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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