Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove.

ABSTRACT: DB921 has a benzimidazole-biphenyl system with terminal amidines that gives the compound a linear conformation with a radius of curvature that does not match the DNA minor groove shape. Surprisingly, the compound binds in the groove with an unusually high equilibrium constant [Miao, Y.; Lee, M. P. H.; Parkinson, G. N.; Batista-Parra, A.; Ismail, M. A.; Neidle, S.; Boykin, D. W.; Wilson, W. D. Biochemistry 2005, 44, 14701-14708]. X-ray crystallographic analysis of DB921 bound to -AATT- in d(CGCGAATTCGCG)(2) showed that the benzimidazole is in position to directly interact with bases at the floor of the groove, while the phenylamidine of DB921 forms indirect contacts with the bases through an interfacial water. The DB921-water pair forms a curved, flexible module with a high K(a) (or a low K

SUBMITTER: Athri P 

PROVIDER: S-EPMC2698132 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature