INCORPORATION OF A NON-NUCLEOTIDE BRIDGE INTO HAIRPIN OLIGONUCLEOTIDES CAPABLE OF HIGH-AFFINITY BINDING TO THE REV PROTEIN OF HIV-1

A bridge containing a rigid trans-stilbene group, 2)(3)NHC(O)-C6H4CH=C HC6H4C(O)NH(CH2)(3)OP(O)(O-)-, has been incorporated into several olig onucleotide sequences based on the minimal Rev Binding Element (RBE) o f HIV-1. This bridge was found to be as effective as a UUCG tetraloop in stabilizing short RNA duplex structures containing mismatched bases and bulged out nucleotide residues and to be more effective than eith er a TTTT loop or a triethyleneglycol linker in stabilizing similar DN A structures. Evaluation of stilbene-containing RNA RBE sequences of v arying length for their ability to bind the Rev protein of HIV-1 showe d that a 22-nucleotide stilbenedicarboxamide conjugate bound Rev almos t as well as a 94-base fragment of the Rev Responsive Element (RRE). A DNA hairpin mimetic with the same sequence was incapable of Rev bindi ng. Taken together, these experiments serve as an example for how in v itro selection and chemical modification can be combined to generate h igh-affinity mimetics of nucleic acid sequence and structure.