New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex.

ABSTRACT: DNA triplexes are formed by both isomorphic (structurally alike) and non-isomorphic (structurally dissimilar) base triplets. It is espoused here that (i) the base triplet non-isomorphism may be articulated in structural terms by a residual twist (Delta(t) degrees), the angle formed by line joining the C1'...C1' atoms of the adjacent Hoogsteen or reverse Hoogsteen (RH) base pairs and the difference in base triplet radius (Delta(r) A), and (ii) their influence on DNA triplex is largely mechanistic, leading to the prediction of a high (t + Delta(t))degrees and low (t - Deltat)degrees twist at the successive steps of Hoogsteen or RH duplex of a parallel or antiparallel triplex. Efficacy of this concept is corroborated by molecular dynamics (MD) simulation of an antiparallel DNA triplex compris

SUBMITTER: Thenmalarchelvi R 

PROVIDER: S-EPMC546132 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature