Sugar-oligoamides: bound-state conformation and DNA minor-groove-binding description by TR-NOESY and differential-frequency saturation-transfer-difference experiments

Chemistry : a European Journal
Florence SouardCristina Vicent

Abstract

Selective-frequency saturation-transfer-difference (STD) spectra allow the description of complexes established between minor-groove binders and long tracts of calf thymus DNA (ct-DNA). Two sets of experiments with selective saturation of either the H1' or H4'/H5'/H5'' proton NMR regions of deoxyribose allow the description of the ligand residues close to the inner (H1') and outer regions (H4'/H5'/H5'') of the minor groove of double-helical DNA. A series of complexes of sugar-oligoamides (2-6) with ct-DNA have been studied by both TR-NOESY and STD experiments. The binding mode of the complexes is similar to that of netropsin (1) and allows us to define a general binding mode for this family of ligands, in which an NH rim points towards the internal area (inner region) and a CH3 rim points towards the external part (outer region) of the minor groove of DNA. Also by means of both TR-NOESY and STD experiments, a description of the asymmetric centers of the sugar residue close to the inner and outer regions of the groove has been achieved. These results confirm that the sugar is responsible for the differences previously found in binding energetics.

References

Dec 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·K J BreslauerL A Marky
Jun 25, 1985·Journal of Molecular Biology·M L KopkaR E Dickerson
Jul 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·L A Marky, K J Breslauer
Nov 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·D J Patel
Sep 11, 1995·Nucleic Acids Research·A Abu-DayaK R Fox
Aug 6, 1996·Proceedings of the National Academy of Sciences of the United States of America·D S PilchP B Dervan
Jun 1, 1997·Current Opinion in Structural Biology·D E Wemmer, P B Dervan
Jul 17, 1998·Current Opinion in Structural Biology·J B Chaires
Dec 28, 1999·Journal of Molecular Biology·N G AbresciaJ A Subirana
Jan 5, 2000·Proceedings of the National Academy of Sciences of the United States of America·L WangW D Wilson
Jul 31, 2001·Natural Product Reports·S Neidle
Sep 13, 2001·Bioorganic & Medicinal Chemistry·P B Dervan
Nov 7, 2002·Journal of the American Chemical Society·Moriz Mayer, Thomas L James
May 8, 2003·Journal of the American Chemical Society·Dorte Renneberg, Peter B Dervan
Jul 2, 2003·Current Opinion in Structural Biology·Peter B Dervan, Benjamin S Edelson
Apr 1, 2004·Journal of the American Chemical Society·Moriz Mayer, Thomas L James
Jun 30, 2005·Journal of the American Chemical Society·Jason N MartinCristina Vicent
Sep 21, 2006·Chemistry & Biology·Moriz MayerThomas L James
Jul 5, 2007·Organic & Biomolecular Chemistry·Mehdi Mobli, Andrew Almond

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Citations

Sep 29, 2011·European Biophysics Journal : EBJ·Jesus Angulo, Pedro M Nieto
Feb 20, 2015·Journal of Molecular Recognition : JMR·Linda CerofoliniMarco Fragai
Nov 2, 2014·Chemistry : a European Journal·M Teresa Blázquez-SánchezCristina Vicent
Nov 11, 2010·Organic & Biomolecular Chemistry·Cristina AiroldiMario Salmona
Nov 15, 2012·The Journal of Organic Chemistry·Concepción BadíaCristina Vicent

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