GQW articles: May 2012 edition

This post includes 33 articles divided by category as follows:

• GQ-Biology (GQB).  8 articles
• GQ-Cations (GQC). 1 article
• GQ-Methods (GQM). 5 articles
• GQ-Nano & Technology (GQNT). 9 articles
• GQ-Recognition (GQR). 5 articles
• GQ-Structure & Dynamics (GQSD). 2 articles
• GQ-Supramolecular (GQS). 3 articles

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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) [8 articles]

1. DNA helicase and helicase–nuclease enzymes with a conserved iron–sulfur cluster. [OA] Yuliang Wu and Robert M. Brosh, Jr. Nucleic Acids Res. 2012; 40:4247-4260.
2. The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary. [OA] E. P. Booy, M. Meier, N. Okun, S. K. Novakowski, S. Xiong, J. Stetefeld, and S. A. McKenna. Nucleic Acids Res. 2012; 40:4110-4124.
3. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals. [OA] Aradhita Baral, Pankaj Kumar, Rashi Halder, Prithvi Mani, Vinod Kumar Yadav, Ankita Singh, Swapan K. Das, and Shantanu Chowdhury. Nucleic Acids Res. 2012; 40: 3800-3811.
4. Autophagy acts as a safeguard mechanism against G-quadruplex ligand-mediated DNA damage. [OA] NI Orlotti, G Cimino-Reale, E Borghini, M Pennati, C Sissi, F Perrone, M Palumbo, MG Daidone, M Folini, and N Zaffaroni. Autophagy. 8 (8) 2012 [Epub Aug 1] PMID: 22627293
5. RTEL1 Dismantles T Loops and Counteracts Telomeric G4-DNA to Maintain Telomere Integrity. JB Vannier, V Pavicic-Kaltenbrunner, MI Petalcorin, H Ding, and SJ Boulton. Cell. 2012; 149 (4): 795-806. PMID: 22579284
6. Promoter G-quadruplex sequences are targets for base oxidation and strand cleavage during hypoxia-induced transcription. DW Clark, T Phang, MG Edwards, MW Geraci, & MN Gillespie. Free Radic Biol Med. 2012. [Epub May 1] PMID: 22583700
7. The human RecQ helicases BLM and RECQL4 cooperate to preserve genome stability. [OA] D Kumar Singh, V Popuri, T Kulikowicz, I Shevelev, AK Ghosh, M Ramamoorthy, ML Rossi, P Janscak, DL Croteau, and VA Bohr. Nucleic Acids Res. 2012.
8. The BLM helicase contributes to telomere maintenance through processing of late-replicating intermediate structures. [OA] Colleen Barefield and Jan Karlseder. Nucleic Acids Res. 2012. [Epub May 10] DOI: 10.1093/nar/gks407

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• GQ-Cations. Studies aimed at elucidating the role of cations in GQ structure and/or dynamics. [1 article]

1. Stable G-quadruplex structure in a hydrated ion pair: cholinium cation and dihydrogen phosphate anion. K Fujita and H Ohno. Chem. Commun. 2012; 48 (46): 5751-5753.  PMID: 22552502

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• GQ-Methods. Application and development of methods and techniques to study GQs. [5 articles]

1. NMR spectroscopy of G-quadruplexes. M Adrian, B Heddi, and AT Phan. Methods. 2012 [Epub May 24] PMID: 22633887
2. Sequence-specific detection of nucleic acids utilizing isothermal enrichment of G-quadruplex DNAzymes. HJ Xiao, HC Hak, DM Kong, and HX Shen. Anal Chim Acta. 729: 67-72. 2012 [Epub Apr 21] PMID: 22595435
3. QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences. Menendez C, Frees S, Bagga PS. Nucleic Acids Res. 2012 May 10. [Epub ahead of print] PMID: 22576365
4. UV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase. Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P. J Phys Chem A. 2012 May 8. [Epub ahead of print] PMID: 22568521
5. Computational Detection and Analysis of Sequences with Duplex-Derived Interstrand G-quadruplex Forming Potential. Cao K, Ryvkin P, Brad Johnson F. Methods. 2012  [Epub May 28] PMID: 22652626

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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. Aptamer-DNAzyme hairpins for biosensing of Ochratoxin A. Yang C, Lates V, Prieto-Simón B, Marty JL, Yang X. Biosens Bioelectron. 2012 Feb 15; 32 (1): 208-212. [Epub 2011 Dec 13] PMID: 22221796
2. Sensitive fluorescence biosensor for folate receptor based on terminal protection of small-molecule-linked DNA. X Wei, W Lin, N Ma, F Luo, Z Lin, L Guo, B Qiu, & G Chen.  Chem. Commun. 2012; 48 (49): 6184-6186. [Epub May 16] PMID: 22590712
3. Structure Formation and Catalytic Activity of DNA Dissolved in Organic Solvents. H Abe, N Abe, A Shibata, K Ito, Y Tanaka, M Ito, H Saneyoshi, S Shuto, and Y Ito. Angew Chem Int Ed Engl. 2012 [Epub May 22] DOI: 10.1002/anie.201201111. PMID: 22615181
4. Photosensitizer-incorporated G-quadruplex DNA-functionalized magnetofluorescent nanoparticles for targeted magnetic resonance/fluorescence multimodal imaging and subsequent photodynamic therapy of cancer. M Yin, Z Li, Z Liu, J Ren, X Yang, and X Qu. Chem. Commun. 2012 [Epub May 24] PMID: 22622597
5. Detection of quadruplex DNA by gold nanoparticles. HF Crouse, A Doudt, C Zerbe, and S Basu. J Anal Methods Chem. 2012; 2012: 327603.
6. Fluorescence Detection of DNA, Adenosine-5′-Triphosphate (ATP) and Telomerase Activity by Zn(II)-Protoporphyrin IX/G-Quadruplex Labels. Z Zhang, E Sharon, R Freeman, X Liu, and I Willner. Anal Chem. 2012.
7. Ultrasensitive detection of potassium ions based on target induced DNA conformational switch enhanced fluorescence polarization. Hu K, Huang Y, Zhao S, Tian J, Wu Q, Zhang G, Jiang J. Analyst. 2012  [Epub May 3] PMID: 22551947
8. Single-molecule analysis using DNA origami. Rajendran A, Endo M, Sugiyama H. Angew Chem Int Ed Engl. 2012 Jan 23;51(4):874-90. doi: 10.1002/anie.201102113. Epub 2011 Nov 25. Review. PMID: 22121063
9. Enantioselective Friedel-Crafts reactions in water catalyzed by a human telomeric G-quadruplex DNA metalloenzyme. C Wang, Y Li, G Jia, Y Liu, S Lu, and C Li. Chem. Commun. 2012 [Epub May 18] PMID: 22595813

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• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry). [5 articles]

1. Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications. Yaku H, Fujimoto T, Murashima T, Miyoshi D, Sugimoto N. Chem. Commun. 2012 [Epub May 15] PMID: 22590705
2. The porphyrin TmPyP4 unfolds the extremely stable G-quadruplex in MT3-MMP mRNA and alleviates its repressive effect to enhance translation in eukaryotic cells. [OA] Mark J. Morris, Katherine L. Wingate, Jagannath Silwal, Thomas C. Leeper, and Soumitra Basu. Nucleic Acids Res. 2012; 40:4137-4145.
3. A New Cationic Porphyrin Derivative (TMPipEOPP) with Large Side Arm Substituents: A Highly Selective G-Quadruplex Optical Probe. [OA] LN Zhu, SJ Zhao, B Wu, XZ Li, and DM Kong. PLoS One. 2012; 7 (5): e35586 [Epub May 22] PMID: 22629300
4. Interaction of Berberine derivative with protein POT1 affect telomere function in cancer cells. Xiao N, Chen S, Ma Y, Qiu J, Tan JH, Ou TM, Gu LQ, Huang ZS, Li D. Biochem Biophys Res Commun. 2012 Mar 16; 419 (3): 567-572. Epub 2012 Feb 17. PMID: 22369941
5. Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS [OA] Raju G, Srinivas R, Santhosh Reddy V, Idris MM, Kamal A, Nagesh N. PLoS One. 2012; 7 (4): e35920. Epub 2012 Apr 27. PMID: 22558271

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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. [2 articles]

1. Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation. [OA] Dengguo Wei, Gary N. Parkinson, Anthony P. Reszka, and Stephen Neidle. Nucleic Acids Res. 2012; 40: 4691-4700.
2. Energetic basis of human telomeric DNA folding into G-quadruplex structures. M Boncina, J Lah, I Prislan, & G Vesnaver. J Am Chem Soc. 2012. [Epub May 17] PMID: 22594380

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• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. (assemblies; molecular devices) [3 articles]

1. Crystal Structure of a Template-Assembled Synthetic G-Quadruplex. M Nikan, BO Patrick, and JC Sherman. Chembiochem. 2012. [Epub May 24] DOI: 10.1002/cbic.201200262. PMID: 22628361
2. Effect of precursor chain-length on the formation and stability of poly(ethylene glycol)-based supramolecular star polymers. Ikhlas Gadwal, Swati De, Mihaiela C. Stuparu, Se Gyu Jang, Roey J. Amir, Anzar Khan. Journal of Polymer Science Part A: Polymer Chemistry. 2012, 50, 2415–2420. DOI: 10.1002/pola.26018
3. Porphyrin-templated synthetic G-quartet (PorphySQ): a second prototype of G-quartet–based G-quadruplex ligand. Xu, H.-J.; Stefan, L.; Haudecoeur, R.; Vuong, S.; Richard, P.; Denat, F.; Barbe, J.-M.; Gros, C. P.; Monchaud, D. Org. Biomol. Chem. 2012. ASAP DOI: 10.1039/C2OB25601K

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[OA] = Open Access

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