Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution.

TLDR

The thrombin‑binding aptamer d(GGTTGGTGTGGTTGG) is part of a 15‑base consensus series that inhibits thrombin‑catalyzed fibrin clot formation in vitro. Understanding its structure could aid development of oligonucleotide‑based thrombin inhibitors. We employed two‑dimensional 1H NMR spectroscopy to probe the aptamer’s conformation in solution. NMR revealed a unimolecular DNA quadruplex with two G‑quartets linked by two TT loops and one TGT loop, a T.T base pair across the top G‑quartet’s diagonal, and complete base pairing of all invariant consensus bases, demonstrating a specific folded structure.

Abstract

We have used two-dimensional 1H NMR spectroscopy to study the conformation of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) in solution. This is one of a series of thrombin-binding DNA aptamers with a consensus 15-base sequence that was recently isolated and shown to inhibit thrombin-catalyzed fibrin clot formation in vitro [Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H. & Toole, J. J. (1992) Nature (London) 355, 564-566]. The oligonucleotide forms a unimolecular DNA quadruplex 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 across 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 further development of oligonucleotide-based thrombin inhibitors.