Publication
Title
Molecular-dynamics studies of single-stranded hexitol, altritol, mannitol, and ribose nucleic acids (HNA, MNA, ANA, and RNA, resp,) and of the stability of HNA center dot RNA, ANA center dot RNA, and MNA center dot RNA duplexes
Author
Abstract
The influence of the orientation of a 3'-OH group on the conformation and stability of hexitol oligonucleotides in complexes with RNA and as single strands in aqueous solution was investigated by molecular-dynamics (MD)simulations with AMBER 4.1. The particle mesh Ewald (PME) method was used for the treatment of long-range electrostatic interactions. An equatorial orientation of the 3'-OH group in the single-stranded D-mannitol nucleic acid (MNA) m(GCGTAGCG) and in the complex with the RNA r(CGCAUCGC) has an unfavorable influence on the helical stability. Frequent I-I-bonds between the 3'-OH group and the O-C(6') of the phosphate backbone of the following nucleotide explain the distorted conformation of the MNA RNA complex as well as that of the single MNA strand. This is consistent with experimental results that show lowered hybridization potentials for MNA RNA complexes. An axial orientation of the 3'-OH group in the D-altritol nucleic acid (ANA) a(GCGTAGCG) leads to a stable complex with the complementary RNA r(CGCAUCGC), as well as to a more highly preorganized single stranded ANA chain. The averaged conformation of the ANA RNA complex is similar to that of A-RNA, with only minor changes in groove width, helical curvature, and H-bonding pattern. The relative stabilities of ANA RNA vs. HNA.RNA (HNA = D-hexitol nucleic acid without 3'-OH group) can be explained by differences in restricted movements, H-bonds, and solvation effects.
Language
English
Source (journal)
Helvetica chimica acta. - Basel
Publication
Basel : 2000
ISSN
0018-019X
Volume/pages
83:9(2000), p. 2153-2182
ISI
000089843100006
Full text (Publishers DOI)
Full text (publishers version - intranet only)
UAntwerpen
Faculty/Department
Publication type
Subject
External links
Web of Science
Record
Identification
Creation 11.12.2013
Last edited 20.04.2017