Consistent Relative Thermodynamic Data for Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Derivatives

An ab initio method is used in a two state model to calculate consistent relative enthalpies and free energies for the stacking of nucleic acid bases in deoxyribose dinucleotides and the Watson-Crick hydrogen bonding interactions between mononucleotides when uncharged and singly charged. Favorable free energy changes are determined for the formation of dimers between mononucleotides by Watson-Crick and stacking interactions. The data is used to compare the free energy changes for the formation of the ten antiparallel dublet deoxyribose nucleotide duplexes with the analogous ten antiparallel dublet ribose nucleotide duplexes. The data is also used to show the predominance of Watson-Crick hydrogen bonding in the formation of the antiparallel triplet deoxyribose nucleotide duplexes and indicate the formation of non Watson-Crick interactions leading to the formation of point mutations such as that found in sickle cell anaemia. The silencing of genes is shown to be viable and the slightly increased stability of the DNA codons and anticodons versus the RNA analogues is established. However, prebiotically the codons and anticodons could not be fully translated without a chance of error. Hybridization of the mRNA triplets with the tRNA triplets is shown to span the entire range of accessible stacking free energies and provide some specificity for the operation of the standard genetic code. The stacking interactions were calculated for the overall enthalpy changes in the ZKE approximation at the HF and MP2 /6-31G* level. Key-Words: Thermodynamic data, base stacking, deoxyribo dinucleotides, duplexes, genetic code.