Analysis of conformational parameters in nucleic acid fragments. II. Co-crystal complexes of nucleic acid bases

On Spectral Identification of DNA-Base Pairs Polymorphism

The results of MNDO-PM3 theoretical study of H-bonds liability of watson-crick base pairs are discussed. Some microwave and IR spectral criteria are suggested for identification of hidden polymorphism of DNA base pairing.

Analysis of conformational parameters in nucleic acid fragments. IV. Intercalating drug complexes of very short chain oligonucleotides

Studies have been made of base-pairing conformational parameters in single crystal structures of very short chain oligonucleotide structures complexed with drug molecules, using data extracted from the Cambridge structural database. The planar portion of the drug has a tendency to intercalate between two bases, utilising strong stacking interactions to stabilise the configuration. The effect of the existence of a formative backbone is seen in the high occurrence of standard base-pairing schemes and a consistent C1'-C1' separation, although the choice of compounds studied does tend to emphasise complementary pairing. In addition to the modulation of the general magnitude which is reduced from that in uncomplexed oligonucleotides, there appears to be some correlation of propeller twist value with the presence of planar groups sandwiching a base-pair. The average twist in such sandwiched pairs is lower than in any other group studied to date.

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.