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Posts Tagged ‘OGQ-ligands’

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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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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Structural studies of naphthalene diimide ligands with telomeric G-Quadruplex DNA

March 15, 2012 13 comments

Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands

Gavin W. Collie, Rossella Promontorio, Sonja M. Hampel, Marialuisa Micco, Stephen Neidle*, and Gary N. Parkinson*

J. Am. Chem. Soc., 2012, 134 (5), 2723; DOI: 10.1021/ja2102423

A synopsis by Maxier Acosta

Previously Neidle had reported a series on naphthalene diimide (ND) oligo G-quadruplex (OGQ) ligands with side-chains (n) of 3-5 carbons with N-methyl-piperazine end groups. They showed experimentally how it inhibited binding of hPOT1 and topoisomerase IIIα to telomeric DNA and inhibited telomerase activity in MCF7 cells via the stabilization of OGQs (DOI: 10.1016/j.bmcl.2010.09.066). Now, in collaboration with Parkinson, they report the crystalline structure of each one of those naphthalene ligands with the addition of a two-carbons side-chain.

They first give an overview of the tendencies of the overall parallel OGQ (Gtel22) with each ND ligand. With the telomere sequence d(AGGG[TTAGGG]3) they highlight the stacking of two OGQs making a dimer interacting from the 5’ terminal G-quartet. But the ratio between the ND and each OGQ is 1:1. Taking this in consideration, when each ND is bound to the quadruplexes, they force the topology of the loops into parallel strands as first proposed in DOI: 10.1016/j.bmcl.2010.09.066. While going more into detail, stability studies via FRET and inhibition studies where done for each ND. In the case of the ND with a two-carbons side-chain, it didn’t enhanced by much the stability of the Gtel22 due to the inappropriate side-chain length to enable effective interactions (in the OGQ groove) between the protonated N-methyl-piperazine and the DNA backbone phosphates. Although the n=5 ND OGQ complex showed poor quality in its crystal diffraction, it was still higher than that corresponding to n=2. For the n=4 ND, the side-chains were too long to fit well into the grooves as indicated by the disorder of the chains leading to a decrease of strong specific contacts, yet it was still more stabilizing than n=5 ND. For n=3 ND, it was observed that the cation-phosphate interactions were specifically coordinated, making it the best ligand of the small library presented in the paper. The structural features for these ND ligands correlated well with the inhibition of two types of cancer cells (MCF7 and A549).

In the discussion they summarized the data in three major topics: (1) the 1:1 binding of ND and OGQs; (2) the importance of the electrostatic side-chain interaction with the groove; and (3) the retention of the parallel topology of the Gtel22. Also, as might be expected for scientists from a pharmacy school they maintain their focus on how biologically relevant these binders could be for anticancer treatments.

In general, I thought that this was a good OGQ-binder structural article. I know that our systems are difficult to crystallize, yet this type of studies can help us to understand them to a new level so we could also start talking about potential inhibitors among other things. In terms of the organization of the paper, I found confusing the fact that they do not address explicitly some of the figures. In the discussion it was not that clear for me why the NDs induced the parallel topology; so, for that I encourage you guys to read the reference that I mentioned at the beginning, which has additional useful experimental data that may help anyone in the same situation. Other than this, I wish I had seen all of the ND side-chains interactions with the groove (some of them are in the supplementary information).

Raiders of the lost G-quadruplexes …in the human genome

March 14, 2012 15 comments

Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

Raphaël Rodriguez, Kyle M Miller, Josep V Forment, Charles R Bradshaw, Mehran Nikan, Sébastien Britton, Tobias Oelschlaegel, Blerta Xhemalce, Shankar Balasubramanian* & Stephen P. Jackson*

Nature Chemical Biology 8, 301–310 (2012) doi: 10.1038/nchembio.780

A synopsis by Diana Silva Brenes

The authors of this week’s paper play detective to find out -with great detail- what exactly happens to a human cell when it’s treated with the versatile, potent GQ-binder, pyridostatin. Using a combination of biomolecular assays, the authors manage to give strong support for the in vivo formation of GQ-DNA in human cells, and show their role in the activity of the new drug.

Pyridostatin is shown to induce damage to cellular DNA, stumping their proliferation. This happens because cellular checkpoints, which revise DNA before continuing the cellular division cycle, detect the damage and signal to the cell that something is wrong. The cell stops in its tracks to try to correct the problem before it continues the cycle. The drug, however, isn’t too toxic and most cells can survive long-term exposition to it without undergoing apoptosis. Interestingly, inhibition of the checkpoints restores cell proliferation.

Many of the results rely on detecting the presence of γH2AX (a protein that indicates double strand breaks in DNA) as a way to follow damage done to DNA. In cells treated with pyridostatin, γH2AX is present during the DNA transcription and replication processes, pointing at damage to DNA occurring during both stages.

Next, the authors wanted to localize where in the DNA is pyridostatin taking effect. Fluorescence labeling of γH2AX and the telomeres (marked by the labeling of a telomere binding protein) didn’t show co-localization. It was, thus, necessary to modify the drug to add direct fluorescence labeling. Addition of an alkyne group to the drug allowed an in cellulo click reaction with an azide containing fluorescent dye. After making sure that the modified pyridostatin did not affect drug activity, staining of pyridostatin was performed and fluorescent spots (foci) were compared with the a fluorescently labeled human helicase reputed to bind and resolve GQ-DNA during replication. Good co-localization was observed, suggesting that pyridostatin was localized mostly at putative GQ-DNA sites. In another experiment they showed that addition of pyridostatin before of after “freezing” the cellular processes in formaldehyde gave almost identical results, suggesting that GQ structures are pre-folded even without addition of pyridostatin.

They then performed ChIP sequencing to try to figure out which genes (aka, DNA segment) were targeted by pyridostatin. They found several specific genes (mostly away from the telomeres) that sustained pyridostatin induced damage to DNA, and all of them had above average putative GQ sequences. However, not all areas enriched in putative GQ sequences were affected, suggesting that there are other important requirements for interaction.

A particularly affected gene was SRC as confirmed by checking for loss of its corresponding mRNA transcription activity. Out of 25 putative GQ sequences estimated for this gene, 23 of them could be observed to form QGs in vitro using CD and NMR spectra.

The effect of pyridostatin on the bioactivity of SRC was also evaluated. SRC is important for wound healing and motility of cells. Cells treated with pyridostatin displayed a reduced ability to heal. As a control, cells treated with another DNA-damaging drug (DOX), didn’t affect healing, proving that the deficiency was not due merely to DNA damage.

It was previously shown that pyridostatin binds to GQs with enough strength to resist polymerases. It is hypothesized that damage to DNA by pyridostatin is due to mechanical forces breaking the DNA during the cell’s attempt to transcribe or replicate DNA. The findings of this paper support the potential drugability of GQs in cells.

The data reported by this paper is really important for the field of GQ binders and raises large hopes for the future of the field. Being able to use GQ to recognize and regulate specific genes is a dream come true in drug design, and the authors present strong data as to the viability of this approach. As a chemist, it’s difficult to get used to the rather indirect type of evidence that supports these findings, making it hard for me to comment on this paper’s methods. However, the controls and the analyses they did appear to be adequate. Overall, I find the results in this paper to be really important to anyone in the GQ field.

Categories: Lab-blog, Uncategorized Tags: , ,

GQW articles: January 2012 edition

February 16, 2012 1 comment

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Following is a (non-comprehensive) list of articles related to G-quadruplex research published (for the first time on the web or “officially” in print) during the month of January 2012. This post includes 21 articles divided by category as follows:

  • GQ-Biology (GQB).  4 articles
  • GQ-Cations (GQC). 3 articles
  • GQ-Methods (GQM). 1 articles
  • GQ-Nano & Technology (GQNT). 7 articles
  • GQ-Recognition (GQR). 4 articles
  • GQ-Structure & Dynamics (GQSD). 2 articles
  • GQ-Supramolecular (GQS). 0 article
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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) [4 articles]

  1. Tools for Investigation of the RNA Endonuclease Activity of Mammalian Argonaute2 Protein. Yang N, Cao Y, Han P, Zhu X, Sun L, Li G. Anal Chem. 2012 Jan 26. [Epub before print] PMID: 22283827
  2. Telomestatin impairs glioma stem cell survival and growth through the disruption of telomeric G-quadruplex and inhibition of the proto-oncogene, c-Myb. Miyazaki T, Pan Y, Joshi K, Purohit D, Hu B, Demir H, Mazumder S, Okabe S, Yamori T, Viapiano MS, Shin-Ya K, Seimiya H, Nakano I. Clin Cancer Res. 2012 Jan 9. [Epub before print] PMID: 22230766
  3. Structure of noncoding RNA is a determinant of function of RNA binding proteins in transcriptional regulation [OA] Oyoshi T, Kurokawa R. Cell Biosci. 2012 Jan 3;2 (1):1. PMID: 22214309
  4. Potential G-quadruplexes in the human long non-coding transcriptome. Jayaraj GG, Pandey S, Scaria V, Maiti S. RNA Biol. 2012 Jan 1; 9 (1). PMID: 22258148
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• GQ-Cations. Studies aimed at elucidating the role of cations in GQ structure and/or dynamics. [3 articles]

  1.  G-Quadruplexes and Metal Ions. Campbell NH, Neidle S. Met Ions Life Sci. 2012;10: 119-134. PMID: 22210337
  2. Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel. Akhshi P, Mosey NJ, Wu G. Angew Chem Int Ed Engl. 2012 Jan 13. doi: 10.1002/anie.201107700. PMID: 22241618
  3. Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb2+ [OA] Liu W, Zhu H, Zheng B, Cheng S, Fu Y, Li W, Lau TC, Liang H. Nucleic Acids Res. 2012 Jan 12. [Epub before print] PMID: 22241774
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• GQ-Methods. Application and development of methods and techniques to study GQs. [1 articles]

  1. G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots [OA] Buscaglia R, Jameson DM, Chaires JB. Nucleic Acids Res. 2012 Jan 12. [Epub before print] PMID: 22241767
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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). [7 articles]

  1. Input-Dependent Induction of Oligonucleotide Structural Motifs for Performing Molecular Logic. [OA] Li T, Ackermann D, Hall AM, Famulok M. J Am Chem Soc. 2012 Jan 31. PMID: 22296341
  2. A novel label-free fluorescent sensor for the detection of potassium ion based on DNAzyme. Fan X, Li H, Zhao J, Lin F, Zhang L, Zhang Y, Yao S. Talanta. 2012 Jan 30;89:57-62. PMID: 22284459
  3. DNA G-quadruplex-templated formation of the fluorescent silver nanocluster and its application to bioimaging. Ai J, Guo W, Li B, Li T, Li D, Wang E. Talanta. 2012 Jan 15;88:450-455. PMID: 22265525
  4. Cationic Conjugated Polyelectrolytes-Triggered Conformational Change of Molecular Beacon Aptamer for Highly Sensitive and Selective Potassium Ion Detection. Kim B, Jung IH, Kang M, Shim HK, Woo HY. J Am Chem Soc. 2012 Jan 14. [Epub before print] PMID: 22280349
  5. Growth Mechanisms of Fluorescent Silver Clusters Regulated by Polymorphic DNA templates: A DFT Study. Wu J, Fu Y, He Z, Han Y, Zheng L, Zhang J, Li W. J Phys Chem B. 2012 Jan 13. PMID: 22242908
  6. G-Quadruplex-Forming Oligonucleotide Conjugated to Magnetic Nanoparticles: Synthesis, Characterization and Enzymatic Stability Assays. Musumeci D, Oliviero G, Roviello GN, Bucci EM, Piccialli G. Bioconjug Chem. 2012 Jan 12. [Epub before print] PMID: 22239558
  7. Studies of the Activity of Peroxidase-Like DNAzyme by Modifying 3′- or 5′-End of Aptamers. Zhang M, Li H, Deng M, Weng X, Ma H, Feng S, Zhou Y, Zhou X. Chem Biodivers. 2012 Jan; 9 (1):170-180. doi: 10.1002/cbdv.201100040. PMID: 22253114
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• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry). [4 articles]

  1.  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] Morris MJ, Wingate KL, Silwal J, Leeper TC, Basu S. Nucleic Acids Res. 2012 Jan 20. [Epub before print] PMID: 22266651
  2. Structural basis for telomeric G-quadruplex targeting by naphthalene diimide ligands. Collie GW, Promontorio R, Hampel SM, Micco M, Neidle S, Parkinson GN. J Am Chem Soc. 2012 Jan 12. [Epub before print] PMID: 22280460
  3. Synthesis and human telomeric G-quadruplex DNA-binding activity of glucosaminosides of shikonin/alkannin. He H, Bai LP, Jiang ZH. Bioorg Med Chem Lett. 2012 Jan 10. [Epub before print] PMID: 22281188
  4. Recognize three different human telomeric G-quadruplex conformations by quinacrine. Sun H, Xiang J, Li Q, Liu Y, Li L, Shang Q, Xu G, Tang Y. Analyst. 2012 Jan 5. [Epub before print] PMID: 22223064
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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. 28 January 2012. [Epub before print]
  2. G-Qadruplexes from Human Telomeric DNA: How Many Conformations in PEG Containing Solutions? Petraccone L, Malafronte A, Amato J, Giancola C. J Phys Chem B. 2012. Jan 23. [Epub before print] PMID: 22268560
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• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. (assemblies; molecular devices) [0 articles]

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[OA] = Open Access