Archive

Posts Tagged ‘G-quadruplex’

GQW articles: June 2013 edition

201306GQW

Just a quick post with a list of 32 articles related to GQs published last June, roughly classified as follows:

  • (B). GQ-Biology: 6 articles
  • (C). GQ-Cations: 1 article
  • (M). GQ-Methods: 3 articles
  • (NT). GQ-Nano & Technology: 9 articles
  • (R). GQ-Recognition. 7 articles
  • (SD). GQ-Structure & Dynamics: 7 articles
  • (S). GQ-Supramolecular: 2 articles

______________________________________________________________________

1. (B) Research shows four-stranded DNA in human cancer cells. Mayor S. Lancet Oncol. 2013 Mar; 14 (3): e91.  PMID: 23580959

2. (SD) A highly sensitive resonance Rayleigh scattering method to discriminate a parallel-stranded G-quadruplex from DNA with other topologies and structures. Shi Y, Luo HQ, Li NB. Chem Commun. 2013 Jun 4. [Epub] PMID: 23736799

3. (NT) A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification. Zhang J, Chai Y, Yuan R, Yuan Y, Bai L, Xie S, Jiang L. Analyst. 2013 Jun 6. [Epub] PMID: 23741737

4. (B) Recognition of intermolecular G-quadruplexes by full length nucleophosmin. Effect of a leukaemia-associated mutation. Bañuelos S, Lectez B, Taneva SG, Ormaza G, Alonso-Mariño M, Calle X, Urbaneja MA. FEBS Lett. 2013 Jun 3. doi:pii: S0014-5793(13)00422-5. 10.1016/j.febslet.2013.05.055. [Epub] PMID: 23742937

5. (NT) Aptamer selection based on g4-forming promoter region. [OA] Yoshida W, Saito T, Yokoyama T, Ferri S, Ikebukuro K. PLoS One. 2013 Jun 4; 8 (6): e65497. doi: 10.1371/journal.pone.0065497. Print 2013. PMID: 23750264

6. (SD; M) Mechanical unfolding of long human telomeric RNA (TERRA). Garavís M, Bocanegra R, Herrero-Galán E, González C, Villasante A, Arias-Gonzalez JR. Chem Commun. 2013 Jun 10. [Epub] PMID: 23748212

7. (NT) A highly sensitive G-quadruplex-based luminescent switch-on probe for the detection of polymerase 3′-5′ proofreading activity. Surnameleung GH, Surnamehe GZ, Surnamezhong GJ, Surnamelu G, Surnamechan GS, Surnamema GL, Surnameleung GH. Methods. 2013 Jun 2. doi:pii: S1046-2023(13)00167-9. 10.1016/j.ymeth.2013.05.017. [Epub] PMID: 23748144

8. (B) Translational halt during elongation caused by G-quadruplex formed by mRNA. Endoh T, Kawasaki Y, Sugimoto N. Methods. 2013 Jun 6. doi:pii: S1046-2023(13)00192-8. 10.1016/j.ymeth.2013.05.026. [Epub] PMID: 23747335

9. (M) Clerocidin-mediated DNA footprinting discriminates among different G-quadruplex conformations and detects tetraplex folding in a duplex environment. Nadai M, Sattin G, Palù G, Palumbo M, Richter SN. Biochim Biophys Acta. 2013 Jun 6. doi:pii: S0304-4165(13)00243-2. 10.1016/j.bbagen.2013.05.039. [Epub] PMID: 23747297

10. (S) Quartet formation of a guanine derivative with an isopropyl group: crystal structures of “naked” G-quartets and thermodynamics of G-quartet formation. Inui Y, Shiro M, Fukuzumi S, Kojima T. Org Biomol Chem. 2013 Feb 7; 11 (5): 758-64. doi: 10.1039/c2ob26877a. Epub 2012 Dec 13. PMID: 23238354

11. (B) DNA2, a new player in telomere maintenance and tumor suppression. Chai W, Zheng L, Shen B. Cell Cycle. 2013 Jun 10; 12 (13). [Epub] PMID: 23759580

12. (NT; S) Guided assembly of tetramolecular G-quadruplexes. Yatsunyk LA, Pietrement O, Albrecht D, Tran PL, Renciuk D, Sugiyama H, Arbona JM, Aimé JP, Mergny JL. ACS Nano. 2013 Jun 13. [Epub] PMID: 23763613

13. (R) Pentose Phosphate Pathway Function Affects Tolerance to the G-Quadruplex Binder TMPyP4. [OA] Andrew EJ, Merchan S, Lawless C, Banks AP, Wilkinson DJ, Lydall D. PLoS One. 2013 Jun 12; 8 (6): e66242. doi: 10.1371/journal.pone.0066242. Print 2013. PMID: 23776642

14. (R) Spectroscopic and Biological Studies of Phenanthroline Compounds: Selective Recognition of Gene-Promoter G-Quadruplex DNAs Preferred over Duplex DNA. Wang L, Wei C. Chem Biodivers. 2013 Jun;10(6):1154-64. doi: 10.1002/cbdv.201200341. PMID: 23776031

15. (SD) Combination of i-Motif and G-Quadruplex Structures within the Same Strand: Formation and Application. Zhou J, Amrane S, Korkut DN, Bourdoncle A, He HZ, Ma DL, Mergny JL. Angew Chem Int Ed Engl. 2013 Jun 14. doi: 10.1002/anie.201301278. [Epub] PMID: 23775868

16. (SD) Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex. Shek YL, Noudeh GD, Nazari M, Heerklotz H, Abu-Ghazalah RM, Dubins DN, Chalikian TV. Biopolymers. 2013 Jun 18. doi: 10.1002/bip.22317. [Epub] PMID: 23775839

17. (B) Mechanistic Studies for the Role of Cellular Nucleic-acid-binding Protein (CNBP) in Regulation of c-myc Transcription. Chen S, Su L, Qiu J, Xiao N, Lin J, Tan JH, Ou TM, Gu LQ, Huang ZS, Li D. Biochim Biophys Acta. 2013 Jun 14. doi:pii: S0304-4165(13)00267-5. 10.1016/j.bbagen.2013.06.007. [Epub] PMID: 23774591

18. (SD) Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences. [OA] König SL, Huppert JL, Sigel RK, Evans AC. Nucleic Acids Res. 2013 Jun 14. [Epub] PMID: 23771141

19. (NT) A dual-functional electrochemical biosensor for the detection of prostate specific antigen and telomerase activity. Liu J, Lu CY, Zhou H, Xu JJ, Wang ZH, Chen HY. Chem Commun. 2013 Jun 14. [Epub] PMID: 23770709

20. (NT) A simple, fast and highly sensitive assay for the detection of telomerase activity. Quach QH, Jung J, Kim H, Chung BH. Chem Commun. 2013 Jun 14. [Epub]  PMID: 23770610

21. (NT) A label-free DNA hairpin biosensor for colorimetric detection of target with suitable functional DNA partners. Nie J, Zhang DW, Tie C, Zhou YL, Zhang XX. Biosens Bioelectron. 2013 May 25;49C:236-242. doi: 10.1016/j.bios.2013.05.020. [Epub]  PMID: 23770395

22. (R) The influence of positional isomerism on G-quadruplex binding and anti-proliferative activity of tetra-substituted naphthalene diimide compounds. Mpima S, Ohnmacht SA, Barletta M, Husby J, Pett LC, Gunaratnam M, Hilton ST, Neidle S. Bioorg Med Chem. 2013 May 25. doi:pii: S0968-0896(13)00463-X. 10.1016/j.bmc.2013.05.027. [Epub] PMID: 23769166

23. (SD) Excimer Formation by Stacking G-Quadruplex Blocks. Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT. ChemPhysChem. 2013 Jun 18. doi: 10.1002/cphc.201300481. [Epub] PMID: 23780713

24. (M) A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction. Li Y, Xu F, Liu C, Xu Y, Feng X, Liu BF. Analyst. 2013 Jun 20. [Epub] PMID: 23785706

25. (B) G-Quadruplex DNA as a Molecular Target for Induced Synthetic Lethality in Cancer Cells. McLuckie KI, Di Antonio M, Zecchini H, Xian J, Caldas C, Krippendorff BF, Tannahill D, Lowe C, Balasubramanian S. J Am Chem Soc. 2013 Jun 19. [Epub] PMID: 23782415

26. (R) Macrocyclic biphenyl tetraoxazoles: Synthesis, evaluation as G-quadruplex stabilizers and cytotoxic activity. Blankson GA, Pilch DS, Liu AA, Liu LF, Rice JE, Lavoie EJ. Bioorg Med Chem. 2013 May 30. doi:pii: S0968-0896(13)00482-3. 10.1016/j.bmc.2013.05.033. [Epub] PMID: 23787291

27. (R) On the interaction between [Ru(NH3)6]3+ and the G-quadruplex forming thrombin binding aptamer sequence. De Rache A, Doneux T, Kejnovská I, Buess-Herman C. J Inorg Biochem. 2013 May 30;126C:84-90. doi: 10.1016/j.jinorgbio.2013.05.014. [Epub] PMID: 23787142

28. (R) V-Shaped Dinuclear Pt(II) Complexes: Selective Interaction with Human Telomeric G-quadruplex and Significant Inhibition towards Telomerase. [OA] Xu CX, Zheng YX, Zheng XH, Hu Q, Zhao Y, Ji LN, Mao ZW. Sci Rep. 2013 Jun 24;3:2060. doi: 10.1038/srep02060. PMID: 23792883

29. (NT; C) A “turn-on” fluorescent sensor for detection of Pb2+ based on graphene oxide and G-quadruplex DNA. Li X, Wang G, Ding X, Chen Y, Gou Y, Lu Y. Phys Chem Chem Phys. 2013 Jun 25. [Epub] PMID: 23799396

30. (SD) Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection. [OA] Buscaglia R, Miller MC, Dean WL, Gray RD, Lane AN, Trent JO, Chaires JB. Nucleic Acids Res. 2013 Jun 26. [Epub] PMID: 23804761

31. (NT) Stable label-free fluorescent sensing of biothiols based on ThT direct inducing conformation-specific G-quadruplex. Tong LL, Li L, Chen Z, Wang Q, Tang B. Biosens Bioelectron. 2013 Jun 10; 49C: 420-425. doi: 10.1016/j.bios.2013.05.051. [Epub] PMID: 23807235

32. (R) Asymmetric distyrylpyridinium dyes as red-emitting fluorescent probes for quadruplex DNA. Xie X, Choi B, Largy E, Guillot R, Granzhan A, Teulade-Fichou MP. Chemistry. 2013 Jan 21; 19 (4): 1214-26. doi: 10.1002/chem.201203710. Epub 2013 Jan 4. PMID: 23292703

______________________________________________________________________

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.

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
_____________________________________

• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
[OA] = Open Access

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.
_____________________________________
• 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.
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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.
_____________________________________
• 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
_____________________________________
• 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
_____________________________________

GQW articles: March 2012 edition


From this post onwards, I intend to classify the monthly references by subtopics. Having the references curated this way makes the initial process a little more time consuming, but, I’m hoping it will pay out in the end by providing a quick reference source in the future.

The initial subtopics, with a basic description and some keywords/tags, are:

  • 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)
  • GQ-Cations. Studies aimed at elucidating the role of cations in GQ structure and/or dynamics.
  • GQ-Methods. Application and development of methods and techniques to study GQs.
  • GQ-Nano & Technology. The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors; molecular machinery).
  • GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (synthesis; design; pharmacology; medicinal chemistry).
  • GQ-Structure & Dynamics. Studies aimed at elucidating the detailed structure and/or dynamics of GQs. This includes experimental techniques such as X-Ray crystallography, NMR, and other spectroscopic methods as well as theoretical approaches such as MD-simulations.
  • 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. (assemblies; molecular devices)

_____________________________________

• 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) [13 articles]


  1. The DEAH-box helicase RHAU is an essential gene and critical for mouse hematopoiesis. Lai JC, Ponti S, Pan D, Kohler H, Skoda RC, Matthias P, Nagamine Y. Blood. 2012 Mar 15. [Epub before print] PMID: 22422825
  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, & S. A. McKenna. Nucleic Acids Res. published 11 January 2012, 10.1093/nar/gkr1306
  3. Cell Cycle Regulation of G-Quadruplex DNA Structures at Telomeres. Juranek SA, Paeschke K. Curr Pharm Des.2012 Feb 27. [Epub before print] PMID: 22376109
  4. New insights into replication origin characteristics in metazoans. Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali M. Cell Cycle. 2012 Feb 15;11(4):658-67. PMID: 22373526
  5. The formation and stabilization of a novel G-quadruplex in the 5′-flanking region of the relaxin gene [OA] Lin S, Gu H, Xu M, Cui X, Zhang Y, Gao W, Yuan G. PLoS One. 2012;7(2):e31201. Epub 2012 Feb 21. PMID: 22363579
  6. Saccharomyces cerevisiae Mph1 helicase on junction-containing DNA structures [OA] Young-Hoon Kang, Palinda Ruvan Munashingha, Chul-Hwan Lee, Tuan Anh Nguyen, & Yeon-Soo Seo. Nucleic Acids Res. 2012; 40: 2089-2106.
  7. Nonspaced inverted DNA repeats are preferential targets for homology-directed gene repair in mammalian cells. [OA] Maarten Holkers, Antoine A. F. de Vries, and Manuel A. F. V. Gonçalves. Nucleic Acids Res. 2012; 40:1984-1999.
  8. Yin Yang 1 contains G-quadruplex structures in its promoter and 5′-UTR and its expression is modulated by G4 resolvase 1. [OA] Weiwei Huang, Philip J. Smaldino, Qiang Zhang, Lance D. Miller, Paul Cao, Kristin Stadelman, Meimei Wan, Banabihari Giri, Ming Lei, Yoshikuni Nagamine, James P. Vaughn, Steven A. Akman, & Guangchao Sui. Nucleic Acids Res. 2012; 40:1033-1049.
  9. Overcoming natural replication barriers: differential helicase requirements [OA] Ranjith P. Anand, Kartik A. Shah, Hengyao Niu, Patrick Sung, Sergei M. Mirkin, & Catherine H. Freudenreich. Nucleic Acids Res. 2012; 40:1091-1105.
  10. 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, & Shantanu Chowdhury. Nucleic Acids Res. published 11 January 2012, [Epub before print]
  11. Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. R Halder, JF Riou, MP Teulade-Fichou, T Frickey, & JS Hartig. BMC Res Notes. 2012; 5: 138.
  12. A telomerase-associated RecQ protein-like helicase resolves telomeric G-quadruplex structures during replication. J Postberg, M Tsytlonok, D Sparvoli, D Rhodes, & HJ Lipps. Gene. 2012. [Epub before print]
  13. DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase. N Sabouri, KR McDonald, CJ Webb, IM Cristea, & VA Zakian. Genes Dev. 2012; 26: 581.
_____________________________________
• GQ-Cations. Studies aimed at elucidating the role of cations in the structure and/or dynamics of GQs. [1 article]

  1. Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb2+ . Wei Liu, Hong Zhu, Bin Zheng, Sheng Cheng, Yan Fu, Wei Li, Tai-Chu Lau, and Haojun Liang. Nucleic Acids Res. published 12 January 2012, 10.1093/nar/gkr1310
_____________________________________
• GQ-Methods. Application and development of methods and techniques to study GQs. [11 articles]

  1. Determination of DNA structural detail using radioprobing. Girard PM, Laughton C, Nikjoo H. Int J Radiat Biol. 2012 Jan;88(1-2):123-128. Epub 2011 Sep 21. PMID: 21823822
  2. Tandem mass spectrometry of platinated quadruplex DNA. Stucki SR, Nyakas A, Schürch S. J Mass Spectrom. 2011 Dec;46 (12):1288-1297. doi: 10.1002/jms.2019. PMID: 22223421
  3. Selective isolation of G-quadruplexes by affinity chromatography. Chang T, Liu X, Cheng X, Qi C, Mei H, Shangguan D. J Chromatogr A. 2012 Feb 16. [Epub before print] PMID: 22398385
  4. Reporter assays for studying quadruplex nucleic acids. Halder K, Benzler M, Hartig JS. Methods. 2012 Feb 23. [Epub ahead of print] PMID: 22388183
  5. G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots [OA] Robert Buscaglia, David M. Jameson, & Jonathan B. Chaires. Nucleic Acids Res. published 12 January 2012, 10.1093/nar/gkr1286
  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. published 12 January 2012, 10.1093/nar/gkr1304
  7. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes. E Largy, F Hamon, & MP Teulade-Fichou. Methods. 2012. [Epub before print]
  8. Methods of studying telomere damage induced by quadruplex-ligand complexes. Rizzo A, Salvati E, Biroccio A. Methods. 2012 Mar 4. [Epub before print] PMID: 22410593
  9. Fluorescence properties of 8-(2-pyridyl)guanine “2PyG” as compared to 2-aminopurine in DNA. Dumas A, Luedtke NW. Chembiochem. 2011 Sep 5;12(13):2044-51. doi: 10.1002/cbic.201100214. Epub 2011 Jul 22. PMID: 21786378
  10. Circular dichroism and guanine quadruplexes. M Vorlickova, I Kejnovska, J Sagi, D Renciuk, K Bednarova, J Motlova, & J Kypr. Methods. 2012. [Epub before print]
  11. Combination of chromatographic and chemometric methods to study the interactions between DNA strands. S Ruiz-Castelar, A Checa, R Gargallo, & J Jaumot. Anal Chim Acta. 2012; 722: 34. PMID: 22444532
_____________________________________
• GQ-Nano & Technology.  The design and development of GQ-based nanostructures. The use of GQs as components in devices (e.g., sensors, aptamers). [17 articles]

  1. Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin. Yuan Y, Yuan R, Chai Y, Zhuo Y, Ye X, Gan X, Bai L. Chem Commun. 2012 Mar 30. [Epub before print] PMID: 22466956
  2. DNAzyme-based turn-on chemiluminescence assays in homogenous media. Zhou M, Liu Y, Tu Y, Tao G, Yan. J. Biosens Bioelectron. 2012 Mar 17. [Epub before print] PMID: 22465444
  3. Label-free Fluorescent Detection of Ions, Proteins and Small Molecules Using Structure-Switching Aptamers, SYBR Gold and Exonuclease Ⅰ. Zheng D, Zou R, Lou X. Anal Chem. 2012 Mar 16. [Epub before print]  PMID: 22424113
  4. The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands. [OA] Virgilio A, Esposito V, Citarella G, Pepe A, Mayol L, Galeone A. Nucleic Acids Res. 2012 Jan; 40 (1):461-75. Epub 2011 Sep 9. PMID: 21908403
  5. Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch. De Rache A, Kejnovská I, Vorlíčková M, Buess-Herman C. Chemistry. 2012 Feb 23. doi: 10.1002/chem.201103381. [Epub ahead of print] PMID: 22362492
  6. Amplified Surface Plasmon Resonance and Electrochemical Detection of Pb2+ Ions Using the Pb2+-Dependent DNAzyme and Hemin/G-Quadruplex as a Label. Pelossof G, Tel-Vered R, Willner I. Anal Chem. 2012 Mar 15. [Epub ahead of print] PMID: 22424055
  7. A G-quadruplex based label-free fluorescent biosensor for lead ion. Guo L, Nie D, Qiu C, Zheng Q, Wu H, Ye P, Hao Y, Fu F, Chen G. Biosens Bioelectron. 2012 Feb 24. [Epub before print] PMID: 22417873
  8. G-Quadruplex as Signal Transducer for Biorecognition Events. Lv L, Guo Z, Wang J, Wang E. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22380517
  9. G-Quadruplex Based Probes for Visual Detection and Sensing. Neo JL, Kamaladasan K, Uttamchandani M. Curr Pharm Des. 2012 Feb 27. [Epub before print] PMID: 22380516
  10. G-quadruplex DNA Aptamers and their Ligands: Structure, Function and Application. Tucker WO, Shum KT, Tanner JA. Curr Pharm Des. 2012 Feb 27. [Epub before print] PMID: 22376117
  11. A label-free, G-quadruplex DNAzyme-based fluorescent probe for signal-amplified DNA detection and turn-on assay of endonuclease. Zhou Z, Du Y, Zhang L, Dong S. Biosens Bioelectron. 2012 Jan 28. [Epub ahead of print] PMID: 22366377
  12. A label-free fluorescence DNA probe based on ligation reaction with quadruplex formation for highly sensitive and selective detection of nicotinamide adenine dinucleotide. J Zhao, L Zhang, J Jiang, G Shen, and R Yu. Chem Commun. 2012.
  13. Label-free Fluorescent Detection of Ions, Proteins and Small Molecules Using Structure-Switching Aptamers, SYBR Gold and Exonuclease. D Zheng, R Zou, and X Lou. Anal Chem. 2012. [Epub before print]
  14. G-Quadruplex as Signal Transducer for Biorecognition Events. L Lv, Z Guo, J Wang, and E Wang. Curr Pharm Des. 2012. [Epub before print]
  15. G-quadruplex DNA Aptamers and their Ligands: Structure, Function and Application. WO Tucker, KT Shum, and JA Tanner. Curr Pharm Des. 2012. [Epub before print]
  16. A novel biosensing strategy for screening G-quadruplex ligands based on graphene oxide sheets. H Wang, T Chen, S Wu, X Chu, and R Yu. Biosens Bioelectron. 2012. [Epub before print]
  17. Single strand DNA catenane synthesis using the formation of G-quadruplex structure. Sannohe Y, Sugiyama H. Bioorg Med Chem. 2012 Feb 1. [Epub before print] PMID: 22364954
_____________________________________
• GQ-Recognition. Discovery and development of (mostly) small molecule ligands that recognize GQs (ynthesis; design; pharmacology; medicinal chemistry). [29 articles]


  1. Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure-Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties. Jain AK, Paul A, Maji B, Muniyappa K, Bhattacharya S. J Med Chem. 2012 Mar 27. [Epub ahead of print]PMID: 22452380
  2. Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes. Campbell NH, Karim NH, Parkinson GN, Gunaratnam M, Petrucci V, Todd AK, Vilar R, Neidle S. J Med Chem. 2012 Jan 12; 55 (1):209-222. Epub 2011 Dec 13. PMID: 22112241
  3. Structural polymorphism of human telomere G-quadruplex induced by a pyridyl carboxamide molecule. Xu L, Xu Z, Shang Y, Feng S, Zhou X. Bioorg Med Chem Lett. 2012 Feb 28. [Epub ahead of print] PMID: 22440628
  4. A Caged Ligand for a Telomeric G-Quadruplex. Nakamura T, Iida K, Tera M, Shin-Ya K, Seimiya H, Nagasawa K. Chembiochem. 2012 Mar 21. doi: 10.1002/cbic.201200013. [Epub ahead of print] PMID: 22438312
  5. Structure, function and targeting of human telomere RNA. Xu Y, Komiyama M. Methods. 2012 Mar 8. [Epub ahead of print] PMID: 22425636
  6. G-quadruplexes: targets and tools in anticancer drug design. Düchler M. J Drug Target. 2012 Mar 19. [Epub ahead of print] PMID: 22424091
  7. Identification of novel telomeric G-quadruplex-targeting chemical scaffolds through screening of three NCI libraries. Rahman KM, Tizkova K, Reszka AP, Neidle S, Thurston DE. Bioorg Med Chem Lett. 2012 Feb 16. [Epub ahead of print] PMID: 22421021
  8. Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. Halder R, Riou JF, Teulade-Fichou MP, Frickey T, Hartig JS. BMC Res Notes. 2012 Mar 13;5(1):138. [Epub ahead of print] PMID: 22414013
  9. Spectroscopic probing of recognition of the G-quadruplex in c-kit promoter by small-molecule natural products. Cui X, Lin S, Yuan G. Int J Biol Macromol. 2012 Mar 3. [Epub ahead of print] PMID: 22405847
  10. In silico screening of quadruplex-binding ligands. Ma DL, Ma VP, Chan DS, Leung KH, Zhong HJ, Leung CH. Methods. 2012 Feb 26. [Epub ahead of print] PMID: 22391485
  11. Heterocyclic Dications as a New Class of Telomeric G-Quadruplex Targeting Agents.  Nanjunda R, Musetti C, Kumar A, Ismail MA, Farahat AA, Wang S, Sissi C, Palumbo M, Boykin DW, Wilson WD. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22380518
  12. Synthesis of Small Molecules Targeting Multiple DNA Structures using Click Chemistry. Howell LA, Bowater RA, O’Connell MA, Reszka AP, Neidle S, Searcey M. ChemMedChem. 2012 Feb 29. doi: 10.1002/cmdc.201200060. [Epub ahead of print] PMID: 22378532
  13. Human Telomere RNA: A Potential Target for Ligand Recognition. Xu Y. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376119
  14. Screening of a Chemical Library by HT-G4-FID for Discovery of Selective G-quadruplex Binders. Largy E, Saettel N, Hamon F, Dubruille S, Teulade-Fichou MP. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376118
  15. Searching Drug-like Anti-cancer Compound(s) Based on G-Quadruplex Ligands. Li Q, Xiang JF, Zhang H, Tang YL. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376116
  16. The Polymorfisms of DNA G-Quadruplex investigated by Docking Experiments with Telomestatin Enantiomers. Alcaro S, Costa G, Distinto S, Moraca F, Ortuso F, Parrotta L, Artese A. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376115
  17. G-Quadruplex Binding Ligands: from Naturally Occurring to Rationally Designed Molecules. Le TV, Han S, Chae J, Park HJ. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376113
  18. Targeting DNA G-Quadruplex Structures with Peptide Nucleic Acids. Panyutin IG, Onyshchenko MI, Englund EA, Appella DH, Neumann RD. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376112
  19. Luminescent G-quadruplex Probes. Ma DL, Chan DS, Yang H, He HZ, Leung CH. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376110
  20. Experimental Methods for Studying the Interactions between G-Quadruplex Structures and Ligands Jaumot J, Gargallo R. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376108
  21. Structure Conversion and Structure Separation of G-Quadruplexes Investigated by Carbazole Derivatives. Chang TC, Chu JF, Tsai YL, Wang ZF. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376106
  22. Recent Developments in the Chemistry and Biology of G-Quadruplexes with Reference to the DNA Groove Binders. Jain AK, Bhattacharya S. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376105
  23. State-of-the-Art Methodologies for the Discovery and Characterization of DNA G-Quadruplex Binder. Pagano B, Cosconati S, Gabelica V, Petraccone L, De Tito S, Marinelli L, La Pietra V, di Leva FS, Lauri I, Trotta R, Novellino E, Giancola C, Randazzo A. Curr Pharm Des. 2012 Feb 27. [Epub ahead of print] PMID: 22376104
  24. Stabilization of G-Quadruplex DNA, Inhibition of Telomerase Activity and Live Cell Imaging Studies of Chiral Ruthenium(II) Complexes. Sun D, Liu Y, Liu D, Zhang R, Yang X, Liu J. Chemistry. 2012 Feb 24. doi: 10.1002/chem.201103156. [Epub ahead of print] PMID: 22367788
  25. Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures. Doria F, Nadai M, Folini M, Di Antonio M, Germani L, Percivalle C, Sissi C, Zaffaroni N, Alcaro S, Artese A, Richter SN, Freccero M. Org Biomol Chem. 2012 Feb 27. [Epub ahead of print] PMID: 22367401
  26. Interaction of human telomeric DNA with N-methyl mesoporphyrin IX. [OA] Nicoludis JM, Barrett SP, Mergny JL, Yatsunyk LA. Nucleic Acids Res. 2012 Feb 23. [Epub ahead of print] PMID: 22362740
  27. Luminescent detection of DNA-binding proteins [OA] Chung-Hang Leung, Daniel Shiu-Hin Chan, Hong-Zhang He, Zhen Cheng, Hui Yang, and Dik-Lung Ma. Nucleic Acids Res. 2012; 40:941-955.
  28. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch [OA] Catherine D. Eichhorn, Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks, III, and Hashim M. Al-Hashimi. Nucleic Acids Res. 2012; 40:1345-1355.
  29. Identifying G-quadruplex-binding ligands using DNA-functionalized gold nanoparticles. Y Qiao, J Deng, Y Jin, G Chen, & L Wang. Analyst. 2012; 137: 1663.
_____________________________________
• 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. [7 articles]

  1. RNA G-Quadruplexes: G-quadruplexes with “U” Turns. Agarwal T, Jayaraj G, Pandey SP, Agarwala P, Maiti S. Curr Pharm Des. 2012 Feb 27. [Epub before print] PMID: 22376111
  2. Formation of pearl-necklace monomorphic G-quadruplexes in the human CEB25 minisatellite. Amrane S, Adrian M, Heddi B, Serero A, Nicolas A, Mergny JL, Phan AT. J Am Chem Soc. 2012 Feb 29. [Epub before print] PMID: 22376028
  3. The Tertiary DNA Structure in the Single-Stranded hTERT Promoter Fragment Unfolds and Refolds by Parallel Pathways via Cooperative or Sequential Events. Yu Z, Gaerig V, Cui Y, Kang H, Gokhale V, Zhao Y, Hurley LH, Mao H. J Am Chem Soc. 2012 Feb 28. [Epub before print] PMID: 22372563
  4. Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study. AK Chaubey, KD Dubey, and RP Ojha. J Comput Aided Mol Des. 2012. [Epub before print]
  5. Studying the effect of crowding and dehydration on DNA G-quadruplexes. L Petraccone, B Pagano, and C Giancola. Methods. 2012. [Epub before print]
  6. Stability and Structure of Long Intramolecular G-quadruplexes. L Payet and JL Huppert. Biochemistry. 2012. [Epub before print]
  7. The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages [OA] GR Clark, PD Pytel, and CJ Squire. Nucleic Acids Res. 2012. [Epub before print]
_____________________________________
• 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. [o articles]


_____________________________________

This post includes 78 articles divided by categories as follows:

  • GQ-Biology.  13 articles
  • GQ-Methods11 articles
  • GQ-Cations1 article
  • GQ-Nano & Technology. 17 articles
  • GQ-Recognition29 articles
  • GQ-Structure & Dynamics7 articles
  • GQ-Supramolecular0 articles
_____________________________________
[OA] = Open Access


GQW articles: January 2012 edition

February 16, 2012 1 comment

Image

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
_____________________________________

• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• 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
_____________________________________
• GQ-Supramolecular. Studies related to the design and applications of GQs in supramolecular chemistry. (assemblies; molecular devices) [0 articles]

_____________________________________
[OA] = Open Access