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Transcriptional control by G-quadruplexes: In vivo roles and perspectives for specific intervention.

Armas P, David A, Calcaterra NB.

Transcription. 2017 Jan;8(1):21-25. doi: 10.1080/21541264.2016.1243505. Epub 2016 Oct 3.


Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA.

Kim M, Kreig A, Lee CY, Rube HT, Calvert J, Song JS, Myong S.

Nucleic Acids Res. 2016 Jun 2;44(10):4807-17. doi: 10.1093/nar/gkw272. Epub 2016 Apr 19.


MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex.

Ho J, Newcomer MB, Ragain CM, Gascon JA, Batista ER, Loria JP, Batista VS.

J Chem Theory Comput. 2014 Nov 11;10(11):5125-35. doi: 10.1021/ct500571k. Epub 2014 Oct 8.


G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence.

Kreig A, Calvert J, Sanoica J, Cullum E, Tipanna R, Myong S.

Nucleic Acids Res. 2015 Sep 18;43(16):7961-70. doi: 10.1093/nar/gkv749. Epub 2015 Jul 21.


Leukocyte telomere length variation due to DNA extraction method.

Denham J, Marques FZ, Charchar FJ.

BMC Res Notes. 2014 Dec 4;7:877. doi: 10.1186/1756-0500-7-877.


G-quadruplex conformation and dynamics are determined by loop length and sequence.

Tippana R, Xiao W, Myong S.

Nucleic Acids Res. 2014 Jul;42(12):8106-14. doi: 10.1093/nar/gku464. Epub 2014 Jun 11.


Effect of sequence and metal ions on UVB-induced anti cyclobutane pyrimidine dimer formation in human telomeric DNA sequences.

Smith JE, Lu C, Taylor JS.

Nucleic Acids Res. 2014 Apr;42(8):5007-19. doi: 10.1093/nar/gku163. Epub 2014 Mar 4.


Structural basis of sodium-potassium exchange of a human telomeric DNA quadruplex without topological conversion.

Wang ZF, Li MH, Hsu ST, Chang TC.

Nucleic Acids Res. 2014 Apr;42(7):4723-33. doi: 10.1093/nar/gku083. Epub 2014 Jan 29.


Automatic workflow for the classification of local DNA conformations.

Čech P, Kukal J, Černý J, Schneider B, Svozil D.

BMC Bioinformatics. 2013 Jun 25;14:205. doi: 10.1186/1471-2105-14-205.


Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species?

Balthasart F, Plavec J, Gabelica V.

J Am Soc Mass Spectrom. 2013 Jan;24(1):1-8. doi: 10.1007/s13361-012-0499-3. Epub 2012 Nov 7.


Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

Wei D, Parkinson GN, Reszka AP, Neidle S.

Nucleic Acids Res. 2012 May;40(10):4691-700. doi: 10.1093/nar/gks023. Epub 2012 Jan 28.


Biochemical characterization of Warsaw breakage syndrome helicase.

Wu Y, Sommers JA, Khan I, de Winter JP, Brosh RM Jr.

J Biol Chem. 2012 Jan 6;287(2):1007-21. doi: 10.1074/jbc.M111.276022. Epub 2011 Nov 18.


Thermodynamics of nucleic acid "shape readout" by an aminosugar.

Xi H, Davis E, Ranjan N, Xue L, Hyde-Volpe D, Arya DP.

Biochemistry. 2011 Oct 25;50(42):9088-113. doi: 10.1021/bi201077h. Epub 2011 Oct 3.


Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.

Cang X, Šponer J, Cheatham TE 3rd.

J Am Chem Soc. 2011 Sep 14;133(36):14270-9. doi: 10.1021/ja107805r. Epub 2011 Aug 19.


Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.

Cang X, Šponer J, Cheatham TE 3rd.

Nucleic Acids Res. 2011 May;39(10):4499-512. doi: 10.1093/nar/gkr031. Epub 2011 Feb 3.


Aminoglycoside binding to Oxytricha nova telomeric DNA.

Ranjan N, Andreasen KF, Kumar S, Hyde-Volpe D, Arya DP.

Biochemistry. 2010 Nov 16;49(45):9891-903. doi: 10.1021/bi101517e. Epub 2010 Oct 22.


Cation involvement in telomestatin binding to g-quadruplex DNA.

Rosu F, Gabelica V, Smargiasso N, Mazzucchelli G, Shin-Ya K, De Pauw E.

J Nucleic Acids. 2010;2010. pii: 121259. doi: 10.4061/2010/121259. Epub 2010 Jun 16.


Stability and kinetics of G-quadruplex structures.

Lane AN, Chaires JB, Gray RD, Trent JO.

Nucleic Acids Res. 2008 Oct;36(17):5482-515. doi: 10.1093/nar/gkn517. Epub 2008 Aug 21. Review.


Mix and measure fluorescence screening for selective quadruplex binders.

Paramasivan S, Bolton PH.

Nucleic Acids Res. 2008 Oct;36(17):e106. doi: 10.1093/nar/gkn487. Epub 2008 Jul 28.


G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA).

Peng CG, Damha MJ.

Nucleic Acids Res. 2007;35(15):4977-88. Epub 2007 Jul 17.

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