| Abstract
| - To better understand the molecular basis for recognition of the DNA minor groove by heterocycliccations, a series of “reversed amidine” substituted heterocycles has been prepared. Amidine derivativesfor targeting the minor groove have the amidine carbon linked to a central heterocyclic system, whereasin the reverse orientation, an amidine nitrogen provides the link. The reverse system has a larger dihedralangle as well as a modified spatial relationship with the groove relative to amidines. Because of the largedihedral, the reversed amidines should have reduced binding to DNA relative to similar amidines. Such areduction is observed in footprinting, circular dichroism (CD), biosensor-surface plasmon resonance (SPR),and isothermal titration calorimetric (ITC) experiments with DB613, which has a central phenyl-furan-phenylheterocyclic system. The reduction is not seen when a pyrrole (DB884) is substituted for the furan. Analysisof a number of derivatives defines the pyrrole and a terminal phenyl substituent on the reversed amidinegroups as critical components in the strong binding of DB884. ITC and SPR comparisons showed that thebetter binding of DB884 was due to a more favorable binding enthalpy and that it had exceptionally slowdissociation from DNA. Crystallographic analysis of DB884 bound to an AATT site shows that the compoundwas bound in the minor groove in a 1:1 complex as suggested by CD solution studies. Surprisingly, unlikethe amidine derivative, the pyrrole −NH of DB884 formed an H-bond with a central T of the AATT site andthis accounts for the enthalpy-driven strong binding. The structural results and molecular modeling studiesprovide an explanation for the differences in binding affinities for related amidine and reversed amidineanalogues.
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