An updated virtual bond scheme has been developed to include “long-range” effects of base stacking in the treatment of the spatial configurations of the polynucleotides. As a consequence of the relative rigidity of rotations about the C-0 bonds (ø’ and ø) of the sugar-phosphate backbone, it is possible to represent the six chemical bonds constituting each nucleotide repeating unit in terms of two virtual bonds of comparable magnitudes (spanning C-C-O-P bond fragments of the chain). The “long-range” (three-bond) interdependence of the alternate C-C and O-P bonds in the polynucleotide backbone somewhat complicates computations of chain averages compared to our previous treatments. Despite this complexity, the “long-range” interactions introduce a novel theoretical probe to deduce the solution conformation of the phosphodiester linkages (ω’ ω) from the experimentally observed conformations of the C-C rotations (ΨΨ). On the basis of hard-core conformational analysis and Karplus treatment of NMR coupling constants, we have modeled the helix-to-coil transition of poly(rA) over the temperature range -12 to 60 °C. At low temperatures the molecule is a flexible helix similar in conformational detail to the A-RNA family of structures. At higher temperatures as the nucleotide residues fluctuate over 12 distinct conformational domains, chain dimensions decrease in accordance with experimental data. In contrast to the conventional concept of unstacked, randomly coiling polynucleotides, these computations describe poly(rA) at high temperatures as a highly stacked system with 5 out of 12 of the nucleotides in such arrangements.
All Science Journal Classification (ASJC) codes
- Organic Chemistry
- Polymers and Plastics
- Inorganic Chemistry
- Materials Chemistry