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
Authors: Froeyen, Mathy ×
Wroblowski, B
Esnouf, R
De Winter, H
Allart, B
Lescrinier, Eveline
Herdewijn, Piet #
Issue Date: 2000
Publisher: Wiley-v c h verlag gmbh
Series Title: Helvetica Chimica Acta vol:83 issue:9 pages:2153-2182
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.
ISSN: 0018-019X
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Medicinal Chemistry (Rega Institute)
× corresponding author
# (joint) last author

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