Analysis of conformational parameters in nucleic acid fragments. III. Very short chain oligonucleotides. The effect of base stacking.

Studies have been made of conformational parameters in single crystal structures of very short chain oligonucleotides consisting of strands with lengths in the range 2-3 bases. Using published data extracted from the Cambridge structural database for 20 such structures, a total of 14 base-pairs were found, of which 10 were hetero-pairs and 4 homo-pairs. Subjecting these to analysis to examine hydrogen bond parameters, propeller twist, buckle and C1'-C1' separation revealed an average propeller twist of 11.6 degrees, with no dependence of this parameter on hydrogen bonding details. In addition, an analysis of base stacking showed there to be no correlation between in-plane geometry and degree of inter-plane overlap.