Heterocyclic diamidine interactions at AT base pairs in the DNA minor groove: effects of heterocycle differences, DNA AT sequence and length.
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 molecule to match DNA for enhanced affinity and sequence recognition.
Liu
Yang
Y
Collar
Catharine J
CJ
Kumar
Arvind
A
Stephens
Chad E
CE
Boykin
David W
DW
Wilson
W David
WD
D000225:Adenine / Q000737:chemistry*; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002151:Calorimetry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D005663:Furans / Q000737:chemistry; D006571:Heterocyclic Compounds / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D016566:Organoselenium Compounds / Q000737:chemistry; D010419:Pentamidine / Q000737:chemistry*; D020349:Surface Plasmon Resonance; D013816:Thermodynamics; D013876:Thiophenes / Q000737:chemistry; D013941:Thymine / Q000737:chemistry*
D005663:Furans; D006571:Heterocyclic Compounds; D016566:Organoselenium Compounds; D013876:Thiophenes; D010419:Pentamidine; D004247:DNA; D000225:Adenine; D013941:Thymine; C039281:furan