THROMBIN-BINDING DNA APTAMER FORMS A UNIMOLECULAR QUADRUPLEX STRUCTURE IN SOLUTION

We have used two-dimensional H-1 NMR spectroscopy to study the conform ation of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) in solution. This is one of a series of thrombin-binding DNA aptamers with a consen sus 15-base sequence that was recently isolated and shown to inhibit t hrombin-catalyzed fibrin clot formation in vitro [Bock, L. C., Griffin , L. C., Latham, J. A., Vermaas, E. B. & Toole, J. J. (1992) Nature (L ondon) 355, 564-566]. The oligonucleotide forms a unimolecular DNA qua druplex consisting of two G-quartets connected by two TT loops and one TGT loop. A potential T.T bp is formed between the two TT loops acros s the diagonal of the top G-quartet. Thus, all of the invariant bases in the consensus sequence are base-paired. This aptamer structure was determined by NMR and illustrates that this molecule forms a specific folded structure. Knowledge of this structure may be used in the furth er development of oligonucleotide-based thrombin inhibitors.