Open AccessStructural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes
Author(s) -
Cheryl A. Hawkins
Publication year - 2001
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/29.4.936
Subject(s) - minor groove , homonuclear molecule , amide , oligonucleotide , stereochemistry , crystallography , hydrogen bond , molecule , biology , dna , binding site , nuclear magnetic resonance spectroscopy , chemistry , biochemistry , organic chemistry
Two-dimensional homonuclear NMR was used to characterize synthetic DNA minor groove-binding ligands in complexes with oligonucleotides containing three different A-T binding sites. The three ligands studied have a C(2) axis of symmetry and have the same general structural motif of a central para-substituted benzene ring flanked by two meta-substituted rings, giving the molecules a crescent shape. As with other ligands of this shape, specificity seems to arise from a tight fit in the narrow minor groove of the preferred A-T-rich sequences. We found that these ligands slide between binding subsites, behavior attributed to the fact that all of the amide protons in the ligand backbone cannot hydrogen bond to the minor groove simultaneously.