DSSR-derived G-quadruplex features in PDB entry 148d
Poster "DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB" presented at the RNA2020 online meeting
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- Three-dimensional solution structure of the thrombin binding DNA aptamer d(ggttggtgtggttgg)
- Schultze, P., Macaya, R.F., Feigon, J.: (1994) "Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)." J.Mol.Biol., 235, 1532-1547.
- 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.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(+Ln+Lw+Ln), chair(2+2), UDUD
1 glyco-bond=s-s- groove=wnwn planarity=0.583 type=other nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=-s-s groove=wnwn planarity=0.526 type=other nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5