Selection of single-stranded DNA molecules that bind and inhibit human thrombin

Abstract

APTAMERS1 are double-stranded DNA or single-stranded RNA molecules that bind specific molecular targets. Large randomly generated populations can be enriched in aptamers by in vitro selection and polymerase chain reaction1–11. But so far single-stranded DNA has not been investigated for aptamer properties, nor has a target protein been considered that does not interact physiologically with nucleic acid. Here we describe the isolation of single-stranded DNA aptamers to the protease thrombin of the blood coagulation cascade and report binding affinities in the range 25–200 nM. Sequence data from 32 thrsombin aptamers, selected from a pool of DNA containing 60 nucleotides of random sequence, displayed a highly conserved 14–17–base region. Several of these aptamers at nanomolar concentrations inhibited thrombin-catalysed fibrin-clot formation in vitro using either purified fibrinogen or human plasma.