Heterocyclic diamidine interactions at AT base pairs in the DNA minor groove: effects of heterocycle differences, DNA AT sequence and length.

The Journal of Physical Chemistry. B
Yang LiuW David Wilson

Abstract

Given the increasing significance of diamidines as DNA-targeted therapeutics and biotechnology reagents, it is important to establish the variations in thermodynamic quantities that characterize the interactions of closely related compounds to different sequence AT binding sites. In this study, an array of methods including biosensor-surface plasmon resonance (SPR), isothermal titration microcalorimetry (ITC), circular dichroism (CD), thermal melting (Tm) and molecular modeling have been used to characterize the binding of dicationic diamidines related to DB75 (amidine-phenyl-furan-phenyl-amidine) with alternating and nonalternating AT sequences. Conversion of the central furan of DB75 to other similar groups, such as thiophene or selenophene, can yield compounds with increased affinity and sequence binding selectivity for the minor groove. Calorimetric measurements revealed that the thermodynamic parameters (Delta G, Delta H, Delta S) that drive diamidine binding to alternating and nonalternating oligomers can be quite different and depend on both DNA sequence and length. Small changes in a compound can have major effects on DNA interactions. By choosing an appropriate central group it is possible to "tune" the shape of the mo...Continue Reading

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Citations

Jun 2, 2011·Journal of the American Chemical Society·Yang LiuW David Wilson
Mar 1, 2012·Journal of the American Chemical Society·Yang LiuW David Wilson
Jul 7, 2009·Nucleic Acids Research·Denise S TevisW David Wilson
Mar 10, 2010·Journal of Molecular Recognition : JMR·Robert J FalconerBrett M Collins
Dec 18, 2009·Journal of Molecular Recognition : JMR·Rebecca L Rich, David G Myszka
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Aug 18, 2018·ACS Chemical Biology·Jana R JenquinJ Andrew Berglund

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