Summary information

PDB id
6jcd
Class
DNA
Method
NMR
Summary
G-quadruplex peripheral knot
Reference
Truong THA, Winnerdy FR, Phan AT (2019): "An Unprecedented Knot-like G-Quadruplex Peripheral Motif." Angew.Chem.Int.Ed.Engl., 58, 13834-13839. doi: 10.1002/anie.201907740.
Abstract
We discovered the formation of a knot-like G-quadruplex peripheral structure by a 7-nt DNA sequence DL7: 5'-d(TGTTGGT)-3', whereby six out of its seven nucleobases participate in compact base pairing interactions. Here, solution 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 structure, including the construction of two sharp turns from the DNA backbone. The formation of this novel structural element highlights the intricate property 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

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=-3-- groove=wnwn planarity=0.222 type=other  nts=4 GGGG A.DG2,A.DG19,A.DG8,A.DG14
 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.180 type=other  nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG13

List of 1 G4-helix

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

 1  glyco-bond=s-s- sugar=-3-- groove=wnwn Major-->WC nts=4 GGGG A.DG2,A.DG19,A.DG8,A.DG14
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG13
  step#1  mm(<>,outward)  area=14.38 rise=4.06 twist=20.0
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG2,A.DG3
  strand#2 DNA glyco-bond=-- sugar=3- nts=2 GG A.DG19,A.DG6
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG8,A.DG9
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG14,A.DG13

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=s-s- sugar=-3-- groove=wnwn Major-->WC nts=4 GGGG A.DG2,A.DG19,A.DG8,A.DG14
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG13
  step#1  mm(<>,outward)  area=14.38 rise=4.06 twist=20.0

Download PDB file
Interactive view in 3Dmol.js

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