MODIFIED NUCLEOSIDES IN TRIPLEX FORMING OLIGONUCLEOTIDES

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DESCRIPTION (Adapted from applicant's abstract):The primary goal of this study is to chemically refine class of sequence-specific, DNA binding, triple helix-forming oligonucleotides (TFOs). The unique feature of these TFOs is that binding of the third strand to its duplex DNA target is pH independent and is stabilized by GGC and TAT triplets such that the preferred orientation places the bound TFO antiparallel with respect to the more purine rich strand of the underlying duplex. In accord with molecular modeling, 2'-deoxyformycin (df) is introduced into 3'-amine modified TFOs at sites engaged in H-bonding where polypurine/polypyrimidine runs in a duplex target are interrupted by a CG inversion. The binding affinity of such a dF-TFO is assessed by band shift analysis and by quantitative DNase I footprinting techniques. The effect of dF upon triplex structure is assessed by local high affinity Cuphenanthroline cleavage. In preliminary studies, a homologue of 3'A-PRE2ap displayed a 10-fold increase in binding affinity due to inclusion of dF at three sites as compared to its unmodified counterpart. In Phase I studies we will confirm these findings and extend the use of dF substitution within TFOs which are specific for epidermal growth factor receptor (EGFR) (EG36ap), mouse insulin receptor (IR) promoter (IR2ap) and HIV-1 (HIV38p) domains. If dF substitution improves triple helix structure and binding affinity, in Phase II Studies the biological effects of such TFOs will be assessed.