DSSR-derived G-quadruplex features in PDB entry 2chj
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.
- nucleic acid
- NMR structure of tglglt quadruplex
- Nielsen, J.T., Arar, K., Petersen, M.: (2006) "NMR Solution Structures of Lna (Locked Nucleic Acid) Modified Quadruplexes." Nucleic Acids Res., 34, 2006-.
- We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of the LNA nucleotides. However, local structural alterations are observed owing to the locked LNA sugars. In particular, a distinct change in the sugar-phosphate backbone is observed at the G2pL3 and L2pL3 base steps and sequence dependent changes in the twist between tetrads are also seen. Both the LNA modified quadruplexes have raised thermostability as compared to the DNA quadruplex. The quadruplex-forming capability of d(TGLGLT) is of particular interest as it expands the design flexibility for stable parallel LNA quadruplexes and shows that LNA nucleotides can be mixed with DNA or other modified nucleic acids. As such, LNA-based quadruplexes can be decorated by a variety of chemical modifications. Such LNA quadruplex scaffolds might find applications in the developing field of nanobiotechnology.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.281 type=other nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20 2 glyco-bond=---- groove=---- planarity=0.313 type=other nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21 3 glyco-bond=---- groove=---- planarity=0.118 type=planar nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22 4 glyco-bond=---- groove=---- planarity=0.241 type=other nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23