St. Cload et A. Schepartz, SELECTION OF STRUCTURE-SPECIFIC INHIBITORS OF THE HIV REV-REV RESPONSE ELEMENT COMPLEX, Journal of the American Chemical Society, 116(2), 1994, pp. 437-442
We devised a single-step selection method to identify short sequences
within the folded Rev response element (RRE) of the human immunodefici
ency virus (HIV) RNA genome that are proximal and able to bind short o
ligonucleotides. The method employed a library of partially randomized
tethered oligonucleotide probes (TOPs) complementary to all regions o
f the RRE and an RNase H cleavage assay which identified those RRE reg
ions preferred by the TOPs. Six short sequences were identified. Two T
OPs synthesized on the basis of this selection, S1-5-S2 and S1-1-S2, w
ere potent, concentration-dependent inhibitors of a RRE function in vi
tro and abolished interaction of the RRE with the HIV regulatory prote
in Rev at nanomolar concentration (25-degrees-C, 0.8 nM RRE, 45 nM Rev
). TOPs S1-5-S2 and S1-1-S2 exhibited greater potency and faster assoc
iation kinetics than traditional oligonucleotides targeted to the same
regions. The random TOP selection procedure described here allows rat
ional design of oligonucleotide-based ligands for RNA that exploit (ra
ther than avoid) the complex structure of the RNA target.