Isomorphic building blocks for information-bearing duplexes—part 2: pyrimidine base pairs with sugar phosphate backbones

Abstract

Earlier searches using DFT had identified two isomorphic H-bonded pyrimidine base pairs B1:B2 and B3:B4 as possible repeat units for macromolecular H-bonded duplexes with a capacity to store information as in DNA. This DFT study seeks to design repeat units with suitable backbones which can hold a sequence of base pairs in desired order. A deoxyribose phosphate backbone and a deoxyallopyranose phosphate backbone are proposed here. These sets of backboned nucleotide pairs are examined for their stability and their isomorphism. The results yield stable H-bonded nucleotide pairs with pairing energies of the order of those for the Watson-Crick DNA base pairs. Isomorphism is examined in the central pyrimidine base pair moiety, in the backbone torsional angles and in the overall topology. Out of three different sets of nucleotide pairs, the anionic deoxyribonucleotide pairs DA1:DA2 and DA3:DA4 emerge as showing the maximal overall isomorphism, while the pyranonucleotide pairs PyA1:PyA2 and PyA3:PyA4 are predicted as the most stable.