Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6jcd
Class
DNA
Method
NMR
Summary
G-quadruplex peripheral knot
Reference
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.
Abstract
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

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 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

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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- groove=wnwn Major-->WC nts=4 GGGG A.DG2,A.DG19,A.DG8,A.DG14
 2  glyco-bond=---s 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- nts=2 GG A.DG2,A.DG3
  strand#2 DNA glyco-bond=-- nts=2 GG A.DG19,A.DG6
  strand#3 DNA glyco-bond=s- nts=2 GG A.DG8,A.DG9
  strand#4 DNA glyco-bond=-s nts=2 GG A.DG14,A.DG13

Download PDB file
Interactive view in 3Dmol.js

1 stacking diagram
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG2,A.DG19,A.DG8,A.DG14
2 glyco-bond=---s 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 0 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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