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.

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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

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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.

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