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

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