Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes.
The sugar puckering of adenosine and uridine nucleosides with an amino group at 2' in the ribo or arabino orientations are determined using high-level quantum mechanical calculations Only the conformations that have dihedrals compatible with their insertion into a duplex are retained. The amino group has always been found to be pyramidal and its orientation governs the conformation of the sugar. The energetically most favorable conformation of the 2'-aminoribonucleosides has the south puckering but must be discarded. For another orientation of the 2'-amino group, the conformation is energetically less favorable but has the north puckering. Calculations performed in the presence of a water molecule give similar results but with a smaller energy gap. The model then explains why the insertion of a 2'-aminoribonucleotide destabilizes double-stranded RNAs and also double-stranded DNAs. In the arabino orientation, an NH(2) substituent at 2' favors north puckering. In contrast to 2'-aminoribonucleosides, deoxynucleosides inserted into a duplex remain in the most energetically favorable conformation compatible with the canonical values of the torsion angles. The whole relaxed potential map, in the amplitude/pseudorotation space, shows that for natural deoxyadenosine there is only one valley in the east running from south to north puckering.
Barbe
Sophie
S
LBPA, CNRS, Ecole Normale Supérieure de Cachan, France.
Le Bret
Marc
M
D001087:Arabinonucleosides / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D011789:Quantum Theory; D012313:RNA / Q000737:chemistry; D012263:Ribonucleosides / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D001087:Arabinonucleosides; D012263:Ribonucleosides; D014867:Water; D012313:RNA; D004247:DNA