148d

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THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA APTAMER D(GGTTGGTGTGGTTGG)

Overview

The DNA oligonucleotide d(GGTTGGTGTGGTTGG) (thrombin aptamer) binds to, thrombin and inhibits its enzymatic activity in the chain of reactions, that lead to blood clotting. Two-dimensional 1H NMR studies indicate that, the oligonucleotide forms a folded structure in solution, composed of two, guanine quartets connected by two T-T loops spanning the narrow grooves at, one end and a T-G-T loop spanning a wide groove at the other end. We, present the assignment strategy used, methods for the structure, determination, and the refined three-dimensional structure of the thrombin, aptamer. The initial structures were generated by metric matrix distance, geometry using distance and dihedral bond angle constraints from NOE and, coupling constants, respectively, and refined by restrained molecular, dynamics and direct NOE refinement. Knowledge of the three-dimensional, structure of this thrombin aptamer may be relevant for the design of, improved thrombin-inhibiting anti-coagulants with similar structural, motifs.

About this Structure

148D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)., Schultze P, Macaya RF, Feigon J, J Mol Biol. 1994 Feb 4;235(5):1532-47. PMID:8107090

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