DSSR-derived G-quadruplex features in PDB entry 6jcd
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.
- G-quadruplex peripheral knot
- Truong, T.H.A., Winnerdy, F.R., Phan, A.T.: (2019) "An Unprecedented Knot-like G-Quadruplex Peripheral Motif." Angew.Chem.Int.Ed.Engl., 58, 13834-13839.
- A knot-like G-quadruplex peripheral structure is formed by a 7-nt DNA sequence DL7 (TGTTGGT), in which six out of its seven nucleobases participate in compact base-pairing interactions. Here, the solution NMR structure of a 24-nt DNA oligonucleotide containing the DL7 sequence shows the interaction between a two-layer anti-parallel G-quadruplex core and the peripheral knot-like structure, including the construction of two sharp turns in the DNA backbone. The formation of this novel structural element highlights the intricate properties of single-stranded DNA folding in presence of G-quadruplex-forming motifs. We demonstrated the compatibility of the DL7 knot-like structure with various G-quadruplexes, which could have implications in drug design and DNA engineering.
- G4 notes
- 2 G-tetrads, 1 G4 helix
1 glyco-bond=s-s- groove=wnwn planarity=0.222 type=other nts=4 GGGG A.DG2,A.DG19,A.DG8,A.DG14 2 glyco-bond=---s groove=--wn planarity=0.180 type=other nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG13
Helix#1, 2 G-tetrad layers, INTRA-molecular
List of 4 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=4 GTTG A.DG3,A.DT4,A.DT5,A.DG6 2 type=V-shaped helix=#1 nts=4 GTGG A.DG6,A.DT7,A.DG8,A.DG9 3 type=lateral helix=#1 nts=5 GTTTG A.DG9,A.DT10,A.DT11,A.DT12,A.DG13 4 type=diagonal helix=#1 nts=6 GTGTTG A.DG14,A.DT15,A.DG16,A.DT17,A.DT18,A.DG19