Paper Citing NAMD - Abstract
Ivanova, Anela; Roesch, Notker
The structure of LNA : DNA hybrids from molecular dynamics simulations: The effect of locked nucleotides
JOURNAL OF PHYSICAL CHEMISTRY A, 111:9307-9319, SEP 27 2007
Locked nucleic acids (LNAs) exhibit a modified sugar fragment that is restrained to the C3 '-endo conformation. LNA-containing duplexes are rather stable and have a more rigid structure than DNA duplexes, with a propensity for A-conformation of the double helix. To gain detailed insight into the local structure of LNA-modified DNA oligomers (as a foundation for subsequent exploration of the electron-transfer capabilities of such modified duplexes), we carried out molecular dynamics simulations on a set of LNA:DNA 9-mer duplexes and analyzed the resulting structures in terms of base step parameters and the conformations of the sugar residues. The perturbation introduced by a single locked nucleotide was found to be fairly localized, extending mostly to the first neighboring base pairs; such duplexes featured a B-type helix. With increasing degree of LNA modification the structure gradually changed; the duplex with one complete LNA strand assumed a typical A-DNA structure. The relative populations of the sugar conformations agreed very well with NMR data, lending credibility to the validity of the computational protocol.
