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.

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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

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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

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