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Archive for August, 2013

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

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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.
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GQW articles: MAY 2013 edition

201305GQW

I can’t believe is almost September already and I still haven’t posted the list of articles for last May (I mean, the previous one took me a year, but I’m trying to improve on that…). Hopefully I’ll have this brief “panoramic” overview of May’s articles finished later this week, but just in case, here is the plain list of the 30 papers published that month, roughly classified by categories as follows:

  • (B). GQ-Biology: 9 articles
  • (C). GQ-Cations: 1 articles
  • (M). GQ-Methods: 6 articles
  • (NT). GQ-Nano & Technology: 7 articles
  • (R). GQ-Recognition. 5 articles
  • (SD). GQ-Structure & Dynamics: 8 articles
  • (S). GQ-Supramolecular: 2 article

Similar to April, studies related to the biological role of GQs continue to dominate the list this month, but there are almost as many contributions on structure & dynamics (SD) and nano & technology (NT) categories. GQ-Recognition (R) always get steady stream of papers, while less common categories (e.g., cations and supramolecular) had at least a few.

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1. (NT) Electrochemical determination of microRNA-21 based on bio bar code and hemin/G-quadruplet DNAenzyme. Meng X, Zhou Y, Liang Q, Qu X, Yang Q, Yin H, Ai S. Analyst. 2013 Jun 21; 138 (12) 3409-3415. doi: 10.1039/c3an36788f. Epub 2013 Apr 30. PMID: 23629000

2. (SD; M) Recent Progress in G-quadruplex DNA in Deep Eutectic Solvent. Zhao C, Qu X. Methods. 2013 Apr 26. doi:pii: S1046-2023(13)00123-0. 10.1016/j.ymeth.2013.04.017. [Epub] PMID: 23628945

3. (SD) Direct Measurement of Sequential Folding Pathway and Energy Landscape of Human Telomeric G-quadruplex Structures. Li W, Hou XM, Wang PY, Xi XG, Li M. J Am Chem Soc. 2013 May 1; 135 (17) 6423-6426. doi: 10.1021/ja4019176. Epub 2013 Apr 23. PMID: 23631592

4. (B) General cell-binding activity of intramolecular g-quadruplexes with parallel structure. [OA] Chang T, Qi C, Meng J, Zhang N, Bing T, Yang X, Cao Z, Shangguan D. PLoS One. 2013 Apr 26; 8 (4) e62348. doi: 10.1371/journal.pone.0062348. Print 2013. PMID: 23638046

5. (R) Human cathelicidin peptide LL37 binds telomeric G-quadruplex. Jana J, Kar RK, Ghosh A, Biswas A, Ghosh S, Bhunia A, Chatterjee S. Mol Biosyst. 2013 May 1. [Epub] PMID: 23636272

6. (SD; M) Self-assembled G-quadruplex nanostructures: AFM and voltammetric characterization. Chiorcea-Paquim AM, Santos PV, Eritja R, Oliveira-Brett AM. Phys Chem Chem Phys. 2013 May 3. [Epub] PMID: 23644414

7. (S) A Photoresponsive Supramolecular G-Quadruplex. Rivera JM, Silva-Brenes D. Org Lett. 2013 May 3. [Epub] PMID: 23642252

8. (NT) Isothermal quadruplex priming amplification for DNA-based diagnostics. Taylor A, Joseph A, Okyere R, Gogichaishvili S, Musier-Forsyth K, Kankia B. Biophys Chem. 2013 Jan; 171: 1-8. doi: 10.1016/j.bpc.2012.11.001. Epub 2012 Nov 14. PMID: 23232099

9. (NT; M) Nanomechanics of surface DNA switches probed by captive contact angle. Maiolo D, Federici S, Ravelli L, Depero LE, Hamad-Schifferli K, Bergese P. J Colloid Interface Sci. 2013 Apr 11. doi:pii: S0021-9797(13)00327-5.10.1016/j.jcis.2013.03.069. [Epub] PMID: 23647692

10. (SD) Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. [OA] Islam B, Sgobba M, Laughton C, Orozco M, Sponer J, Neidle S, Haider S. Nucleic Acids Res. 2013 Feb 1; 41 (4) 2723-35. doi: 10.1093/nar/gks1331. Epub 2013 Jan 4. PMID: 23293000

11. (B) G-quadruplex structures are stable and detectable in human genomic DNA. Lam EY, Beraldi D, Tannahill D, Balasubramanian S. Nat Commun. 2013; 4:1796. doi: 10.1038/ncomms2792. PMID: 23653208

12. (B) Pif1 family helicases suppress genome instability at G-quadruplex motifs. Paeschke K, Bochman ML, Garcia PD, Cejka P, Friedman KL, Kowalczykowski SC, Zakian VA. Nature. 2013 May 8. doi: 10.1038/nature12149. [Epub] PMID: 23657261

13. (B) Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy. [OA] Yuan L, Tian T, Chen Y, Yan S, Xing X, Zhang Z, Zhai Q, Xu L, Wang S, Weng X, Yuan B, Feng Y, Zhou X. Sci Rep. 2013 May 9;3:1811. doi: 10.1038/srep01811. PMID: 23657205

14. (R) Structure-activity relationships of novel substituted naphthalene diimides as anticancer agents. Milelli A, Tumiatti V, Micco M, Rosini M, Zuccari G, Raffaghello L, Bianchi G, Pistoia V, Fernando Díaz J, Pera B, Trigili C, Barasoain I, Musetti C, Toniolo M, Sissi C, Alcaro S, Moraca F, Zini M, Stefanelli C, Minarini A. Eur J Med Chem. 2012 Nov;57:417-28. doi: 10.1016/j.ejmech.2012.06.045. Epub 2012 Jul 4. PMID: 22819507

15. (NT) Label-free electrochemiluminescent detection of DNA by hybridization with a molecular beacon to form hemin/G-quadruplex architecture for signal inhibition. Deng S, Cheng L, Lei J, Cheng Y, Huang Y, Ju H. Nanoscale. 2013 May 10. [Epub] PMID: 23662297

16. (SD; S) G-quadruplex formation of entirely hydrophobic DNA in organic solvents. Shibata T, Dohno C, Nakatani K. Chem Commun. 2013 May 10. [Epub] PMID: 23660830

17. (B) Beyond the Binding Site: In Vivo Identification of tbx2, smarca5 and wnt5b as Molecular Targets of CNBP during Embryonic Development. [OA] Armas P, Margarit E, Mouguelar VS, Allende ML, Calcaterra NB. PLoS One. 2013 May 7; 8 (5) e63234. doi: 10.1371/journal.pone.0063234. Print 2013. PMID: 23667590

18. (NT) A visible multi-digit DNA keypad lock based on split G-quadruplex DNAzyme and silver microspheres. Zhu J, Yang X, Zhang L, Zhang L, Lou B, Dong S, Wang E. Chem Commun. 2013 May 13. [Epub] PMID: 23665889

19. (NT; C) Aptamer biosensor for label-free impedance spectroscopy detection of potassium ion based on DNA G-quadruplex conformation. Chen Z, Chen L, Ma H, Zhou T, Li X. Biosens Bioelectron. 2013 Apr 17;48C:108-112. doi: 10.1016/j.bios.2013.04.007. [Epub] PMID: 23665159

20. (B) Interaction of G-quadruplex with RecA Protein Studied in Bulk Phase and at Single-Molecule Level. Tanaka A, Choi J, Kim SK, Majima T. J Phys Chem B. 2013 May 10. [Epub] PMID: 23662701

21. (M; NT) Capillary Electrophoresis-Systematic Evolution of Ligands by Exponential Enrichment Selection of Base- and Sugar-Modified DNA Aptamers: Target Binding Dominated by 2′-O,4′-C-Methylene-Bridged/Locked Nucleic Acid Primer. Kasahara Y, Irisawa Y, Fujita H, Yahara A, Ozaki H, Obika S, Kuwahara M. Anal Chem. 2013 May 10. [Epub] PMID: 23662585

22. (SD) Effect of Loops, G-Quartets on the Stability of RNA G-Quadruplexes. Pandey S, Agarwala P, Maiti S. J Phys Chem B. 2013 May 17. [Epub] PMID: 23683360

23. (M; SD) Interactions of the human telomere sequence with the nanocavity of the α-hemolysin ion channel reveal structure-dependent electrical signatures for hybrid folds. An N, Fleming AM, Burrows CJ. J Am Chem Soc. 2013 May 17. [Epub] PMID: 23682802

24. (SD; M) Structural characterization of quadruplex DNA with in-cell EPR approaches. Holder IT, Drescher M, Hartig JS. Bioorg Med Chem. 2013 Apr 16. doi:pii: S0968-0896(13)00331-3. 10.1016/j.bmc.2013.04.014. [Epub] PMID: 23693068

25. (B) Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns. [OA] Savage AL, Bubb VJ, Breen G, Quinn JP. BMC Evol Biol. 2013 May 21;13(1):101. [Epub] PMID: 23692647

26. (B) On the origin of the eukaryotic chromosome: the role of non-canonical DNA structures in telomere evolution. [OA] Garavís M, González C, Villasante A. Genome Biol Evol. 2013 May 22. [Epub] PMID: 23699225

27. (R) Dual recognition of the human telomeric G-quadruplex by a neomycin-anthraquinone conjugate. Ranjan N, Davis E, Xue L, Arya DP. Chem Commun. 2013 May 22. [Epub] PMID: 23698792

28. (R) Ellipticine binds to human telomere sequence – an additional mode of action as a putative anticancer agent? Ghosh S, Kar A, Chowdhury S, Dasgupta D. Biochemistry. 2013 May 22. [Epub] PMID: 23697684

29. (R) RPA-Mediated Unfolding of Systematically Varying G-Quadruplex Structures. Ray S, Qureshi MH, Malcolm DW, Budhathoki JB, Celik U, Balci H. Biophys J. 2013 May 21;104 (10) 2235-2245. doi: 10.1016/j.bpj.2013.04.004. PMID: 23708363

30. (B) DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix. [OA] Zhang C, Liu HH, Zheng KW, Hao YH, Tan Z. Nucleic Acids Res. 2013 May 28. [Epub] PMID: 23716646

______________________________________________________________________

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.
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