DSSR-derived G-quadruplex features in PDB entry 2kvy
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.
- NMR solution structure of the 4:1 complex between an uncharged distamycin a analogue and [d(tggggt)]4
- Cosconati, S., Marinelli, L., Trotta, R., Virno, A., De Tito, S., Romagnoli, R., Pagano, B., Limongelli, V., Giancola, C., Baraldi, P.G., Mayol, L., Novellino, E., Randazzo, A.: (2010) "Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle." J.Am.Chem.Soc., 132, 6425-6433.
- The study of DNA G-quadruplex stabilizers has enjoyed a great momentum in the late years due to their application as anticancer agents. The recognition of the grooves of these structural motifs is expected to result in a higher degree of selectivity over other DNA structures. Therefore, to achieve an enhanced knowledge on the structural and conformational requisites for quadruplex groove recognition, distamycin A, the only compound for which a pure groove binding has been proven, has been chemically modified. Surprisingly, structural and thermodynamic studies revealed that the absence of Coulombic interactions results in an unprecedented binding position in which both the groove and the 3' end of the DNA are occupied. This further contribution adds another piece to the so far elusive puzzle of the recognition between ligands and DNA quadruplexes and will serve as a platform for a rational design of new groove binders.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.216 type=other nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14 2 glyco-bond=---- groove=---- planarity=0.226 type=other nts=4 GGGG A.DG3,D.DG21,B.DG9,C.DG15 3 glyco-bond=---- groove=---- planarity=0.379 type=other nts=4 GGGG A.DG4,D.DG22,B.DG10,C.DG16 4 glyco-bond=---- groove=---- planarity=0.855 type=bowl nts=4 GGGG A.DG5,D.DG23,B.DG11,C.DG17