Exploring the periodic table with supramolecular G-quadruplexes

Exploring the periodic table with supramolecular G-quadruplexes.

via Exploring the periodic table with supramolecular G-quadruplexes.

GQW articles: August 2013 edition

Following is a list of 37 articles related to GQs published last August, roughly classified as follows:

• (B). GQ-Biology: 8 articles
• (NT). GQ-Nano & Technology: 7 articles
• (R). GQ-Recognition. 12 articles
• (SD). GQ-Structure & Dynamics: 9 articles
• (S). GQ-Supramolecular: 3 articles

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(B). GQ-Biology: Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs).

1. (B) ATRX: the case of a peculiar chromatin remodeler. Ratnakumar K, Bernstein E. Epigenetics. 2013 Jan; 8 (1): 3-9. doi: 10.4161/epi.23271. Epub 2012 Dec 18. Review. PMID: 23249563
2. (B) Specialization Among Iron-Sulfur Cluster Helicases to Resolve G-Quadruplex DNA Structures that Threaten Genomic Stability. Bharti SK, Sommers JA, Kuper J, Hamon F, Shin-Ya K, Teulade-Fichou MP, Kisker C, Brosh RM Jr. J Biol Chem. 2013 Aug 9. [Epub] PMID: 23935105
3. (B) Binding to G-quadruplex RNA activates the mitochondrial GTPase NOA1. Al-Furoukh N, Goffart S, Szibor M, Wanrooij S, Braun T. Biochim Biophys Acta. 2013 Aug 7. doi:pii: S0167-4889(13)00297-8. 10.1016/j.bbamcr.2013.07.022. [Epub] PMID: 23933583
4. (B) DNA replication: driving past four-stranded snags. Mirkin SM. Nature. 2013 May 23; 497 (7450): 449-450. doi: 10.1038/nature12244. Epub 2013 May 8. PMID: 23657255
5. (B) Light-mediated in cell downregulation of G-quadruplex-containing genes using a photo-caged ligand. Murat P, Gormally MV, Sanders D, Antonio MD, Balasubramanian S. Chem Commun. 2013 Aug 15. [Epub] PMID: 23949446
6. (B) Enhanced Cytotoxicity from Deoxyguanosine-Enriched T-oligo in Prostate Cancer Cells. [OA] Rankin AM, Forman L, Sarkar S, Faller DV. Nucleic Acid Ther. 2013 Aug 24. [Epub] PMID: 23971906
7. (B) Association between hTERT rs2736100 polymorphism and sensitivity to anti-cancer agents. Kim J, Jones-Hall YL, Wei R, Myers J, Qi Y, Knipp GT, Liu W. Front Genet. 2013 Aug 26;4:162. doi: 10.3389/fgene.2013.00162. PMID: 23986774
8. (B) Suggested role for G4 DNA in recombinational switching at the antigenic variation locus of the Lyme disease spirochete. [OA] Walia R, Chaconas G. PLoS One. 2013; 8 (2): e57792. doi: 10.1371/journal.pone.0057792. Epub 2013 Feb 28. PMID: 23469068

(NT). GQ-Nano & Technology: The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors, aptamers).

1. (NT) Closer to nature: an ATP-driven bioinspired catalytic oxidation process. Stefan L, Duret D, Spinelli N, Defrancq E, Monchaud D. Chem Commun. 2013 Feb 21; 49 (15): 1500-1502. doi: 10.1039/c2cc38317a. PMID: 23325338
2. (NT) Effects of polymorphic DNA on the fluorescent properties of silver nanoclusters. Li W, Liu L, Fu Y, Sun Y, Zhang J, Zhang R. Photochem Photobiol Sci. 2013 Aug 14. [Epub] PMID: 23946050
3. (NT) The influence of G-quadruplex structure on DNA-based asymmetric catalysis using the G-quadruplex-bound cationic porphyrin TMPyP4·Cu. Wilking M, Hennecke U. Org Biomol Chem. 2013 Aug 20. [Epub] PMID: 23959382
4. (NT) A label-free biosensor for DNA detection based on ligand-responsive G-quadruplex formation. Guo Y, Xu P, Hu H, Zhou X, Hu J. Talanta. 2013 Sep 30; 114: 138-142. doi: 10.1016/j.talanta.2013.04.003. Epub 2013 Apr 12. PMID: 23953453
5. (NT) Metamaterials-Based Label-Free Nanosensor for Conformation and Affinity Biosensing. Cao C, Zhang J, Wen X, Dodson SL, Dao NT, Wong LM, Wang S, Li S, Phan AT, Xiong Q. ACS Nano. 2013 Aug 17. [Epub] PMID: 23952283
6. (NT) Detection of 3’→5′ exonuclease activity using a metal-based luminescent switch-on probe. He HZ, Chan WI, Mak TY, Liu LJ, Wang M, Chan DS, Ma DL, Leung CH. Methods. 2013 Aug 21. doi:pii: S1046-2023(13)00316-2. 10.1016/j.ymeth.2013.08.011. [Epub] PMID: 23973810

(R). GQ-Recognition.Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry).

1. (R) Multiple and Cooperative Binding of Fluorescence Light-up Probe Thioflavin T with Human Telomere DNA G-Quadruplex. Gabelica V, Maeda R, Fujimoto T, Yaku H, Murashima T, Sugimoto N, Miyoshi D. Biochemistry. 2013 Aug 2. [Epub] PMID: 23909872
2. (R) Ni2+ and Cu2+ complexes of a phenanthroline-based ligand bind to G-quadruplexes at non-overlapping sites. Bianco S, Musetti C, Krapcho AP, Palumbo M, Sissi C. Chem Commun. 2013 Aug 7. [Epub] PMID: 23925422
3. (R) Synthesis, cytotoxicity and DNA-binding properties of Pd(II), Cu(II) and Zn(II) complexes with 4′-(4-(2-(piperidin-1-yl)ethoxy)phenyl)-2,2′:6′,2″-terpyridine. Chu W, Wang Y, Liu S, Yang X, Wang S, Li S, Zhou G, Qin X, Zhou C, Zhang J. Bioorg Med Chem Lett. 2013 Jul 12. doi:pii: S0960-894X(13)00837-8. 10.1016/j.bmcl.2013.07.003. [Epub] PMID: 23927970
4. (R) Synthesis, G-Quadruplex Stabilisation, Docking Studies, and Effect on Cancer Cells of Indolo[3,2-b]quinolines with One, Two, or Three Basic Side Chains. Lavrado J, Borralho PM, Ohnmacht SA, Castro RE, Rodrigues CM, Moreira R, Santos DJ, Neidle S, Paulo A. ChemMedChem. 2013 Aug 19. doi: 10.1002/cmdc.201300288. [Epub] PMID: 23960016
5. (R) Molecular basis of recognition of quadruplexes human telomere and c-myc promoter by the putative anticancer agent sanguinarine. Ghosh S, Pradhan SK, Kar A, Chowdhury S, Dasgupta D. Biochim Biophys Acta. 2013 Aug; 1830 (8): 4189-4201. doi: 10.1016/j.bbagen.2013.03.027. Epub 2013 Apr 4. PMID: 23562763
6. (R) Drug repositioning by structure-based virtual screening. Ma DL, Chan DS, Leung CH. Chem Soc Rev. 2013 Mar 7; 42 (5): 2130-41. doi: 10.1039/c2cs35357a. Epub 2013 Jan 4. [Review] PMID: 23288298
7. (R) Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2. [OA] Le VH, Nagesh N, Lewis EA. PLoS One. 2013 Aug 20; 8 (8): e72462. doi: 10.1371/journal.pone.0072462. PMID: 23977303
8. (R) Phenyl 1,2,3-Triazole-Thymidine Ligands Stabilize G-Quadruplex DNA, Inhibit DNA Synthesis and Potentially Reduce Tumor Cell Proliferation over 3′-Azido Deoxythymidine. [OA] Mahesh Kumar J, Idris MM, Srinivas G, Vinay Kumar P, Meghah V, Kavitha M, Reddy CR, Mainkar PS, Pal B, Chandrasekar S, Nagesh N. PLoS One. 2013 Aug 19; 8 (8): e70798. doi: 10.1371/journal.pone.0070798. PMID: 23976957
9. (R) Toward the design of new DNA G-quadruplex ligands through rational analysis of polymorphism and binding data. Artese A, Costa G, Distinto S, Moraca F, Ortuso F, Parrotta L, Alcaro S. Eur J Med Chem. 2013 Aug 11; 68C: 139-149. doi: 10.1016/j.ejmech.2013.07.022. [Epub] PMID: 23974014
10. (R) Optimization of anti-proliferative activity using a screening approach with a series of bis-heterocyclic G-quadruplex ligands. Ohnmacht SA, Ciancimino C, Vignaroli G, Gunaratnam M, Neidle S. Bioorg Med Chem Lett. 2013 Aug 1. doi:pii: S0960-894X(13)00902-5. 10.1016/j.bmcl.2013.07.057. [Epub] PMID: 23972440
11. (R) DNA G-Quadruplex binders: a patent review. Yan Y, Tan J, Ou T, Huang Z, Gu L. Expert Opin Ther Pat. 2013 Aug 23. [Epub] PMID: 23972147

(SD). GQ-Structure & Dynamics: Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations.

1. (SD) A novel equilibrium relating to the helix handedness in G-quadruplexes formed by heterochiral oligonucleotides with an inversion of polarity site. Virgilio A, Esposito V, Mangoni A, Mayol L, Galeone A. Chem Commun. 2013 Jul 30. [Epub] PMID: 23900626
2. (SD) DNA gyrase-driven generation of a G-quadruplex from plasmid DNA. Lv B, Li D, Zhang H, Lee JY, Li T. Chem Commun. 2013 Jul 31. [Epub] PMID: 23903590
3. (SD) Electron Hole Transfer in G-Quadruplexes with Different Tetrad Stacking Geometries: A Combined QM and MD Study. Lech CJ, Phan AT, Michel-Beyerle ME, Voityuk AA. J Phys Chem B. 2013 Aug 1. [Epub] PMID: 23906279
4. (SD; R) Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative. Chung WJ, Heddi B, Tera M, Iida K, Nagasawa K, Phan AT. J Am Chem Soc. 2013 Aug 2. [Epub] PMID: 23909929
5. (SD) G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold. Marusic M, Veedu RN, Wengel J, Plavec J. Nucleic Acids Res. 2013 Aug 8. [Epub] PMID: 23935071
6. (SD) Structural dynamics of human telomeric g-quadruplex loops studied by molecular dynamics simulations. [OA] Zhu H, Xiao S, Liang H. PLoS One. 2013 Aug 8; 8 (8): e71380. doi: 10.1371/journal.pone.0071380. PMID: 23951152
7. (SD) The critical effect of polarization on the dynamical structure of guanine quadruplex DNA. Song J, Ji C, Zhang JZ. Phys Chem Chem Phys. 2013 Mar 21; 15 (11): 3846-3854. doi: 10.1039/c2cp44100d. PMID: 23399949
8. (SD) Sequence and Solvent Effects on Telomeric DNA Bimolecular G-Quadruplex Folding Kinetics. Marchand A, Ferreira R, Tateishi-Karimata H, Miyoshi D, Sugimoto N, Gabelica V. J Phys Chem B. 2013 Aug 26. [Epub] PMID: 23978125
9. (SD) Effect of external electric field on H-bonding and π-stacking interactions in guanine aggregates. Jissy AK, Datta A. Chemphyschem. 2012 Dec 21; 13 (18): 4163-4172. doi: 10.1002/cphc.201200690. Epub 2012 Oct 12. PMID: 23065813

(S). GQ-Supramolecular: Studies related to the design and applications of GQs in supramolecular chemistry. Of particular interest are studies on the use of independent guanosine subunits to guide the self-assembly of complex structures.

1. (S) Multitasking Water-Soluble Synthetic G-Quartets: From Preferential RNA-Quadruplex Interaction to Biocatalytic Activity. Haudecoeur R, Stefan L, Monchaud D. Chemistry. 2013 Aug 6. doi: 10.1002/chem.201300791. [Epub] PMID: 23922305
2. (S; NT) Photonic DNA-Chromophore Nanowire Networks: Harnessing Multiple Supramolecular Assembly Modes. Zhang N, Chu X, Fathalla M, Jayawickramarajah J. Langmuir. 2013 Aug 27; 29 (34): 10796-806. doi: 10.1021/la402214p. Epub 2013 Aug 15. PMID: 23895408
3. (S) Extending Photo-induced Charge Separation Lifetimes by using Supramolecular Design: Guanine-Perylenediimide G-Quadruplex. Wu YL, Brown KE, Wasielewski MR. J Am Chem Soc. 2013 Aug 27. [Epub] PMID: 23978062

GQW articles: July 2013 edition

Following is a list of 35 articles related to GQs published last July, roughly classified as follows:

• (B). GQ-Biology: 6 articles
• (C). GQ-Cations:  2 articles
• (M). GQ-Methods: 2 articles
• (NT). GQ-Nano & Technology: 15 articles
• (R). GQ-Recognition. 9 articles
• (SD). GQ-Structure & Dynamics: 5 articles
• (S). GQ-Supramolecular: 1 article

______________________________________________________________________

(B). GQ-Biology: Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs).

1. (B) G4-quadruplexes and genome instability. Zybaĭlov BL, Sherpa MD, Glazko GV, Raney KD, Glazko VI. Mol Biol (Mosk). 2013 Mar-Apr; 47 (2): 224-31. [Article in Russian]. PMID: 23808155
2. (B) A dynamic G-quadruplex region regulates the HIV-1 long terminal repeat promoter. Perrone R, Nadai M, Frasson I, Poe JA, Butovskaya E, Smithgall TE, Palumbo M, Palù G, Richter SN. J Med Chem. 2013 Jul 18. [Epub] PMID: 23865750
3. (B; R; M) Targeting Non-B-Form DNA in Living Cells. Du Y, Zhou X. Chem Rec. 2013 Jul 4. doi: 10.1002/tcr.201300005. [Epub] PMID: 23828823
4. (B) A versatile microsatellite instability reporter system in human cells. [OA] Koole W, Schäfer HS, Agami R, van Haaften G, Tijsterman M. Nucleic Acids Res. 2013 Jul 16. [Epub]  PMID: 23861444
5. (B) The Cell’s Nucleolus: an Emerging Target for Chemotherapeutic Intervention. Pickard AJ, Bierbach U. ChemMedChem. 2013 Jul 23. doi: 10.1002/cmdc.201300262. [Epub] PMID: 23881648
6. (B) Screening for long-lived genes identifies Oga1, a guanine-quadruplex associated protein that affects the chronological lifespan of the fission yeast Schizosaccharomyces pombe. Ohtsuka H, Ogawa S, Kawamura H, Sakai E, Ichinose K, Murakami H, Aiba H. Mol Genet Genomics. 2013 Jun; 288 (5-6): 285-95. doi: 10.1007/s00438-013-0748-6. Epub 2013 May 3. PMID: 23640107

(C). GQ-Cations: Studies aimed at elucidating the role of cations in the structure and/or dynamics of GQs.

1. (C; SD) Atomic-scale structures and interactions between the guanine quartet and potassium. Xu W, Tan Q, Yu M, Sun Q, Kong H, Lægsgaard E, Stensgaard I, Kjems J, Wang JG, Wang C, Besenbacher F. Chem Commun. 2013 Jul 10. [Epub] PMID: 23841112

(NT). GQ-Nano & Technology: The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors, aptamers).

1. (NT) An aptasensing platform for simultaneous detection of multiple analytes based on the amplification of exonuclease-catalyzed target recycling and DNA concatemers. Jiang L, Peng J, Yuan R, Chai Y, Yuan Y, Bai L, Wang Y. Analyst. 2013 Jul 1. [Epub] PMID: 23817314
2. (NT; C) Colorimetric detection of potassium ions using aptamer-functionalized gold nanoparticles. Chen Z, Huang Y, Li X, Zhou T, Ma H, Qiang H, Liu Y. Anal Chim Acta. 2013 Jul 17; 787: 189-192. doi: 10.1016/j.aca.2013.05.020. Epub 2013 May 21. PMID: 23830438
3. (NT) Tetra(p-tolyl)borate-Functionalized Solvent Polymeric Membrane: A Facile and Sensitive Sensing Platform for Peroxidase and Peroxidase Mimetics. Wang X, Qin W. Chemistry. 2013 Jul 22; 19 (30): 9979-9986. doi: 10.1002/chem.201300284. Epub 2013 Jun 12. PMID: 23852960
4. (NT) A difunctional DNA-AuNP dendrimer coupling DNAzyme with intercalators for femtomolar detection of nucleic acids. Xu M, Zhuang J, Chen X, Chen G, Tang D. Chem Commun. 2013 Jul 12. [Epub] PMID: 23852135
5. (NT) An ultrasensitive electrochemical aptasensor with autonomous assembly of hemin-G-quadruplex DNAzyme nanowires for pseudo triple-enzyme cascade electrocatalytic amplification. Yuan Y, Chai Y, Yuan R, Zhuo Y, Gan X. Chem Commun. 2013 Jul 15. [Epub] PMID: 23851915
6. (NT) Ultrasensitive label-free amplified colorimetric detection of p53 based on G-quadruplex MBzymes. Li H, Wu Z, Qiu L, Liu J, Wang C, Shen G, Yu R. Biosens Bioelectron. 2013 Jun 29; 50C: 180-185. doi: 10.1016/j.bios.2013.06.041. [Epub] PMID: 23850786
7. (NT) Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages. Varizhuk AM, Tsvetkov VB, Tatarinova ON, Kaluzhny DN, Florentiev VL, Timofeev EN, Shchyolkina AK, Borisova OF, Smirnov IP, Grokhovsky SL, Aseychev AV, Pozmogova GE. Eur J Med Chem. 2013 Jun 25;67C:90-97. doi: 10.1016/j.ejmech.2013.06.034. [Epub] PMID: 23850569
8. (NT) Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame. [OA] Rajendran A, Endo M, Hidaka K, Lan Thao Tran P, Mergny JL, Sugiyama H. Nucleic Acids Res. 2013 Jul 17. [Epub] PMID: 23863846
9. (NT) Rational design of a thrombin electrochemical aptasensor by conjugating two DNA aptamers with G-quadruplex halves. Yan Z, Han Z, Huang H, Shen H, Lu X. Anal Biochem. 2013 Jul 16. doi:pii: S0003-2697(13)00328-X. 10.1016/j.ab.2013.06.021. [Epub] PMID: 23872010
10. (NT) A label-free and colorimetric turn-on assay for coralyne based on coralyne-induced formation of peroxidase-mimicking split DNAzyme. Hou T, Wang X, Liu X, Liu S, Du Z, Li F. Analyst. 2013 Jul 19. [Epub] PMID: 23869385
11. (NT) A parallel G-quadruplex-selective luminescent probe for the detection of nanomolar calcium(II) ion. He HZ, Wang M, Chan DS, Leung CH, Lin X, Lin JM, Ma DL. Methods. 2013 Jul 19. doi:pii: S1046-2023(13)00270-3. 10.1016/j.ymeth.2013.07.021. [Epub] PMID: 23876936
12. (NT; M) Factors influencing the performance of G-quadruplex DNAzyme-based sensors. Kong DM. Methods. 2013 Jul 16. doi:pii: S1046-2023(13)00262-4.10.1016/j.ymeth.2013.07.013. [Epub] PMID: 23872055
13. (NT; C) Highly Sensitive Simultaneous Detection of Lead(II) and Barium(II) with G-Quadruplex DNA in α-Hemolysin Nanopore. Yang C, Liu L, Zeng T, Yang D, Yao Z, Zhao Y, Wu HC. Anal Chem. 2013 Jul 29. [Epub] PMID: 23895278
14. (NT) A label-free G-quadruplex-based luminescent switch-on assay for the selective detection of histidine. He HZ, Wang M, Chan DS, Leung CH, Qiu JW, Ma DL. Methods. 2013 Jul 24. doi: pii: S1046-2023(13)00272-7. 10.1016/j.ymeth.2013.07.023. [Epub]  PMID: 23891801
15. (NT) A homogeneous hemin/G-quadruplex DNAzyme based turn-on chemiluminescence aptasensor for interferon-gamma detection via in-situ assembly of luminol functionalized gold nanoparticles, deoxyribonucleic acid, interferon-gamma and hemin. Jiang J, He Y, Yu X, Zhao J, Cui H. Anal Chim Acta. 2013 Aug 12;791:60-4. doi: 10.1016/j.aca.2013.06.048. Epub 2013 Jul 5. PMID: 23890607

(R). GQ-Recognition.Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry).

1. (R) A cyclometallated platinum complex as a selective optical switch for quadruplex DNA. Suntharalingam K, Łęczkowska A, Furrer MA, Wu Y, Kuimova MK, Therrien B, White AJ, Vilar R. Chemistry. 2012 Dec 14; 18 (51): 16277-16282. doi: 10.1002/chem.201202990. Epub 2012 Nov 20. PMID: 23165895
2. (R) Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1. [OA] Edwards JM, Long J, de Moor CH, Emsley J, Searle MS. Nucleic Acids Res. 2013 Jun 6. [Epub] PMID: 23748565
3. (R) Conformational switch for cisplatin with hemin/G-quadruplex DNAzyme supersandwich structure. Wang G, He X, Chen L, Zhu Y, Zhang X, Wang L. Biosens Bioelectron. 2013 Jun 29; 50C: 210-216. doi: 10.1016/j.bios.2013.06.046. [Epub]  PMID: 23859921
4. (R) Phenolic promiscuity in the cell nucleus–epigallocatechingallate (EGCG) and theaflavin-3,3′-digallate from green and black tea bind to model cell nuclear structures including histone proteins, double stranded DNA and telomeric quadruplex DNA. Mikutis G, Karaköse H, Jaiswal R, LeGresley A, Islam T, Fernandez-Lahore M, Kuhnert N. Food Funct. 2013 Feb; 4 (2): 328-337. doi: 10.1039/c2fo30159h. PMID: 23172122
5. (R) Study of the synthesis, antiproliferative properties, and interaction with DNA and polynucleotides of cisplatin-like Pt(II) complexes containing carcinogenic polyaromatic amines. Gabano E, Gama S, Mendes F, Gariboldi MB, Monti E, Bombard S, Bianco S, Ravera M. J Biol Inorg Chem. 2013 Jul 20. [Epub]  PMID: 23873259
6. (R) The role of positive charges on G-quadruplex binding small molecules: Learning from bisaryldiketene derivatives. Chen SB, Shi QX, Peng D, Huang SY, Ou TM, Li D, Tan JH, Gu LQ, Huang ZS. Biochim Biophys Acta. 2013 Jul 20. doi:pii: S0304-4165(13)00315-2. 10.1016/j.bbagen.2013.07.012. [Epub] PMID: 23880070
7. (R) A Fluorescent Guanosine Dinucleoside as a Selective Switch-On Sensor for c-myc G-Quadruplex DNA with Potent Anticancer Activities. Kumar YP, Bhowmik S, Das RN, Bessi I, Paladhi S, Ghosh R, Schwalbe H, Dash J. Chemistry. 2013 Jul 29. doi: 10.1002/chem.201302107. [Epub]  PMID: 23897752
8. (R) [Complexes of antiparallel telomeric G-quadruplex d(TTAGGG)4 with carboxymethyl tetracationic porphyrins]. Kovaleva OA, Shchelkina AK, Mamaeva OK, Ol’shevskaia VA, Makarenkov AV, Semeĭkin AS, Shtil’ AA, Borisova OF, Kaliuzhnyĭ DN. Mol Biol (Mosk). 2013 May-Jun; 47 (3): 513-521. [Article in Russian]. PMID: 23888784

(SD). GQ-Structure & Dynamics: Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations.

1. (SD) G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch. Yan YY, Tan JH, Lu YJ, Yan SC, Wong KY, Li D, Gu LQ, Huang ZS. Biochim Biophys Acta. 2013 Jun 26. doi:pii: S0304-4165(13)00279-1. 10.1016/j.bbagen.2013.06.019. [Epub] PMID: 23811336
2. (SD) When secondary comes first–the importance of non-canonical DNA structures. Saini N, Zhang Y, Usdin K, Lobachev KS. Biochimie. 2013 Feb; 95 (2): 117-123. doi: 10.1016/j.biochi.2012.10.005. Epub 2012 Oct 16. PMID: 23084930
3. (SD) DNA structure: Visualizing the quadruplex. Siddiqui-Jain A, Hurley LH. Nat Chem. 2013 Mar; 5 (3): 153-155. doi: 10.1038/nchem.1587. PMID: 23422553
4. (SD) Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics. Husby J, Todd AK, Platts JA, Neidle S. Biopolymers. 2013 Jul 5. doi: 10.1002/bip.22340. [Epub]  PMID: 23828641

(S). GQ-Supramolecular: Studies related to the design and applications of GQs in supramolecular chemistry. Of particular interest are studies on the use of independent guanosine subunits to guide the self-assembly of complex structures.

1. (S) Synthesis of a Single G-Quartet Platform in Water. Bare GA, Liu B, Sherman JC. J Am Chem Soc. 2013 Jul 16. [Epub] PMID: 23859130

GQW articles: June 2013 edition

Just a quick post with a list of 32 articles related to GQs published last June, roughly classified as follows:

• (B). GQ-Biology: 6 articles
• (C). GQ-Cations: 1 article
• (M). GQ-Methods: 3 articles
• (NT). GQ-Nano & Technology: 9 articles
• (R). GQ-Recognition. 7 articles
• (SD). GQ-Structure & Dynamics: 7 articles
• (S). GQ-Supramolecular: 2 articles

______________________________________________________________________

1. (B) Research shows four-stranded DNA in human cancer cells. Mayor S. Lancet Oncol. 2013 Mar; 14 (3): e91.  PMID: 23580959

2. (SD) A highly sensitive resonance Rayleigh scattering method to discriminate a parallel-stranded G-quadruplex from DNA with other topologies and structures. Shi Y, Luo HQ, Li NB. Chem Commun. 2013 Jun 4. [Epub] PMID: 23736799

3. (NT) A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification. Zhang J, Chai Y, Yuan R, Yuan Y, Bai L, Xie S, Jiang L. Analyst. 2013 Jun 6. [Epub] PMID: 23741737

4. (B) Recognition of intermolecular G-quadruplexes by full length nucleophosmin. Effect of a leukaemia-associated mutation. Bañuelos S, Lectez B, Taneva SG, Ormaza G, Alonso-Mariño M, Calle X, Urbaneja MA. FEBS Lett. 2013 Jun 3. doi:pii: S0014-5793(13)00422-5. 10.1016/j.febslet.2013.05.055. [Epub] PMID: 23742937

5. (NT) Aptamer selection based on g4-forming promoter region. [OA] Yoshida W, Saito T, Yokoyama T, Ferri S, Ikebukuro K. PLoS One. 2013 Jun 4; 8 (6): e65497. doi: 10.1371/journal.pone.0065497. Print 2013. PMID: 23750264

6. (SD; M) Mechanical unfolding of long human telomeric RNA (TERRA). Garavís M, Bocanegra R, Herrero-Galán E, González C, Villasante A, Arias-Gonzalez JR. Chem Commun. 2013 Jun 10. [Epub] PMID: 23748212

7. (NT) A highly sensitive G-quadruplex-based luminescent switch-on probe for the detection of polymerase 3′-5′ proofreading activity. Surnameleung GH, Surnamehe GZ, Surnamezhong GJ, Surnamelu G, Surnamechan GS, Surnamema GL, Surnameleung GH. Methods. 2013 Jun 2. doi:pii: S1046-2023(13)00167-9. 10.1016/j.ymeth.2013.05.017. [Epub] PMID: 23748144

8. (B) Translational halt during elongation caused by G-quadruplex formed by mRNA. Endoh T, Kawasaki Y, Sugimoto N. Methods. 2013 Jun 6. doi:pii: S1046-2023(13)00192-8. 10.1016/j.ymeth.2013.05.026. [Epub] PMID: 23747335

9. (M) Clerocidin-mediated DNA footprinting discriminates among different G-quadruplex conformations and detects tetraplex folding in a duplex environment. Nadai M, Sattin G, Palù G, Palumbo M, Richter SN. Biochim Biophys Acta. 2013 Jun 6. doi:pii: S0304-4165(13)00243-2. 10.1016/j.bbagen.2013.05.039. [Epub] PMID: 23747297

10. (S) Quartet formation of a guanine derivative with an isopropyl group: crystal structures of “naked” G-quartets and thermodynamics of G-quartet formation. Inui Y, Shiro M, Fukuzumi S, Kojima T. Org Biomol Chem. 2013 Feb 7; 11 (5): 758-64. doi: 10.1039/c2ob26877a. Epub 2012 Dec 13. PMID: 23238354

11. (B) DNA2, a new player in telomere maintenance and tumor suppression. Chai W, Zheng L, Shen B. Cell Cycle. 2013 Jun 10; 12 (13). [Epub] PMID: 23759580

12. (NT; S) Guided assembly of tetramolecular G-quadruplexes. Yatsunyk LA, Pietrement O, Albrecht D, Tran PL, Renciuk D, Sugiyama H, Arbona JM, Aimé JP, Mergny JL. ACS Nano. 2013 Jun 13. [Epub] PMID: 23763613

13. (R) Pentose Phosphate Pathway Function Affects Tolerance to the G-Quadruplex Binder TMPyP4. [OA] Andrew EJ, Merchan S, Lawless C, Banks AP, Wilkinson DJ, Lydall D. PLoS One. 2013 Jun 12; 8 (6): e66242. doi: 10.1371/journal.pone.0066242. Print 2013. PMID: 23776642

14. (R) Spectroscopic and Biological Studies of Phenanthroline Compounds: Selective Recognition of Gene-Promoter G-Quadruplex DNAs Preferred over Duplex DNA. Wang L, Wei C. Chem Biodivers. 2013 Jun;10(6):1154-64. doi: 10.1002/cbdv.201200341. PMID: 23776031

15. (SD) Combination of i-Motif and G-Quadruplex Structures within the Same Strand: Formation and Application. Zhou J, Amrane S, Korkut DN, Bourdoncle A, He HZ, Ma DL, Mergny JL. Angew Chem Int Ed Engl. 2013 Jun 14. doi: 10.1002/anie.201301278. [Epub] PMID: 23775868

16. (SD) Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex. Shek YL, Noudeh GD, Nazari M, Heerklotz H, Abu-Ghazalah RM, Dubins DN, Chalikian TV. Biopolymers. 2013 Jun 18. doi: 10.1002/bip.22317. [Epub] PMID: 23775839

17. (B) Mechanistic Studies for the Role of Cellular Nucleic-acid-binding Protein (CNBP) in Regulation of c-myc Transcription. Chen S, Su L, Qiu J, Xiao N, Lin J, Tan JH, Ou TM, Gu LQ, Huang ZS, Li D. Biochim Biophys Acta. 2013 Jun 14. doi:pii: S0304-4165(13)00267-5. 10.1016/j.bbagen.2013.06.007. [Epub] PMID: 23774591

18. (SD) Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences. [OA] König SL, Huppert JL, Sigel RK, Evans AC. Nucleic Acids Res. 2013 Jun 14. [Epub] PMID: 23771141

19. (NT) A dual-functional electrochemical biosensor for the detection of prostate specific antigen and telomerase activity. Liu J, Lu CY, Zhou H, Xu JJ, Wang ZH, Chen HY. Chem Commun. 2013 Jun 14. [Epub] PMID: 23770709

20. (NT) A simple, fast and highly sensitive assay for the detection of telomerase activity. Quach QH, Jung J, Kim H, Chung BH. Chem Commun. 2013 Jun 14. [Epub]  PMID: 23770610

21. (NT) A label-free DNA hairpin biosensor for colorimetric detection of target with suitable functional DNA partners. Nie J, Zhang DW, Tie C, Zhou YL, Zhang XX. Biosens Bioelectron. 2013 May 25;49C:236-242. doi: 10.1016/j.bios.2013.05.020. [Epub]  PMID: 23770395

22. (R) The influence of positional isomerism on G-quadruplex binding and anti-proliferative activity of tetra-substituted naphthalene diimide compounds. Mpima S, Ohnmacht SA, Barletta M, Husby J, Pett LC, Gunaratnam M, Hilton ST, Neidle S. Bioorg Med Chem. 2013 May 25. doi:pii: S0968-0896(13)00463-X. 10.1016/j.bmc.2013.05.027. [Epub] PMID: 23769166

23. (SD) Excimer Formation by Stacking G-Quadruplex Blocks. Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT. ChemPhysChem. 2013 Jun 18. doi: 10.1002/cphc.201300481. [Epub] PMID: 23780713

24. (M) A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction. Li Y, Xu F, Liu C, Xu Y, Feng X, Liu BF. Analyst. 2013 Jun 20. [Epub] PMID: 23785706

25. (B) G-Quadruplex DNA as a Molecular Target for Induced Synthetic Lethality in Cancer Cells. McLuckie KI, Di Antonio M, Zecchini H, Xian J, Caldas C, Krippendorff BF, Tannahill D, Lowe C, Balasubramanian S. J Am Chem Soc. 2013 Jun 19. [Epub] PMID: 23782415

26. (R) Macrocyclic biphenyl tetraoxazoles: Synthesis, evaluation as G-quadruplex stabilizers and cytotoxic activity. Blankson GA, Pilch DS, Liu AA, Liu LF, Rice JE, Lavoie EJ. Bioorg Med Chem. 2013 May 30. doi:pii: S0968-0896(13)00482-3. 10.1016/j.bmc.2013.05.033. [Epub] PMID: 23787291

27. (R) On the interaction between [Ru(NH3)6]3+ and the G-quadruplex forming thrombin binding aptamer sequence. De Rache A, Doneux T, Kejnovská I, Buess-Herman C. J Inorg Biochem. 2013 May 30;126C:84-90. doi: 10.1016/j.jinorgbio.2013.05.014. [Epub] PMID: 23787142

28. (R) V-Shaped Dinuclear Pt(II) Complexes: Selective Interaction with Human Telomeric G-quadruplex and Significant Inhibition towards Telomerase. [OA] Xu CX, Zheng YX, Zheng XH, Hu Q, Zhao Y, Ji LN, Mao ZW. Sci Rep. 2013 Jun 24;3:2060. doi: 10.1038/srep02060. PMID: 23792883

29. (NT; C) A “turn-on” fluorescent sensor for detection of Pb2+ based on graphene oxide and G-quadruplex DNA. Li X, Wang G, Ding X, Chen Y, Gou Y, Lu Y. Phys Chem Chem Phys. 2013 Jun 25. [Epub] PMID: 23799396

30. (SD) Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection. [OA] Buscaglia R, Miller MC, Dean WL, Gray RD, Lane AN, Trent JO, Chaires JB. Nucleic Acids Res. 2013 Jun 26. [Epub] PMID: 23804761

31. (NT) Stable label-free fluorescent sensing of biothiols based on ThT direct inducing conformation-specific G-quadruplex. Tong LL, Li L, Chen Z, Wang Q, Tang B. Biosens Bioelectron. 2013 Jun 10; 49C: 420-425. doi: 10.1016/j.bios.2013.05.051. [Epub] PMID: 23807235

32. (R) Asymmetric distyrylpyridinium dyes as red-emitting fluorescent probes for quadruplex DNA. Xie X, Choi B, Largy E, Guillot R, Granzhan A, Teulade-Fichou MP. Chemistry. 2013 Jan 21; 19 (4): 1214-26. doi: 10.1002/chem.201203710. Epub 2013 Jan 4. PMID: 23292703

______________________________________________________________________

Key:

• (B). GQ-Biology: Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs).
• (C). GQ-Cations: Studies aimed at elucidating the role of cations in the structure and/or dynamics of GQs.
• (M). GQ-Methods: Application and development of methods and techniques to study GQs.
• (NT). GQ-Nano & Technology: The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors, aptamers).
• (R). GQ-Recognition.Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry).
• (SD). GQ-Structure & Dynamics: Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations.
• (S). GQ-Supramolecular: Studies related to the design and applications of GQs in supramolecular chemistry. Of particular interest are studies on the use of independent guanosine subunits to guide the self-assembly of complex structures.

GQW articles: MAY 2013 edition

I can’t believe is almost September already and I still haven’t posted the list of articles for last May (I mean, the previous one took me a year, but I’m trying to improve on that…). Hopefully I’ll have this brief “panoramic” overview of May’s articles finished later this week, but just in case, here is the plain list of the 30 papers published that month, roughly classified by categories as follows:

• (B). GQ-Biology: 9 articles
• (C). GQ-Cations: 1 articles
• (M). GQ-Methods: 6 articles
• (NT). GQ-Nano & Technology: 7 articles
• (R). GQ-Recognition. 5 articles
• (SD). GQ-Structure & Dynamics: 8 articles
• (S). GQ-Supramolecular: 2 article

Similar to April, studies related to the biological role of GQs continue to dominate the list this month, but there are almost as many contributions on structure & dynamics (SD) and nano & technology (NT) categories. GQ-Recognition (R) always get steady stream of papers, while less common categories (e.g., cations and supramolecular) had at least a few.

______________________________________________________________________

1. (NT) Electrochemical determination of microRNA-21 based on bio bar code and hemin/G-quadruplet DNAenzyme. Meng X, Zhou Y, Liang Q, Qu X, Yang Q, Yin H, Ai S. Analyst. 2013 Jun 21; 138 (12) 3409-3415. doi: 10.1039/c3an36788f. Epub 2013 Apr 30. PMID: 23629000

2. (SD; M) Recent Progress in G-quadruplex DNA in Deep Eutectic Solvent. Zhao C, Qu X. Methods. 2013 Apr 26. doi:pii: S1046-2023(13)00123-0. 10.1016/j.ymeth.2013.04.017. [Epub] PMID: 23628945

3. (SD) Direct Measurement of Sequential Folding Pathway and Energy Landscape of Human Telomeric G-quadruplex Structures. Li W, Hou XM, Wang PY, Xi XG, Li M. J Am Chem Soc. 2013 May 1; 135 (17) 6423-6426. doi: 10.1021/ja4019176. Epub 2013 Apr 23. PMID: 23631592

4. (B) General cell-binding activity of intramolecular g-quadruplexes with parallel structure. [OA] Chang T, Qi C, Meng J, Zhang N, Bing T, Yang X, Cao Z, Shangguan D. PLoS One. 2013 Apr 26; 8 (4) e62348. doi: 10.1371/journal.pone.0062348. Print 2013. PMID: 23638046

5. (R) Human cathelicidin peptide LL37 binds telomeric G-quadruplex. Jana J, Kar RK, Ghosh A, Biswas A, Ghosh S, Bhunia A, Chatterjee S. Mol Biosyst. 2013 May 1. [Epub] PMID: 23636272

6. (SD; M) Self-assembled G-quadruplex nanostructures: AFM and voltammetric characterization. Chiorcea-Paquim AM, Santos PV, Eritja R, Oliveira-Brett AM. Phys Chem Chem Phys. 2013 May 3. [Epub] PMID: 23644414

7. (S) A Photoresponsive Supramolecular G-Quadruplex. Rivera JM, Silva-Brenes D. Org Lett. 2013 May 3. [Epub] PMID: 23642252

8. (NT) Isothermal quadruplex priming amplification for DNA-based diagnostics. Taylor A, Joseph A, Okyere R, Gogichaishvili S, Musier-Forsyth K, Kankia B. Biophys Chem. 2013 Jan; 171: 1-8. doi: 10.1016/j.bpc.2012.11.001. Epub 2012 Nov 14. PMID: 23232099

9. (NT; M) Nanomechanics of surface DNA switches probed by captive contact angle. Maiolo D, Federici S, Ravelli L, Depero LE, Hamad-Schifferli K, Bergese P. J Colloid Interface Sci. 2013 Apr 11. doi:pii: S0021-9797(13)00327-5.10.1016/j.jcis.2013.03.069. [Epub] PMID: 23647692

10. (SD) Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. [OA] Islam B, Sgobba M, Laughton C, Orozco M, Sponer J, Neidle S, Haider S. Nucleic Acids Res. 2013 Feb 1; 41 (4) 2723-35. doi: 10.1093/nar/gks1331. Epub 2013 Jan 4. PMID: 23293000

11. (B) G-quadruplex structures are stable and detectable in human genomic DNA. Lam EY, Beraldi D, Tannahill D, Balasubramanian S. Nat Commun. 2013; 4:1796. doi: 10.1038/ncomms2792. PMID: 23653208

12. (B) Pif1 family helicases suppress genome instability at G-quadruplex motifs. Paeschke K, Bochman ML, Garcia PD, Cejka P, Friedman KL, Kowalczykowski SC, Zakian VA. Nature. 2013 May 8. doi: 10.1038/nature12149. [Epub] PMID: 23657261

13. (B) Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy. [OA] Yuan L, Tian T, Chen Y, Yan S, Xing X, Zhang Z, Zhai Q, Xu L, Wang S, Weng X, Yuan B, Feng Y, Zhou X. Sci Rep. 2013 May 9;3:1811. doi: 10.1038/srep01811. PMID: 23657205

14. (R) Structure-activity relationships of novel substituted naphthalene diimides as anticancer agents. Milelli A, Tumiatti V, Micco M, Rosini M, Zuccari G, Raffaghello L, Bianchi G, Pistoia V, Fernando Díaz J, Pera B, Trigili C, Barasoain I, Musetti C, Toniolo M, Sissi C, Alcaro S, Moraca F, Zini M, Stefanelli C, Minarini A. Eur J Med Chem. 2012 Nov;57:417-28. doi: 10.1016/j.ejmech.2012.06.045. Epub 2012 Jul 4. PMID: 22819507

15. (NT) Label-free electrochemiluminescent detection of DNA by hybridization with a molecular beacon to form hemin/G-quadruplex architecture for signal inhibition. Deng S, Cheng L, Lei J, Cheng Y, Huang Y, Ju H. Nanoscale. 2013 May 10. [Epub] PMID: 23662297

16. (SD; S) G-quadruplex formation of entirely hydrophobic DNA in organic solvents. Shibata T, Dohno C, Nakatani K. Chem Commun. 2013 May 10. [Epub] PMID: 23660830

17. (B) Beyond the Binding Site: In Vivo Identification of tbx2, smarca5 and wnt5b as Molecular Targets of CNBP during Embryonic Development. [OA] Armas P, Margarit E, Mouguelar VS, Allende ML, Calcaterra NB. PLoS One. 2013 May 7; 8 (5) e63234. doi: 10.1371/journal.pone.0063234. Print 2013. PMID: 23667590

18. (NT) A visible multi-digit DNA keypad lock based on split G-quadruplex DNAzyme and silver microspheres. Zhu J, Yang X, Zhang L, Zhang L, Lou B, Dong S, Wang E. Chem Commun. 2013 May 13. [Epub] PMID: 23665889

19. (NT; C) Aptamer biosensor for label-free impedance spectroscopy detection of potassium ion based on DNA G-quadruplex conformation. Chen Z, Chen L, Ma H, Zhou T, Li X. Biosens Bioelectron. 2013 Apr 17;48C:108-112. doi: 10.1016/j.bios.2013.04.007. [Epub] PMID: 23665159

20. (B) Interaction of G-quadruplex with RecA Protein Studied in Bulk Phase and at Single-Molecule Level. Tanaka A, Choi J, Kim SK, Majima T. J Phys Chem B. 2013 May 10. [Epub] PMID: 23662701

21. (M; NT) Capillary Electrophoresis-Systematic Evolution of Ligands by Exponential Enrichment Selection of Base- and Sugar-Modified DNA Aptamers: Target Binding Dominated by 2′-O,4′-C-Methylene-Bridged/Locked Nucleic Acid Primer. Kasahara Y, Irisawa Y, Fujita H, Yahara A, Ozaki H, Obika S, Kuwahara M. Anal Chem. 2013 May 10. [Epub] PMID: 23662585

22. (SD) Effect of Loops, G-Quartets on the Stability of RNA G-Quadruplexes. Pandey S, Agarwala P, Maiti S. J Phys Chem B. 2013 May 17. [Epub] PMID: 23683360

23. (M; SD) Interactions of the human telomere sequence with the nanocavity of the α-hemolysin ion channel reveal structure-dependent electrical signatures for hybrid folds. An N, Fleming AM, Burrows CJ. J Am Chem Soc. 2013 May 17. [Epub] PMID: 23682802

24. (SD; M) Structural characterization of quadruplex DNA with in-cell EPR approaches. Holder IT, Drescher M, Hartig JS. Bioorg Med Chem. 2013 Apr 16. doi:pii: S0968-0896(13)00331-3. 10.1016/j.bmc.2013.04.014. [Epub] PMID: 23693068

25. (B) Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns. [OA] Savage AL, Bubb VJ, Breen G, Quinn JP. BMC Evol Biol. 2013 May 21;13(1):101. [Epub] PMID: 23692647

26. (B) On the origin of the eukaryotic chromosome: the role of non-canonical DNA structures in telomere evolution. [OA] Garavís M, González C, Villasante A. Genome Biol Evol. 2013 May 22. [Epub] PMID: 23699225

27. (R) Dual recognition of the human telomeric G-quadruplex by a neomycin-anthraquinone conjugate. Ranjan N, Davis E, Xue L, Arya DP. Chem Commun. 2013 May 22. [Epub] PMID: 23698792

28. (R) Ellipticine binds to human telomere sequence – an additional mode of action as a putative anticancer agent? Ghosh S, Kar A, Chowdhury S, Dasgupta D. Biochemistry. 2013 May 22. [Epub] PMID: 23697684

29. (R) RPA-Mediated Unfolding of Systematically Varying G-Quadruplex Structures. Ray S, Qureshi MH, Malcolm DW, Budhathoki JB, Celik U, Balci H. Biophys J. 2013 May 21;104 (10) 2235-2245. doi: 10.1016/j.bpj.2013.04.004. PMID: 23708363

30. (B) DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix. [OA] Zhang C, Liu HH, Zheng KW, Hao YH, Tan Z. Nucleic Acids Res. 2013 May 28. [Epub] PMID: 23716646

______________________________________________________________________

Key:

• (B). GQ-Biology: Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs).
• (C). GQ-Cations: Studies aimed at elucidating the role of cations in the structure and/or dynamics of GQs.
• (M). GQ-Methods: Application and development of methods and techniques to study GQs.
• (NT). GQ-Nano & Technology: The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors, aptamers).
• (R). GQ-Recognition.Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry).
• (SD). GQ-Structure & Dynamics: Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations.
• (S). GQ-Supramolecular: Studies related to the design and applications of GQs in supramolecular chemistry. Of particular interest are studies on the use of independent guanosine subunits to guide the self-assembly of complex structures.

Celebrating a one year anniversary of not posting… GQW articles: April 2013 edition

It’s been a year since my last post here (talk about procrastination!), and I can go on forever with the reasons why it’s taken so long, but if I do, I’ll probably never make this post. Nonetheless, one of the biggest obstacles in getting this lists posted used to be how long it took for me to browse/read the articles, sort them out, and then compile a cleaned up version of each reference. Afterwards, I would cross-check to minimize redundancy from previous posts (since I rely on email updates from various sources, combined with the individual browsing of multiple journals). The whole process was just too complicated and it always found its way to the bottom of the ‘To do’ list…

So, I decided to streamline the process to see if I can post more regularly. From now on the list will only  contain references from the email updates I get from PubMed. I will not double check for redundancy relative to previous posts (this shouldn’t be a problem since many times it takes more than one look to really notice something). I’ll also do the sorting by simply placing a one- or two-letter code (see below) next to the corresponding reference. The new system makes the process and allows me to classify an article in more than one category.

Following is the list corresponding to last month (April 2013. The interest in determining the biological role of GQs continues unabated as evidenced by the fact that most articles can be broadly classified in this area. In a close second, the search for better ligands (and some not so much better) also continues to be a popular sub-area of research within the field.

______________________________________________________________________

This post includes 31 articles divided by category as follows:

(B). GQ-Biology: 13 articles

(C). GQ-Cations: 0 article

(M). GQ-Methods: 5 articles

(NT). GQ-Nano & Technology: 4 articles

(R). GQ-Recognition. 11 articles

(SD). GQ-Structure & Dynamics: 6 articles

(S). GQ-Supramolecular: 0 articles

______________________________________________________________________

1. (R) Ruthenium (II) polypyridyl complexes stabilize the bcl-2 promoter quadruplex and induce apoptosis of Hela tumor cells. Wang C, Yu Q, Yang L, Liu Y, Sun D, Huang Y, Zhou Y, Zhang Q, Liu J. Biometals. 2013 Mar 30. [Epub] PMID: 23543383

2. (B) A Novel Role for the RNA-Binding Protein FXR1P in Myoblasts Cell-Cycle Progression by Modulating p21/Cdkn1a/Cip1/Waf1 mRNA Stability. [OA] Davidovic L, Durand N, Khalfallah O, Tabet R, Barbry P, Mari B, Sacconi S, Moine H, Bardoni B. PLoS Genet. 2013 Mar; 9 (3) e1003367. doi: 10.1371/journal.pgen.1003367. Epub 2013 Mar 21. PMID: 23555284

3. (R) Structure and stability of human telomeric g-quadruplex with preclinical 9-amino acridines. [OA] Ferreira R, Artali R, Benoit A, Gargallo R, Eritja R, Ferguson DM, Sham YY, Mazzini S. PLoS One. 2013; 8 (3) e57701. doi: 10.1371/journal.pone.0057701. Epub 2013 Mar 15. PMID: 23554865

4. (SD) Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study. [OA] Palacký J, Vorlíčková M, Kejnovská I, Mojzeš P. Nucleic Acids Res. 2013 Jan; 41 (2) 1005-1016. doi: 10.1093/nar/gks1135. Epub 2012 Nov 27. PMID: 23193257

5. (R; NT) Detection of base excision repair enzyme activity using a luminescent G-quadruplex selective switch-on probe. Leung KH, He HZ, Ma VP, Zhong HJ, Chan DS, Zhou J, Mergny JL, Leung CH, Ma DL. Chem Commun. 2013 Apr 5. [Epub] PMID: 23559154

6. (SD; M) Structural probes in quadruplex nucleic acid structure determination by NMR. [OA] Karsisiotis AI, Webba da Silva M. Molecules. 2012 Nov 5; 17 (11) 13073-86. doi: 10.3390/molecules171113073. Review. PMID: 23128087

7. (SD; M) Circular dichroism spectroscopy of DNA: from duplexes to quadruplexes. Vorlíčková M, Kejnovská I, Bednářová K, Renčiuk D, Kypr J. Chirality. 2012 Sep; 24 (9) 691-698. doi: 10.1002/chir.22064. Epub 2012 Jun 14. (Review) PMID: 22696273

8. (B) Atrx deficiency induces telomere dysfunction, endocrine defects, and reduced life span. [OA] Watson LA, Solomon LA, Li JR, Jiang Y, Edwards M, Shin-Ya K, Beier F, Bérubé NG. J Clin Invest. 2013 Apr 8. doi: 65634.10.1172/JCI65634. [Epub] PMID: 23563309

9. (SD; R) Study on Effects of Molecular Crowding on G-quadruplex-ligand Binding and Ligand-mediated Telomerase Inhibition. Yaku H, Murashima T, Tateishi-Karimata H, Nakano SI, Miyoshi D, Sugimoto N. Methods. 2013 Apr 2. doi: S1046-2023(13)00097-2.10.1016/j.ymeth.2013.03.028. [Epub] PMID: 23562626

10. (R; NT) Quantification of the Na+/K+ ratio based on the different response of a newly identified G-quadruplex to Na+ and K+. Sun H, Xiang J, Gai W, Liu Y, Guan A, Yang Q, Li Q, Shang Q, Su H, Tang Y, Xu G. Chem Commun. 2013 Apr 10. [Epub] PMID: 23577345

11. (SD; M) The effect of size on the optical properties of guanine nanostructures: a femtosecond to nanosecond study. Hua Y, Changenet-Barret P, Gustavsson T, Markovitsi D. Phys Chem Chem Phys. 2013 Apr 12. [Epub] PMID: 23580086

12. (R) A Pt(ii)-Dip complex stabilizes parallel c-myc G-quadruplex. Wang J, Lu K, Xuan S, Toh Z, Zhang D, Shao F. Chem Commun. 2013 Apr 15. [Epub] PMID: 23586078

13. (B) Co-transcriptional formation of DNA: RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Zheng KW, Xiao S, Liu JQ, Zhang JY, Hao YH, Tan Z. Nucleic Acids Res. 2013 Apr 12. [Epub] PMID: 23585281

14. (R) Evaluation of the Interaction between Long Telomeric DNA and Macrocyclic Hexaoxazole (6OTD) Dimer of a G-quadruplex Ligand. [OA] Iida K, Majima S, Nakamura T, Seimiya H, Nagasawa K. Molecules. 2013 Apr 12;18(4):4328-41. doi: 10.3390/molecules18044328. PMID: 23584054

15. (M) Single molecule FRET data analysis procedures for FRET efficiency determination: Probing the conformations of nucleic acid structures. Krüger AC, Birkedal V. Methods. 2013 Apr 11. doi:pii: S1046-2023(13)00105-9. 10.1016/j.ymeth.2013.04.001. [Epub] PMID: 23583888

16. (B) Suppression of Gene Expression by G-Quadruplexes in Open Reading Frames Depends on G-Quadruplex Stability. Endoh T, Kawasaki Y, Sugimoto N. Angew Chem Int Ed Engl. 2013 Apr 15. doi: 10.1002/anie.201300058. [Epub] PMID: 23589400

17. (M; R) Direct visualization of the quadruplex structures in human chromosome using FRET: Application of quadruplex stabilizer and duplex-binding fluorophore. Chan YC, Chen JW, Su SY, Chang CC. Biosens Bioelectron. 2013 Mar 29. doi: S0956-5663(13)00211-X. 10.1016/j.bios.2013.03.041. [Epub] PMID: 23591020

18. (B) The g4 genome. PLoS Genet. [OA] Maizels N, Gray LT. 2013 Apr 18; 9 (4) e1003468. doi: 10.1371/journal.pgen.1003468. [Epub] PMID: 23637633

19. (B) Mammalian DNA2 helicase/nuclease cleaves G-quadruplex DNA and is required for telomere integrity. Lin W, Sampathi S, Dai H, Liu C, Zhou M, Hu J, Huang Q, Campbell J, Shin-Ya K, Zheng L, Chai W, Shen B. EMBO J. 2013 Apr 19. doi: 10.1038/emboj.2013.88. [Epub] PMID: 23604072

20. (B; R) Mitochondrial dysfunction and nuclear-mitochondrial shuttling of TERT are involved in cell proliferation arrest induced by G-quadruplex ligands. Zhuang XY, Yao YG. FEBS Lett. 2013 Apr 18. doi:pii: S0014-5793(13)00295-0. 10.1016/j.febslet.2013.04.010. [Epub] PMID: 23603390

21. (NT) Selective, colorimetric assay of glucose in urine using G-quadruplex-based DNAzymes and 10-acetyl-3,7-dihydroxy phenoxazine. Bo H, Wang C, Gao Q, Qi H, Zhang C. Talanta. 2013 Apr 15; 108: 131-135. doi: 10.1016/j.talanta.2013.03.001. Epub 2013 Mar 13. PMID: 23601880

22. (B) Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA. Curtis EA, Liu DR. Chem Biol. 2013 Apr 18; 20 (4) 521-532. doi: 10.1016/j.chembiol.2013.02.015. PMID: 23601641

23. (B) Exploring mRNA 3′-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Beaudoin JD, Perreault JP. Nucleic Acids Res. 2013 Apr 22. [Epub] PMID: 23609544

24. (R) Studies on the interaction mechanism of aminopyrene derivatives with human tumor-related DNA. Li L, Lu J, Zhou W, Li H, Yang X. J Photochem Photobiol B. 2013 Apr 4;123C:32-40. doi: 10.1016/j.jphotobiol.2013.03.009. [Epub] PMID: 23608671

25. (R) 4-(1H-Imidazo[4,5-f]-1,10-phenanthrolin-2-yl)phenol-based G-quadruplex DNA binding agents: Telomerase inhibition, cytotoxicity and DNA-binding studies. Wei CY, Wang JH, Wen Y, Liu J, Wang LH. Bioorg Med Chem. 2012 Dec 11. doi:pii: S0968-0896(12)00963-7. 10.1016/j.bmc.2012.11.059. [Epub] PMID: 23611765

26. (B) The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. [OA] Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM. Nucleic Acids Res. 2013 Apr 25. [Epub] PMID: 23620297

27. (B) Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α. [OA] Endoh T, Kawasaki Y, Sugimoto N. Nucleic Acids Res. 2013 Apr 24. [Epub] PMID: 23620292

28. (B; M; SD) Modelling the regulation of telomere length: the effects of telomerase and G-quadruplex stabilising drugs. [OA] Hirt BV, Wattis JA, Preston SP. J Math Biol. 2013 Apr 26. [Epub] PMID: 23620229

29. (B) Evidence for G-Quadruplex DNA in Human Cells. Xu Y, Komiyama M. Chembiochem. 2013 Apr 25. doi: 10.1002/cbic.201300157. [Epub] PMID: 23619895

30. (SD) Effect of Loop Sequence and Loop Length on the Intrinsic Fluorescence of G-Quadruplexes. Kwok CK, Sherlock ME, Bevilacqua PC. Biochemistry. 2013 Apr 26. [Epub] PMID: 23621657

31. (NT) High-throughput quantitative screening of peroxidase-mimicking DNAzymes on a microarray using electrochemical detection. Kaneko N, Horii K, Kato S, Akitomi J, Waga I. Anal Chem. 2013 Apr 28. [Epub] PMID: 23621546

GQW articles: May 2012 edition

This post includes 33 articles divided by category as follows:

• GQ-Biology (GQB).  8 articles
• GQ-Cations (GQC). 1 article
• GQ-Methods (GQM). 5 articles
• GQ-Nano & Technology (GQNT). 9 articles
• GQ-Recognition (GQR). 5 articles
• GQ-Structure & Dynamics (GQSD). 2 articles
• GQ-Supramolecular (GQS). 3 articles

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• GQ-Biology. Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs) [8 articles]

1. DNA helicase and helicase–nuclease enzymes with a conserved iron–sulfur cluster. [OA] Yuliang Wu and Robert M. Brosh, Jr. Nucleic Acids Res. 2012; 40:4247-4260.
2. The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary. [OA] E. P. Booy, M. Meier, N. Okun, S. K. Novakowski, S. Xiong, J. Stetefeld, and S. A. McKenna. Nucleic Acids Res. 2012; 40:4110-4124.
3. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals. [OA] Aradhita Baral, Pankaj Kumar, Rashi Halder, Prithvi Mani, Vinod Kumar Yadav, Ankita Singh, Swapan K. Das, and Shantanu Chowdhury. Nucleic Acids Res. 2012; 40: 3800-3811.
4. Autophagy acts as a safeguard mechanism against G-quadruplex ligand-mediated DNA damage. [OA] NI Orlotti, G Cimino-Reale, E Borghini, M Pennati, C Sissi, F Perrone, M Palumbo, MG Daidone, M Folini, and N Zaffaroni. Autophagy. 8 (8) 2012 [Epub Aug 1] PMID: 22627293
5. RTEL1 Dismantles T Loops and Counteracts Telomeric G4-DNA to Maintain Telomere Integrity. JB Vannier, V Pavicic-Kaltenbrunner, MI Petalcorin, H Ding, and SJ Boulton. Cell. 2012; 149 (4): 795-806. PMID: 22579284
6. Promoter G-quadruplex sequences are targets for base oxidation and strand cleavage during hypoxia-induced transcription. DW Clark, T Phang, MG Edwards, MW Geraci, & MN Gillespie. Free Radic Biol Med. 2012. [Epub May 1] PMID: 22583700
7. The human RecQ helicases BLM and RECQL4 cooperate to preserve genome stability. [OA] D Kumar Singh, V Popuri, T Kulikowicz, I Shevelev, AK Ghosh, M Ramamoorthy, ML Rossi, P Janscak, DL Croteau, and VA Bohr. Nucleic Acids Res. 2012.
8. The BLM helicase contributes to telomere maintenance through processing of late-replicating intermediate structures. [OA] Colleen Barefield and Jan Karlseder. Nucleic Acids Res. 2012. [Epub May 10] DOI: 10.1093/nar/gks407

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• GQ-Cations. Studies aimed at elucidating the role of cations in GQ structure and/or dynamics. [1 article]

1. Stable G-quadruplex structure in a hydrated ion pair: cholinium cation and dihydrogen phosphate anion. K Fujita and H Ohno. Chem. Commun. 2012; 48 (46): 5751-5753.  PMID: 22552502

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• GQ-Methods. Application and development of methods and techniques to study GQs. [5 articles]

1. NMR spectroscopy of G-quadruplexes. M Adrian, B Heddi, and AT Phan. Methods. 2012 [Epub May 24] PMID: 22633887
2. Sequence-specific detection of nucleic acids utilizing isothermal enrichment of G-quadruplex DNAzymes. HJ Xiao, HC Hak, DM Kong, and HX Shen. Anal Chim Acta. 729: 67-72. 2012 [Epub Apr 21] PMID: 22595435
3. QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences. Menendez C, Frees S, Bagga PS. Nucleic Acids Res. 2012 May 10. [Epub ahead of print] PMID: 22576365
4. UV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase. Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P. J Phys Chem A. 2012 May 8. [Epub ahead of print] PMID: 22568521
5. Computational Detection and Analysis of Sequences with Duplex-Derived Interstrand G-quadruplex Forming Potential. Cao K, Ryvkin P, Brad Johnson F. Methods. 2012  [Epub May 28] PMID: 22652626

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• GQ-Nano & Technology. The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors). [9 articles]

1. Aptamer-DNAzyme hairpins for biosensing of Ochratoxin A. Yang C, Lates V, Prieto-Simón B, Marty JL, Yang X. Biosens Bioelectron. 2012 Feb 15; 32 (1): 208-212. [Epub 2011 Dec 13] PMID: 22221796
2. Sensitive fluorescence biosensor for folate receptor based on terminal protection of small-molecule-linked DNA. X Wei, W Lin, N Ma, F Luo, Z Lin, L Guo, B Qiu, & G Chen.  Chem. Commun. 2012; 48 (49): 6184-6186. [Epub May 16] PMID: 22590712
3. Structure Formation and Catalytic Activity of DNA Dissolved in Organic Solvents. H Abe, N Abe, A Shibata, K Ito, Y Tanaka, M Ito, H Saneyoshi, S Shuto, and Y Ito. Angew Chem Int Ed Engl. 2012 [Epub May 22] DOI: 10.1002/anie.201201111. PMID: 22615181
4. Photosensitizer-incorporated G-quadruplex DNA-functionalized magnetofluorescent nanoparticles for targeted magnetic resonance/fluorescence multimodal imaging and subsequent photodynamic therapy of cancer. M Yin, Z Li, Z Liu, J Ren, X Yang, and X Qu. Chem. Commun. 2012 [Epub May 24] PMID: 22622597
5. Detection of quadruplex DNA by gold nanoparticles. HF Crouse, A Doudt, C Zerbe, and S Basu. J Anal Methods Chem. 2012; 2012: 327603.
6. Fluorescence Detection of DNA, Adenosine-5′-Triphosphate (ATP) and Telomerase Activity by Zn(II)-Protoporphyrin IX/G-Quadruplex Labels. Z Zhang, E Sharon, R Freeman, X Liu, and I Willner. Anal Chem. 2012.
7. Ultrasensitive detection of potassium ions based on target induced DNA conformational switch enhanced fluorescence polarization. Hu K, Huang Y, Zhao S, Tian J, Wu Q, Zhang G, Jiang J. Analyst. 2012  [Epub May 3] PMID: 22551947
8. Single-molecule analysis using DNA origami. Rajendran A, Endo M, Sugiyama H. Angew Chem Int Ed Engl. 2012 Jan 23;51(4):874-90. doi: 10.1002/anie.201102113. Epub 2011 Nov 25. Review. PMID: 22121063
9. Enantioselective Friedel-Crafts reactions in water catalyzed by a human telomeric G-quadruplex DNA metalloenzyme. C Wang, Y Li, G Jia, Y Liu, S Lu, and C Li. Chem. Commun. 2012 [Epub May 18] PMID: 22595813

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• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry). [5 articles]

1. Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications. Yaku H, Fujimoto T, Murashima T, Miyoshi D, Sugimoto N. Chem. Commun. 2012 [Epub May 15] PMID: 22590705
2. The porphyrin TmPyP4 unfolds the extremely stable G-quadruplex in MT3-MMP mRNA and alleviates its repressive effect to enhance translation in eukaryotic cells. [OA] Mark J. Morris, Katherine L. Wingate, Jagannath Silwal, Thomas C. Leeper, and Soumitra Basu. Nucleic Acids Res. 2012; 40:4137-4145.
3. A New Cationic Porphyrin Derivative (TMPipEOPP) with Large Side Arm Substituents: A Highly Selective G-Quadruplex Optical Probe. [OA] LN Zhu, SJ Zhao, B Wu, XZ Li, and DM Kong. PLoS One. 2012; 7 (5): e35586 [Epub May 22] PMID: 22629300
4. Interaction of Berberine derivative with protein POT1 affect telomere function in cancer cells. Xiao N, Chen S, Ma Y, Qiu J, Tan JH, Ou TM, Gu LQ, Huang ZS, Li D. Biochem Biophys Res Commun. 2012 Mar 16; 419 (3): 567-572. Epub 2012 Feb 17. PMID: 22369941
5. Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS [OA] Raju G, Srinivas R, Santhosh Reddy V, Idris MM, Kamal A, Nagesh N. PLoS One. 2012; 7 (4): e35920. Epub 2012 Apr 27. PMID: 22558271

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• GQ-Structure & Dynamics. Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations. [2 articles]

1. Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation. [OA] Dengguo Wei, Gary N. Parkinson, Anthony P. Reszka, and Stephen Neidle. Nucleic Acids Res. 2012; 40: 4691-4700.
2. Energetic basis of human telomeric DNA folding into G-quadruplex structures. M Boncina, J Lah, I Prislan, & G Vesnaver. J Am Chem Soc. 2012. [Epub May 17] PMID: 22594380

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• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. (assemblies; molecular devices) [3 articles]

1. Crystal Structure of a Template-Assembled Synthetic G-Quadruplex. M Nikan, BO Patrick, and JC Sherman. Chembiochem. 2012. [Epub May 24] DOI: 10.1002/cbic.201200262. PMID: 22628361
2. Effect of precursor chain-length on the formation and stability of poly(ethylene glycol)-based supramolecular star polymers. Ikhlas Gadwal, Swati De, Mihaiela C. Stuparu, Se Gyu Jang, Roey J. Amir, Anzar Khan. Journal of Polymer Science Part A: Polymer Chemistry. 2012, 50, 2415–2420. DOI: 10.1002/pola.26018
3. Porphyrin-templated synthetic G-quartet (PorphySQ): a second prototype of G-quartet–based G-quadruplex ligand. Xu, H.-J.; Stefan, L.; Haudecoeur, R.; Vuong, S.; Richard, P.; Denat, F.; Barbe, J.-M.; Gros, C. P.; Monchaud, D. Org. Biomol. Chem. 2012. ASAP DOI: 10.1039/C2OB25601K

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[OA] = Open Access

GQW articles: April 2012 edition

This post includes 43 articles divided by category as follows:

• GQ-Biology (GQB).  9 articles
• GQ-Methods (GQM). 6 articles
• GQ-Cations (GQC). 0 articles
• GQ-Nano & Technology (GQNT). 9 articles
• GQ-Recognition (GQR). 10 articles
• GQ-Structure & Dynamics (GQSD). 8 articles
• GQ-Supramolecular (GQS). 1 article

April wasn’t as busy a month as March, where I listed 78 articles (!) for the month, but it was the second busiest month of this year in terms of publications related to GQs. The distribution of articles for April is more or less even, with the exception of the GQC and GQS, with a grand total of just one paper. This contrasts the the distribution of articles for March where the GQNT and GQR categories comprised more than half of all publications in the list. I haven’t classified (although I hope to do so soon…) the articles from January and February, but just to put in perspective how ‘busy’ March was, in those two months I listed 21 and 14 articles, respectively. So, I better stop writing and continue reading because I have a lot of catching up to do.

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• GQ-Biology. Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs) [9 articles]

1. The human RecQ helicases BLM and RECQL4 cooperate to preserve genome stability. Dharmendra Kumar Singh, Venkateswarlu Popuri, Tomasz Kulikowicz, Igor Shevelev, Avik K. Ghosh, Mahesh Ramamoorthy, Marie L. Rossi, Pavel Janscak, Deborah L. Croteau, & Vilhelm A. Bohr; Nucleic Acids Res. 28 April 2012 [Epub before print]
2. Replication Protein A Unfolds G-Quadruplex Structures with a Varying Degree of Efficiency. Qureshi MH, Ray S, Sewell AL, Basu S, Balci H. J Phys Chem B. 2012 Apr 14. [Epub ahead of print] PMID: 22500657
3.  G-quadruplexes in RNA biology; Millevoi S, Moine H, Vagner S. Wiley Interdiscip Rev RNA. 2012 Apr 4. doi: 10.1002/wrna.1113. [Epub before print] PMID: 22488917
4. Searching for Non-B DNA-Forming Motifs Using nBMST (Non-B DNA Motif Search Tool). Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins JR, Stephens RM. Curr Protoc Hum Genet. 2012 Apr; Chapter 18:Unit18.7. PMID: 22470144
5. Human telomeres replicate using chromosome-specific, rather than universal, replication programs. WC Drosopoulos, ST Kosiyatrakul, Z Yan, SG Calderano, & CL Schildkraut. J Cell Biol. 2012; 197: 253.
6. Telomere maintenance mechanisms in malignant peripheral nerve sheath tumors: expression and prognostic relevance. L Venturini, MG Daidone, R Motta, G Cimino-Reale, SF Hoare, A Gronchi, M Folini, WN Keith, and N Zaffaroni; Neuro Oncol. 2012. [Epub before print]
7. Functional binding of hexanucleotides to 3C protease of hepatitis A virus. Bärbel S. Blaum, Winfried Wünsche, Andrew J. Benie, Yuri Kusov, Hannelore Peters, Verena Gauss-Müller, Thomas Peters, and Georg Sczakiel. Nucleic Acids Res. 2012; 40:3042-3055.
8. Overcoming natural replication barriers: differential helicase requirements. Ranjith P. Anand, Kartik A. Shah, Hengyao Niu, Patrick Sung, Sergei M. Mirkin, & Catherine H. Freudenreich. Nucleic Acids Res. 2012 Feb; 40 (3):1091-1105. Epub 2011 Oct 7.
9. The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA. Béatrice Matot, Yann-Vaï Le Bihan, Rachel Lescasse, Javier Pérez, Simona Miron, Gabriel David, Bertrand Castaing, Patrick Weber, Bertrand Raynal, Sophie Zinn-Justin, Sylvaine Gasparini, and Marie-Hélène Le Du. Nucleic Acids Res. 2012; 40:3197-3207.

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• GQ-Methods. Application and development of methods and techniques to study GQs. [6 articles]

1. Isothermal folding of G-quadruplexes. Gray RD, Chaires JB. Methods. 2012 Apr 16. [Epub ahead of print] PMID: 22525787
2. Single-molecule investigation of G-quadruplex using a nanopore sensor. Shim J, Gu LQ. Methods. 2012 Apr 2. [Epub before print]  PMID: 22487183
3. Normalized Affymetrix expression data are biased by G-quadruplex formation. Hugh P. Shanahan, Farhat N. Memon, Graham J. G. Upton, & Andrew P. Harrison. Nucleic Acids Res. 2012; 40:3307-3315.
4. High-resolution 39K NMR spectroscopy of bio-organic solids. Wu G, Gan Z, Kwan IC, Fettinger JC, Davis JT. J Am Chem Soc. 2011 Dec 14;133(49):19570-3. Epub 2011 Aug 12. PMID: 21819148
5. Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT). R Ferreira, A Marchand, & V Gabelica. Methods. 2012. [Epub before print] PMID: 22465284
6. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. J Sponer, X Cang, and TE Cheatham 3rd. Methods. 2012. [Epub before print] PMID: 22525788

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• GQ-Nano & Technology. The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors). [9 articles]

1. Fluorescence Detection of DNA, Adenosine-5′-Triphosphate (ATP) and Telomerase Activity by Zn(II)-Protoporphyrin IX/G-Quadruplex Labels. Zhang Z, Sharon E, Freeman R, Liu X, Willner I. Anal Chem. 2012 Apr 29. [Epub before print]  PMID: 22540661
2. Label-Free Ultrasensitive Detection of Human Telomerase Activity Using Porphyrin-Functionalized Graphene and Electrochemiluminescence Technique. Wu L, Wang J, Feng L, Ren J, Wei W, Qu X. Adv Mater. 2012 Apr 10. doi: 10.1002/adma.201200412. [Epub before print] PMID: 22488983
3. A simple, post-additional antioxidant capacity assay using adenosine triphosphate-stabilized 2,2′-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) radical cation in a G-quadruplex DNAzyme catalyzed ABTS-H(2)O(2) system. Jia SM, Liu XF, Kong DM, Shen HX. Biosens Bioelectron. 2012 Mar 23. [Epub ahead of print] PMID: 22487010
4. Colorimetric detection of cholesterol with G-quadruplex-based DNAzymes and ABTS(2-). Li R, Xiong C, Xiao Z, Ling L. Anal Chim Acta. 2012 Apr 29;724:80-5. Epub 2012 Feb 27. PMID: 22483213
5. DNA origami as biocompatible surface to match single-molecule and ensemble experiments. Andreas Gietl, Phil Holzmeister, Dina Grohmann, & Philip Tinnefeld. Nucleic Acids Res. published 20 April 2012, 10.1093/nar/gks326
6. Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method. Laura G. Carrascosa, S. Gómez-Montes, A. Aviñó, A. Nadal, M. Pla, R. Eritja, & L. M. Lechuga. Nucleic Acids Res. 2012; 40:e56.
7.  DNA origami as biocompatible surface to match single-molecule and ensemble experiments. Andreas Gietl, Phil Holzmeister, Dina Grohmann, & Philip Tinnefeld. Nucleic Acids Res. published 20 April 2012. [Epub before print]
8. Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin. Y Yuan, R Yuan, Y Chai, Y Zhuo, X Ye, X Gan, & L Bai. Chem Commun. 2012. [Epub before print]
9. DNAzyme-based turn-on chemiluminescence assays in homogenous media. M Zhou, Y Liu, Y Tu, G Tao, and J Yan Biosens Bioelectron. 2012. [Epub before print] PMID: 22465444

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• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry). [10 articles]

1. Recent Progress and Future Potential for Metal Complexes as Anticancer Drugs Targeting G-quadruplex DNA. Zhang J, Zhang F, Li H, Liu C, Xia J, Ma L, Chu W, Zhang Z, Chen C, Li S, Wang S. Curr Med Chem. 2012 Apr 20. [Epub ahead of print] PMID: 22519400
2. 12-N-Methylated 5,6-dihydrobenzo[c]acridine derivatives: A new class of highly selective ligands for c-myc G-quadruplex DNA. Liao SR, Zhou CX, Wu WB, Ou TM, Tan JH, Li D, Gu LQ, Huang ZS. Eur J Med Chem. 2012 Mar 30. [Epub before print] PMID: 22513122
3. Induction of senescence in cancer cells by a G-quadruplex stabilizer BMVC4 is independent of its telomerase inhibitory activity. Huang FC, Chang CC, Wang JM, Chang TC, Lin JJ. Br J Pharmacol. 2012 Apr 18. doi: 10.1111/j.1476-5381.2012.01997.x. [Epub before print] PMID: 22509942
4. d(TGGGAG) with 5′-nucleobase-attached large hydrophobic groups as potent inhibitors for HIV-1 envelop proteins mediated cell-cell fusion. Chen W, Xu L, Cai L, Zheng B, Wang K, He J, Liu K. Bioorg Med Chem Lett. 2011 Oct 1;21(19):5762-5764. Epub 2011 Aug 8. PMID: 21873060
5. Spectroscopic, molecular modeling and NMR-spectroscopic investigation of the binding mode of the natural alkaloids berberine and sanguinarine to human telomeric G-quadruplex DNA. Bessi I, Bazzicalupi C, Richter C, Jonker HR, Saxena K, Sissi C, Chioccioli M, Bianco S, Bilia AR, Schwalbe H, Gratteri P. ACS Chem Biol. 2012 Apr 9. [Epub before print]  PMID: 22486369
6. Disubstituted 1,8-dipyrazolcarbazole derivatives as a new type of c-myc G-quadruplex binding ligands. Chen WJ, Zhou CX, Yao PF, Wang XX, Tan JH, Li D, Ou TM, Gu LQ, Huang ZS. Bioorg Med Chem. 2012 Mar 21. [Epub before print] PMID: 22484007
7. The impact of the G-quadruplex conformation in the development of novel therapeutic and diagnostic agents. Alcaro S. Curr Pharm Des. 2012 May 1;18(14):1865-6. PMID: 22471996
8. The Interaction of Telomeric DNA and C-myc22 G-Quadruplex with 11 Natural Alkaloids. Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. Nucleic Acid Ther. 2012 Apr;22(2):127-36. PMID: 22480315
9. Water soluble extended naphthalene diimides as pH fluorescent sensors and G-quadruplex ligands. Doria F, Nadai M, Sattin G, Pasotti L, Richter SN, Freccero M. Org Biomol Chem. 2012 Apr 3. [Epub before print] PMID: 22469919
10. Structure of Musashi1 in a complex with target RNA: the role of aromatic stacking interactions. Takako Ohyama, Takashi Nagata, Kengo Tsuda, Naohiro Kobayashi, Takao Imai, Hideyuki Okano, Toshio Yamazaki, and Masato Katahira. Nucleic Acids Res. 2012; 40:3218-3231.

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• GQ-Structure & Dynamics. Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations. [8 articles]

1. Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule level using single-pair FRET. Tomás Fessl, Frantisek Adamec, Tomás Polívka, Silvie Foldynová-Trantírková, Frantisek Vácha, & Lukás Trantírek. Nucleic Acids Res. 28 April 2012 [Epub before print]
2. 8-Oxo-7,8-dihydrodeoxyadenosine: The first example of a native DNA lesion that stabilizes human telomeric G-quadruplex DNA. Aggrawal M, Joo H, Liu W, Tsai J, Xue L. Biochem Biophys Res Commun. 2012 Apr 19. [Epub before print] PMID: 22538366
3. Time-resolved NMR spectroscopic studies of DNA i-motif folding reveal kinetic partitioning. Lieblein AL, Buck J, Schlepckow K, Fürtig B, Schwalbe H. Angew Chem Int Ed Engl. 2012 Jan 2; 51 (1):250-253. doi: 10.1002/anie.201104938. PMID: 22095623
4. The Guanine Bases in DNA G-Quadruplex Adopt Non-Planar Geometries Owing to Solvation and Base Pairing. Sychrovsky V, Sochorová Vokáčová Z, Trantirek L. J Phys Chem A. 2012 Apr 3. [Epub before print] PMID: 22471881
5. Conformations of individual quadruplex units studied in the context of extended human telomeric DNA. Singh V, Azarkh M, Drescher M, Hartig JS. Chem Commun. 2012 Apr 24. [Epub before print]  PMID: 22531827
6. Molecular dynamics studies of the STAT3 homodimer:DNA complex: relationships between STAT3 mutations and protein-DNA recognition. J Husby, AK Todd, SM Haider, G Zinzella, DE Thurston, and S Neidle. J Chem Inf Model. 2012. [Epub before print]
7. Replication Protein A Unfolds G-Quadruplex Structures with a Varying Degree of Efficiency. MH Qureshi, S Ray, AL Sewell, S Basu, and H Balci. J Phys Chem B. 2012. [Epub before print]
8. Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops. Maja Marusic, Primoz Sket, Lubos Bauer, Viktor Viglasky, & Janez Plavec. Nucleic Acids Res. 24 April 2012. [Epub before print] PMID: 22532609

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• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. (assemblies; molecular devices) [1 article]

1. Molecular “light switch” for G-quadruplex DNA: cycling the switch on and off. Shi S, Zhao J, Gao X, Lv C, Yang L, Hao J, Huang H, Yao J, Sun W, Yao T, Ji L. Dalton Trans. 2012 Apr 10. [Epub before print] PMID: 22488166

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GQW articles: March 2012 edition

From this post onwards, I intend to classify the monthly references by subtopics. Having the references curated this way makes the initial process a little more time consuming, but, I’m hoping it will pay out in the end by providing a quick reference source in the future.

The initial subtopics, with a basic description and some keywords/tags, are:

• GQ-Biology. Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs)
• GQ-Cations. Studies aimed at elucidating the role of cations in GQ structure and/or dynamics.
• GQ-Methods. Application and development of methods and techniques to study GQs.
• GQ-Nano & Technology. The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors; molecular machinery).
• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry).
• GQ-Structure & Dynamics. Studies aimed at elucidating the detailed structure and/or dynamics of GQs. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations.
• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. Of particular interest are studies on the use of independent guanosine subunits to guide the self-assembly of complex structures. (assemblies; molecular devices)

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• GQ-Biology. Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs) [13 articles]

1. The DEAH-box helicase RHAU is an essential gene and critical for mouse hematopoiesis. Lai JC, Ponti S, Pan D, Kohler H, Skoda RC, Matthias P, Nagamine Y. Blood. 2012 Mar 15. [Epub before print] PMID: 22422825
2. The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary. [OA] E. P. Booy, M. Meier, N. Okun, S. K. Novakowski, S. Xiong, J. Stetefeld, & S. A. McKenna. Nucleic Acids Res. published 11 January 2012, 10.1093/nar/gkr1306
3. Cell Cycle Regulation of G-Quadruplex DNA Structures at Telomeres. Juranek SA, Paeschke K. Curr Pharm Des.2012 Feb 27. [Epub before print] PMID: 22376109
4. New insights into replication origin characteristics in metazoans. Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali M. Cell Cycle. 2012 Feb 15;11(4):658-67. PMID: 22373526
5. The formation and stabilization of a novel G-quadruplex in the 5′-flanking region of the relaxin gene [OA] Lin S, Gu H, Xu M, Cui X, Zhang Y, Gao W, Yuan G. PLoS One. 2012;7(2):e31201. Epub 2012 Feb 21. PMID: 22363579
6. Saccharomyces cerevisiae Mph1 helicase on junction-containing DNA structures [OA] Young-Hoon Kang, Palinda Ruvan Munashingha, Chul-Hwan Lee, Tuan Anh Nguyen, & Yeon-Soo Seo. Nucleic Acids Res. 2012; 40: 2089-2106.
7. Nonspaced inverted DNA repeats are preferential targets for homology-directed gene repair in mammalian cells. [OA] Maarten Holkers, Antoine A. F. de Vries, and Manuel A. F. V. Gonçalves. Nucleic Acids Res. 2012; 40:1984-1999.
8. Yin Yang 1 contains G-quadruplex structures in its promoter and 5′-UTR and its expression is modulated by G4 resolvase 1. [OA] Weiwei Huang, Philip J. Smaldino, Qiang Zhang, Lance D. Miller, Paul Cao, Kristin Stadelman, Meimei Wan, Banabihari Giri, Ming Lei, Yoshikuni Nagamine, James P. Vaughn, Steven A. Akman, & Guangchao Sui. Nucleic Acids Res. 2012; 40:1033-1049.
9. Overcoming natural replication barriers: differential helicase requirements [OA] Ranjith P. Anand, Kartik A. Shah, Hengyao Niu, Patrick Sung, Sergei M. Mirkin, & Catherine H. Freudenreich. Nucleic Acids Res. 2012; 40:1091-1105.
10. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals. [OA] Aradhita Baral, Pankaj Kumar, Rashi Halder, Prithvi Mani, Vinod Kumar Yadav, Ankita Singh, Swapan K. Das, & Shantanu Chowdhury. Nucleic Acids Res. published 11 January 2012, [Epub before print]
11. Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. R Halder, JF Riou, MP Teulade-Fichou, T Frickey, & JS Hartig. BMC Res Notes. 2012; 5: 138.
12. A telomerase-associated RecQ protein-like helicase resolves telomeric G-quadruplex structures during replication. J Postberg, M Tsytlonok, D Sparvoli, D Rhodes, & HJ Lipps. Gene. 2012. [Epub before print]
13. DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase. N Sabouri, KR McDonald, CJ Webb, IM Cristea, & VA Zakian. Genes Dev. 2012; 26: 581.

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• GQ-Cations. Studies aimed at elucidating the role of cations in the structure and/or dynamics of GQs. [1 article]

1. Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb²⁺ . Wei Liu, Hong Zhu, Bin Zheng, Sheng Cheng, Yan Fu, Wei Li, Tai-Chu Lau, and Haojun Liang. Nucleic Acids Res. published 12 January 2012, 10.1093/nar/gkr1310

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• GQ-Methods. Application and development of methods and techniques to study GQs. [11 articles]

1. Determination of DNA structural detail using radioprobing. Girard PM, Laughton C, Nikjoo H. Int J Radiat Biol. 2012 Jan;88(1-2):123-128. Epub 2011 Sep 21. PMID: 21823822
2. Tandem mass spectrometry of platinated quadruplex DNA. Stucki SR, Nyakas A, Schürch S. J Mass Spectrom. 2011 Dec;46 (12):1288-1297. doi: 10.1002/jms.2019. PMID: 22223421
3. Selective isolation of G-quadruplexes by affinity chromatography. Chang T, Liu X, Cheng X, Qi C, Mei H, Shangguan D. J Chromatogr A. 2012 Feb 16. [Epub before print] PMID: 22398385
4. Reporter assays for studying quadruplex nucleic acids. Halder K, Benzler M, Hartig JS. Methods. 2012 Feb 23. [Epub ahead of print] PMID: 22388183
5. G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots [OA] Robert Buscaglia, David M. Jameson, & Jonathan B. Chaires. Nucleic Acids Res. published 12 January 2012, 10.1093/nar/gkr1286
6. Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method. Laura G. Carrascosa, S. Gómez-Montes, A. Aviñó, A. Nadal, M. Pla, R. Eritja, & L. M. Lechuga. Nucleic Acids Res. published 12 January 2012, 10.1093/nar/gkr1304
7. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes. E Largy, F Hamon, & MP Teulade-Fichou. Methods. 2012. [Epub before print]
8. Methods of studying telomere damage induced by quadruplex-ligand complexes. Rizzo A, Salvati E, Biroccio A. Methods. 2012 Mar 4. [Epub before print] PMID: 22410593
9. Fluorescence properties of 8-(2-pyridyl)guanine “2PyG” as compared to 2-aminopurine in DNA. Dumas A, Luedtke NW. Chembiochem. 2011 Sep 5;12(13):2044-51. doi: 10.1002/cbic.201100214. Epub 2011 Jul 22. PMID: 21786378
10. Circular dichroism and guanine quadruplexes. M Vorlickova, I Kejnovska, J Sagi, D Renciuk, K Bednarova, J Motlova, & J Kypr. Methods. 2012. [Epub before print]
11. Combination of chromatographic and chemometric methods to study the interactions between DNA strands. S Ruiz-Castelar, A Checa, R Gargallo, & J Jaumot. Anal Chim Acta. 2012; 722: 34. PMID: 22444532

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• GQ-Nano & Technology.  The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors, aptamers). [17 articles]

1. Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin. Yuan Y, Yuan R, Chai Y, Zhuo Y, Ye X, Gan X, Bai L. Chem Commun. 2012 Mar 30. [Epub before print] PMID: 22466956
2. DNAzyme-based turn-on chemiluminescence assays in homogenous media. Zhou M, Liu Y, Tu Y, Tao G, Yan. J. Biosens Bioelectron. 2012 Mar 17. [Epub before print] PMID: 22465444
3. Label-free Fluorescent Detection of Ions, Proteins and Small Molecules Using Structure-Switching Aptamers, SYBR Gold and Exonuclease Ⅰ. Zheng D, Zou R, Lou X. Anal Chem. 2012 Mar 16. [Epub before print]  PMID: 22424113
4. The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands. [OA] Virgilio A, Esposito V, Citarella G, Pepe A, Mayol L, Galeone A. Nucleic Acids Res. 2012 Jan; 40 (1):461-75. Epub 2011 Sep 9. PMID: 21908403
5. Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch. De Rache A, Kejnovská I, Vorlíčková M, Buess-Herman C. Chemistry. 2012 Feb 23. doi: 10.1002/chem.201103381. [Epub ahead of print] PMID: 22362492
6. Amplified Surface Plasmon Resonance and Electrochemical Detection of Pb2+ Ions Using the Pb2+-Dependent DNAzyme and Hemin/G-Quadruplex as a Label. Pelossof G, Tel-Vered R, Willner I. Anal Chem. 2012 Mar 15. [Epub ahead of print] PMID: 22424055
7. A G-quadruplex based label-free fluorescent biosensor for lead ion. Guo L, Nie D, Qiu C, Zheng Q, Wu H, Ye P, Hao Y, Fu F, Chen G. Biosens Bioelectron. 2012 Feb 24. [Epub before print] PMID: 22417873
8. G-Quadruplex as Signal Transducer for Biorecognition Events. Lv L, Guo Z, Wang J, Wang E. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22380517
9. G-Quadruplex Based Probes for Visual Detection and Sensing. Neo JL, Kamaladasan K, Uttamchandani M. Curr Pharm Des. 2012 Feb 27. [Epub before print] PMID: 22380516
10. G-quadruplex DNA Aptamers and their Ligands: Structure, Function and Application. Tucker WO, Shum KT, Tanner JA. Curr Pharm Des. 2012 Feb 27. [Epub before print] PMID: 22376117
11. A label-free, G-quadruplex DNAzyme-based fluorescent probe for signal-amplified DNA detection and turn-on assay of endonuclease. Zhou Z, Du Y, Zhang L, Dong S. Biosens Bioelectron. 2012 Jan 28. [Epub ahead of print] PMID: 22366377
12. A label-free fluorescence DNA probe based on ligation reaction with quadruplex formation for highly sensitive and selective detection of nicotinamide adenine dinucleotide. J Zhao, L Zhang, J Jiang, G Shen, and R Yu. Chem Commun. 2012.
13. Label-free Fluorescent Detection of Ions, Proteins and Small Molecules Using Structure-Switching Aptamers, SYBR Gold and Exonuclease. D Zheng, R Zou, and X Lou. Anal Chem. 2012. [Epub before print]
14. G-Quadruplex as Signal Transducer for Biorecognition Events. L Lv, Z Guo, J Wang, and E Wang. Curr Pharm Des. 2012. [Epub before print]
15. G-quadruplex DNA Aptamers and their Ligands: Structure, Function and Application. WO Tucker, KT Shum, and JA Tanner. Curr Pharm Des. 2012. [Epub before print]
16. A novel biosensing strategy for screening G-quadruplex ligands based on graphene oxide sheets. H Wang, T Chen, S Wu, X Chu, and R Yu. Biosens Bioelectron. 2012. [Epub before print]
17. Single strand DNA catenane synthesis using the formation of G-quadruplex structure. Sannohe Y, Sugiyama H. Bioorg Med Chem. 2012 Feb 1. [Epub before print] PMID: 22364954

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• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (ynthesis; design; pharmacology; medicinal chemistry). [29 articles]

1. Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure-Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties. Jain AK, Paul A, Maji B, Muniyappa K, Bhattacharya S. J Med Chem. 2012 Mar 27. [Epub ahead of print]PMID: 22452380
2. Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes. Campbell NH, Karim NH, Parkinson GN, Gunaratnam M, Petrucci V, Todd AK, Vilar R, Neidle S. J Med Chem. 2012 Jan 12; 55 (1):209-222. Epub 2011 Dec 13. PMID: 22112241
3. Structural polymorphism of human telomere G-quadruplex induced by a pyridyl carboxamide molecule. Xu L, Xu Z, Shang Y, Feng S, Zhou X. Bioorg Med Chem Lett. 2012 Feb 28. [Epub ahead of print] PMID: 22440628
4. A Caged Ligand for a Telomeric G-Quadruplex. Nakamura T, Iida K, Tera M, Shin-Ya K, Seimiya H, Nagasawa K. Chembiochem. 2012 Mar 21. doi: 10.1002/cbic.201200013. [Epub ahead of print] PMID: 22438312
5. Structure, function and targeting of human telomere RNA. Xu Y, Komiyama M. Methods. 2012 Mar 8. [Epub ahead of print] PMID: 22425636
6. G-quadruplexes: targets and tools in anticancer drug design. Düchler M. J Drug Target. 2012 Mar 19. [Epub ahead of print] PMID: 22424091
7. Identification of novel telomeric G-quadruplex-targeting chemical scaffolds through screening of three NCI libraries. Rahman KM, Tizkova K, Reszka AP, Neidle S, Thurston DE. Bioorg Med Chem Lett. 2012 Feb 16. [Epub ahead of print] PMID: 22421021
8. Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. Halder R, Riou JF, Teulade-Fichou MP, Frickey T, Hartig JS. BMC Res Notes. 2012 Mar 13;5(1):138. [Epub ahead of print] PMID: 22414013
9. Spectroscopic probing of recognition of the G-quadruplex in c-kit promoter by small-molecule natural products. Cui X, Lin S, Yuan G. Int J Biol Macromol. 2012 Mar 3. [Epub ahead of print] PMID: 22405847
10. In silico screening of quadruplex-binding ligands. Ma DL, Ma VP, Chan DS, Leung KH, Zhong HJ, Leung CH. Methods. 2012 Feb 26. [Epub ahead of print] PMID: 22391485
11. Heterocyclic Dications as a New Class of Telomeric G-Quadruplex Targeting Agents.  Nanjunda R, Musetti C, Kumar A, Ismail MA, Farahat AA, Wang S, Sissi C, Palumbo M, Boykin DW, Wilson WD. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22380518
12. Synthesis of Small Molecules Targeting Multiple DNA Structures using Click Chemistry. Howell LA, Bowater RA, O’Connell MA, Reszka AP, Neidle S, Searcey M. ChemMedChem. 2012 Feb 29. doi: 10.1002/cmdc.201200060. [Epub ahead of print] PMID: 22378532
13. Human Telomere RNA: A Potential Target for Ligand Recognition. Xu Y. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376119
14. Screening of a Chemical Library by HT-G4-FID for Discovery of Selective G-quadruplex Binders. Largy E, Saettel N, Hamon F, Dubruille S, Teulade-Fichou MP. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376118
15. Searching Drug-like Anti-cancer Compound(s) Based on G-Quadruplex Ligands. Li Q, Xiang JF, Zhang H, Tang YL. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376116
16. The Polymorfisms of DNA G-Quadruplex investigated by Docking Experiments with Telomestatin Enantiomers. Alcaro S, Costa G, Distinto S, Moraca F, Ortuso F, Parrotta L, Artese A. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376115
17. G-Quadruplex Binding Ligands: from Naturally Occurring to Rationally Designed Molecules. Le TV, Han S, Chae J, Park HJ. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376113
18. Targeting DNA G-Quadruplex Structures with Peptide Nucleic Acids. Panyutin IG, Onyshchenko MI, Englund EA, Appella DH, Neumann RD. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376112
19. Luminescent G-quadruplex Probes. Ma DL, Chan DS, Yang H, He HZ, Leung CH. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376110
20. Experimental Methods for Studying the Interactions between G-Quadruplex Structures and Ligands Jaumot J, Gargallo R. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376108
21. Structure Conversion and Structure Separation of G-Quadruplexes Investigated by Carbazole Derivatives. Chang TC, Chu JF, Tsai YL, Wang ZF. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376106
22. Recent Developments in the Chemistry and Biology of G-Quadruplexes with Reference to the DNA Groove Binders. Jain AK, Bhattacharya S. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376105
23. State-of-the-Art Methodologies for the Discovery and Characterization of DNA G-Quadruplex Binder. Pagano B, Cosconati S, Gabelica V, Petraccone L, De Tito S, Marinelli L, La Pietra V, di Leva FS, Lauri I, Trotta R, Novellino E, Giancola C, Randazzo A. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376104
24. Stabilization of G-Quadruplex DNA, Inhibition of Telomerase Activity and Live Cell Imaging Studies of Chiral Ruthenium(II) Complexes. Sun D, Liu Y, Liu D, Zhang R, Yang X, Liu J. Chemistry. 2012 Feb 24. doi: 10.1002/chem.201103156. [Epub ahead of print] PMID: 22367788
25. Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures. Doria F, Nadai M, Folini M, Di Antonio M, Germani L, Percivalle C, Sissi C, Zaffaroni N, Alcaro S, Artese A, Richter SN, Freccero M. Org Biomol Chem. 2012 Feb 27. [Epub ahead of print] PMID: 22367401
26. Interaction of human telomeric DNA with N-methyl mesoporphyrin IX. [OA] Nicoludis JM, Barrett SP, Mergny JL, Yatsunyk LA. Nucleic Acids Res. 2012 Feb 23. [Epub ahead of print] PMID: 22362740
27. Luminescent detection of DNA-binding proteins [OA] Chung-Hang Leung, Daniel Shiu-Hin Chan, Hong-Zhang He, Zhen Cheng, Hui Yang, and Dik-Lung Ma. Nucleic Acids Res. 2012; 40:941-955.
28. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch [OA] Catherine D. Eichhorn, Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks, III, and Hashim M. Al-Hashimi. Nucleic Acids Res. 2012; 40:1345-1355.
29. Identifying G-quadruplex-binding ligands using DNA-functionalized gold nanoparticles. Y Qiao, J Deng, Y Jin, G Chen, & L Wang. Analyst. 2012; 137: 1663.

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• GQ-Structure & Dynamics. Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations. [7 articles]

1. RNA G-Quadruplexes: G-quadruplexes with “U” Turns. Agarwal T, Jayaraj G, Pandey SP, Agarwala P, Maiti S. Curr Pharm Des. 2012 Feb 27. [Epub before print] PMID: 22376111
2. Formation of pearl-necklace monomorphic G-quadruplexes in the human CEB25 minisatellite. Amrane S, Adrian M, Heddi B, Serero A, Nicolas A, Mergny JL, Phan AT. J Am Chem Soc. 2012 Feb 29. [Epub before print] PMID: 22376028
3. The Tertiary DNA Structure in the Single-Stranded hTERT Promoter Fragment Unfolds and Refolds by Parallel Pathways via Cooperative or Sequential Events. Yu Z, Gaerig V, Cui Y, Kang H, Gokhale V, Zhao Y, Hurley LH, Mao H. J Am Chem Soc. 2012 Feb 28. [Epub before print] PMID: 22372563
4. Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study. AK Chaubey, KD Dubey, and RP Ojha. J Comput Aided Mol Des. 2012. [Epub before print]
5. Studying the effect of crowding and dehydration on DNA G-quadruplexes. L Petraccone, B Pagano, and C Giancola. Methods. 2012. [Epub before print]
6. Stability and Structure of Long Intramolecular G-quadruplexes. L Payet and JL Huppert. Biochemistry. 2012. [Epub before print]
7. The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages [OA] GR Clark, PD Pytel, and CJ Squire. Nucleic Acids Res. 2012. [Epub before print]

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• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. Of particular interest are studies on the use of independent guanosine subunits to guide the self-assembly of complex structures. [o articles]

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This post includes 78 articles divided by categories as follows:

• GQ-Biology.  13 articles
• GQ-Methods. 11 articles
• GQ-Cations. 1 article
• GQ-Nano & Technology. 17 articles
• GQ-Recognition. 29 articles
• GQ-Structure & Dynamics. 7 articles
• GQ-Supramolecular. 0 articles

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[OA] = Open Access

GQW articles: February 2012 edition

Following is a list of articles related to G-quadruplex research published (for the first time on the web or “officially” in print) during the month of February 2012. This post includes 14 articles divided by category as follows:

• GQ-Biology (GQB).  6 articles
• GQ-Cations (GQC). 1 articles
• GQ-Methods (GQM). 1 articles
• GQ-Nano & Technology (GQNT). 3 articles
• GQ-Recognition (GQR). 2 articles
• GQ-Structure & Dynamics (GQSD). 1 articles
• GQ-Supramolecular (GQS). 0 article

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• GQ-Biology. Studies aimed at the discovery of GQs in living organisms and the elucidation of their role in biological processes. (putative quadruplex sequences in genomes; proteins that recognize GQs; in vitro and in vivo studies of GQs) [6 articles]

1. Charge and substituent effects on the stability of porphyrin/G-quadruplex adducts. Ramos CI, Tomé JP, Santana-Marques MG. J Mass Spectrom. 2012 Feb;47(2):173-179. doi: 10.1002/jms.2048. PMID: 22359326
2. Self-entanglement of long linear DNA vectors using transient non-B-DNA attachment points: A new concept for improvement of non-viral therapeutic gene delivery. Tolmachov OE. Med Hypotheses. 2012 Feb 20. [Epub before print] PMID: 22356834
3.  5′-UTR RNA G-quadruplexes: translation regulation and targeting. [OA] Bugaut A, Balasubramanian S. Nucleic Acids Res. 2012 Feb 20. [Epub before print] PMID: 22351747
4. A telomerase-associated RecQ protein-like helicase resolves telomeric G-quadruplex structures during replication. Postberg J, Tsytlonok M, Sparvoli D, Rhodes D, Lipps HJ. Gene. 2012 Feb 2. [Epub before print] PMID: 22327026
5. New insights into replication origin characteristics in metazoans. [OA] Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali M. Cell Cycle. 2012 Feb 15; 11 (4). PMID: 22307000
6. A G-Rich Element Forms a G-Quadruplex and Regulates Bace1 mRNA Alternative Splicing. Fisette JF, Montagna DR, Mihailescu MR, Wolfe MS. J Neurochem. 2012 Feb 3. [Epub before print] doi: 10.1111/j.1471-4159.2012.07680.x. PMID: 22303960

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• GQ-Cations. Studies aimed at elucidating the role of cations in GQ structure and/or dynamics. [1 articles]

1. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. [OA] Reshetnikov RV, Sponer J, Rassokhina OI, Kopylov AM, Tsvetkov PO, Makarov AA, Golovin AV. Nucleic Acids Res. 2011 Dec;39 (22):9789-9802. Epub 2011 Sep 5. PMID: 21893589

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• GQ-Methods. Application and development of methods and techniques to study GQs. [1 articles]

1.  Experimental approaches to identify cellular G-quadruplex structures and functions. Antonio MD, Rodriguez R, Balasubramanian S. Methods. 2012 Feb 11. [Epub before print] PMID: 22343041

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• GQ-Nano & Technology. The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors). [3 articles]

1. Following Glucose Oxidase Activity by Chemiluminescence and Chemiluminescence Resonance Energy Transfer (CRET) Processes Involving Enzyme-DNAzyme Conjugates. [OA] Niazov A, Freeman R, Girsh J, Willner I. Sensors. 2011;11(11):10388-97. Epub 2011 Oct 31. PMID: 22346648
2. A label-free G-quadruplex-based switch-on fluorescence assay for the selective detection of ATP. He HZ, Pui-Yan Ma V, Leung KH, Shiu-Hin Chan D, Yang H, Cheng Z, Leung CH, Ma DL. Analyst. 2012 Feb 20. [Epub before print] PMID: 22343772
3. A novel biosensing strategy for screening G-quadruplex ligands based on graphene oxide sheets. Wang H, Chen T, Wu S, Chu X, Yu R. Biosens Bioelectron. 2012 Jan 26. [Epub before print] PMID: 22336439

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• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry). [2 articles]

1. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Britton S, Oelschlaegel T, Xhemalce B, Balasubramanian S, Jackson SP. Nat Chem Biol. 2012 Feb 5. doi: 10.1038/nchembio.780 [Epub before print] PMID: 22306580
2.  Alternative DNA structures: G4 DNA in cells: itae missa est? Jean-Louis Mergny. Nature Chemical Biology 8, 225–226 (2012) doi:10.1038/nchembio.793 Published online 15 February 2012

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• GQ-Structure & Dynamics. Studies aimed at elucidating structure and/or dynamics GQ. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations. [1 articles]

1.  Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from intron of N-myc gene. Trajkovski M, Webba da Silva M, Plavec J. J Am Chem Soc. 2012 Feb 3. [Epub before print] PMID: 22303871

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• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. (assemblies; molecular devices) [0 articles]

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[OA] = Open Access