DSSR-derived G-quadruplex features in PDB entry 2led
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.
- Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from intron of n-myc gene
- Trajkovski, M., Webba da Silva, M., Plavec, J.: (2012) "Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene." J.Am.Chem.Soc., 134, 4132-4141.
- A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K(+), NH(4)(+), and Na(+) ions. A monomeric G-quadruplex formed in K(+) ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K(+) ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 3'/5'
1 glyco-bond=---- groove=---- planarity=0.399 type=other nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7 2 glyco-bond=---- groove=---- planarity=0.447 type=bowl nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8 3 glyco-bond=---- groove=---- planarity=0.313 type=other nts=4 GGGG A.DG5,A.DG9,B.DG5,B.DG9 4 glyco-bond=---- groove=---- planarity=0.188 type=other nts=4 GGGG A.DG11,A.DG15,B.DG11,B.DG15 5 glyco-bond=---- groove=---- planarity=0.229 type=bowl nts=4 GGGG A.DG12,A.DG16,B.DG12,B.DG16 6 glyco-bond=---- groove=---- planarity=0.447 type=bowl nts=4 GGGG A.DG13,A.DG17,B.DG13,B.DG17
Helix#1, 6 G-tetrad layers, inter-molecular, with 2 stems
Stem#1, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
Stem#2, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [3'/5']