title: DNA triple-helix formation at target sites containing duplex mismatches.
abstract: 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.
authors.affiliation: School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Rusling
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Keith R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D020137:Base Pair Mismatch; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D013696:Temperature
chemical_list: D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA