Energy and structural analysis of double nucleic acid triplets

In order to investigate the energy and structural character of RNA–RNA triplets and RNA–DNA duplex base triplets, 64 sets of three-dimensional models of RNA–DNA duplex base triplets and mRNA–tRNA triplex base triplets were constructed and optimized by homologous modeling method using the software InsightII. The comparative statistical method and cluster analysis were adopted to study these features. The result showed: (i) all energy parameters of monomer RNA–DNA hybrid triplets and ternary complexes appeared significantly different; and some parameters related with overall molecules such as overall energy, bond energy and coulomb energy have statistically significant correlations between the structures in vacuum and aquatic solutions while other parameters, including theta energy, phi energy, hydrogen bond energy and non-bond energy, changed significantly, but not continuously. (ii) However, the case of mRNA–tRNA triplets was much more complicated in that only the bond energy's correlation coefficient is −0.8. Typically, the main contribution of GC pairs and G/A/U bases were interesting. The models of RNA–DNA hybrid triplets and mRNA–tRNA triplet should be helpful for the study of base pairing in codons and the biological effectiveness of antisense nucleic acids.