Analysis of Nearest Neighbor Interactions in the Pyrimidine Triple Helix Motif by Affinity Cleaving

Abstract : Oligonucleotide-directed sequence specific recognition of double helical DNA is length and sequence composition dependent. In order to dissect the relative importance of nearest neighbor interactions on triplet stabilities, binding by oligonucleotides of different sequence composition has been characterized by affinity cleaving. Several groups of target duplexes were synthesized with a central base triplet held constant and the adjacent 3' and 5' triplets systematically varied. By incorporating a thymidine residue with the Deovy Ribonucleic acids DNA-cleaving moiety EDTA in the third strand, the relative stabilities of Hoogsteen base triplets T.AT and C+GC as well as the newly discovered base triplets G.TA, Z.TA, and D3.CG were assessed in the context of different sequences.