Nucleic Acids Research, 1985, Vol. 13, No. 13 4811-4824
© 1985
Articles |
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,D
Department of Chemistry and Laboratory of Chemical Biodynamics, University of California Berkeley, CA 94720 Amgen, Inc., 1900 Oak Terrace Lane, Thousand Oaks, CA 91320, USA
Received March 18, 1985. Accepted June 4, 1985.
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 
is more stable than 
and is similar in stability to 
, 
, 
, 
; 
and 
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.
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