SINGLE-STRAND TARGETED TRIPLEX FORMATION - TARGETING PURINE-PYRIMIDINE MIXED SEQUENCES USING ABASIC LINKERS

Foldback tripler-forming oligonucleotides (FTFOs) that contain an abas ic linker, [2-(4-aminobutyr-1-yl)-1,3-propanediol] (APD linker), in th e Hoogsteen domain against pyrimidine bases of a C:G and a T:A base pa ir were studied for their relative stability and sequence specificity of tripler formation, In general, the APD linker has less destabilizin g effect against a C:G base pair than a T:A base pair, Incorporation o f three APD linker moieties resulted in decreased binding to the targe t, which was comparable to results observed with three imperfectly mat ched natural base triplets, The APD linker incorporation did not resul t in the loss of sequence specificity of FTFOs, unlike in the case of normal tripler-forming oligonucleotides (TFOs), The introduction of a positively charged abasic linker, however, resulted in decreased stabi lity of the tripler, because of loss of hydrogen bonding and stacking interactions in the major groove, The results of a molecular modeling study show that APD linker can be readily incorporated without any cha nge in the conformation of the natural sugar-phosphate backbone conser ving overall triple helix geometry, Further, the modeling study sugges ts a hydrogen bond formation between the amino group of linker and N4 of cytosine mediated by a solvent molecule (water) in the floor of the base triplet in addition to a contribution from the positive charge o n the APD linker amino group, Either a direct or water-mediated hydrog en bond between the amino group of the APD linker and the O4 of thymin e is unlikely when the linker is placed against a T:A base pair.