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Published July 1996 | public
Journal Article

Simultaneous binding of a polyamide dimer and an oligonucleotide in the minor and major grooves of DNA

Abstract

The effect of the polyamide ImPyPy-Dp (Im = N-methylimidazole-2-carboxamide, Py = N-methylpyrrole-2-carboxamide, and Dp = dimethylaminopropylamide), which binds as an antiparallel dimer in the Watson—Crick minor groove, on pyrimidine • purine • pyrimidine triple helix stability was investigated. A DNA restriction fragment was designed which contained two triple helix sites, one which overlapped a minor groove ligand site (proximal), and a control site 13 base pairs away (distal). Using quantitative DNase I footprint titration experiments the equilibrium association constant of oligonucleotide 5′-TTTTTm5CTTTm5CTTTm5CT-3′ (1) to each site was measured in the absence and presence of the polyamide dimer. Our data indicate that triple helix formation is compatible with a polyamide dimer binding in the minor groove of DNA at an overlapping site. No cooperative effect of the polyamide dimer on the equilibrium association constant of oligonucleotide 1 was observed.

Additional Information

Copyright © 1996 Published by Elsevier Ltd. Received 20 March 1996, Accepted 21 March 1996, Available online 12 December 1998 We are grateful to the National Institutes of Health (GM-27681) for research support and a research service award to M.E.P.

Additional details

Created:
August 19, 2023
Modified:
October 18, 2023