Summary information and primary citation
- PDB-id
-
148d;
SNAP-derived features in text and
JSON formats
- Class
- DNA
- Method
- NMR
- Summary
- Three-dimensional solution structure of the thrombin
binding DNA aptamer d(ggttggtgtggttgg)
- Reference
-
Schultze P, Macaya RF, Feigon J (1994): "Three-dimensional
solution structure of the thrombin-binding DNA aptamer
d(GGTTGGTGTGGTTGG)." J.Mol.Biol.,
235, 1532-1547. doi: 10.1006/jmbi.1994.1105.
- Abstract
- 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.
