DSSR-derived G-quadruplex features in PDB entry 2idn
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- NMR structure of a new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site
- Martino, L., Virno, A., Randazzo, A., Virgilio, A., Esposito, V., Giancola, C., Bucci, M., Cirino, G., Mayol, L.: (2006) "A new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site." Nucleic Acids Res., 34, 6653-6662.
- The solution structure of a new modified thrombin binding aptamer (TBA) containing a 5'-5' inversion of polarity site, namely d(3'GGT5'-5'TGGTGTGGTTGG3'), is reported. NMR and CD spectroscopy, as well as molecular dynamic and mechanic calculations, have been used to characterize the 3D structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT and TT loops. d(3'GGT5'-5'TGGTGTGGTTGG3') is characterized by an unusual folding, being three strands parallel to each other and only one strand oriented in opposite manner. This led to an anti-anti-anti-syn and syn-syn-syn-anti arrangement of the Gs in the two tetrads. The thermal stability of the modified oligonucleotide is 4 degrees C higher than the corresponding unmodified TBA. d(3'GGT5'-5'TGGTGTGGTTGG3') continues to display an anticoagulant activity, even if decreased with respect to the TBA.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-Lw-Ln), UD3(1+3), DDUD
1 glyco-bond=--s- groove=-wn- planarity=0.412 type=bowl nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15 2 glyco-bond=s.-s groove=..n- planarity=0.380 type=other nts=4 GGGG A.DG2,A.DG5,A.DG11,A.DG14
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.