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

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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) 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

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