Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,D

Abstract

Thermodynamic parameters for double strand formation have been measured for the sixteen double helices of the sequence dCA₃XA₃G·dCT₃YT₃G, with each of the bases A, C, G and T at the positions labelled X and Y. The results are analyzed in terms of nearest-neighbors and are compared with thermodynamic parameters for RNA secondary structure. At room temperature the sequence $-A-A--T•-T•-$ is more stable than $-A-A--U•-U•-$ and is similar in stability to $-A-C--T•-G•-$ , $-C-A--G•-T•-$ , $-A-G--T•-C•-$ , $-G-A--C•-T•-$ ; $-A-T--T•-A•-$ and $-T-A--A•-T•-$ are least stable. At higher temperatures the sequences containing a G·C base pair become more stable than those containing only A·T. All molecules containing mismatches are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. At room temperature the most stable mismatches are those containing guanine (G·T, G·C, G·A); the least stable contain cytosine (C·A, C·C). At higher temperatures pyrimidine-pyrimidine mismatches become the least stable.