A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
The base sequence dependent flexibility of linear single-stranded oligoribonucleotides correlates with the reactivity of the phosphodiester bond
Tekijät: Kaukinen U, Venalainen T, Lonnberg H, Perakyla M
Kustantaja: ROYAL SOC CHEMISTRY
Julkaisuvuosi: 2003
Journal: Organic and Biomolecular Chemistry
Tietokannassa oleva lehden nimi: ORGANIC & BIOMOLECULAR CHEMISTRY
Lehden akronyymi: ORG BIOMOL CHEM
Vuosikerta: 1
Numero: 14
Aloitussivu: 2439
Lopetussivu: 2447
Sivujen määrä: 9
ISSN: 1477-0520
DOI: https://doi.org/10.1039/b302751a
Tiivistelmä
The effect of base sequence on the structure and flexibility of linear single-stranded RNA molecules and the influence of the base sequence on phosphodiester bond reactivity have been studied. Molecular dynamics simulations of 2.1 ns were carried out for nine chimeric oligonucleotides containing only one unsubstituted ribo unit, all the rest of sugars being 2'-O-methylated. The base sequence has recently been reported to make a big contribution to the reactivity of these compounds. A detailed examination of the interaction energies between the base moieties shows that base stacking is strongly context-dependent and cooperative. The strength of stacking at the site susceptible to chain cleavage by intramolecular transesterification was observed to be dependent on both the flanking bases of the cleavage site and those further apart in the molecule. The interaction energies between the bases in the vicinity of the scissile linkage were found to correlate well with the experimental phosphodiester bond cleavage rates: the stronger the bases close to the cleavage site are stacked, the slower the cleavage rate is.
The effect of base sequence on the structure and flexibility of linear single-stranded RNA molecules and the influence of the base sequence on phosphodiester bond reactivity have been studied. Molecular dynamics simulations of 2.1 ns were carried out for nine chimeric oligonucleotides containing only one unsubstituted ribo unit, all the rest of sugars being 2'-O-methylated. The base sequence has recently been reported to make a big contribution to the reactivity of these compounds. A detailed examination of the interaction energies between the base moieties shows that base stacking is strongly context-dependent and cooperative. The strength of stacking at the site susceptible to chain cleavage by intramolecular transesterification was observed to be dependent on both the flanking bases of the cleavage site and those further apart in the molecule. The interaction energies between the bases in the vicinity of the scissile linkage were found to correlate well with the experimental phosphodiester bond cleavage rates: the stronger the bases close to the cleavage site are stacked, the slower the cleavage rate is.
Turun yliopiston Tutkimustietojärjestelmän portaali