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We have studied the formation of DNA triple helices at target sites that contain mismatches in the duplex target. Fluorescence melting studies were used to examine a series of parallel triple helices that contain all 64 N.XZ triplet combinations at the centre (where N, X and Z are each of the four natural DNA bases in turn). Similar experiments were also performed with N=bis-amino-U (BAU) (for stable recognition of AT base pairs) and N=S (for recognition of TA inversions). We find that the introduction of a duplex mismatch destabilises the C+.GZ, T.AZ and G.TZ triplets. A similar effect is seen with BAU.AZ triplets. In contrast, other base combinations, based on non-standard triplets such as C.AZ, T.TZ, G.CZ and A.CZ are stabilised by the presence of a duplex mismatch. In each case S binds to sites containing duplex mismatches better than the corresponding Watson-Crick base pairs.

Original publication

DOI

10.1016/j.bpc.2006.04.016

Type

Journal article

Journal

Biophys Chem

Publication Date

20/09/2006

Volume

123

Pages

134 - 140

Keywords

Base Pair Mismatch, Binding Sites, DNA, Hydrogen Bonding, Molecular Conformation, Nucleic Acid Conformation, Oligonucleotides, Temperature