Summary information and primary citation

PDB-id
5j4p
Class
DNA
Method
NMR
Summary
Diy g-quadruplexes: solution structure of d(ggtttggttttggtttgg) in sodium
Reference
Dvorkin SA, Karsisiotis AI, Webba da Silva M (2018): "Encoding canonical DNA quadruplex structure." Sci Adv, 4, eaat3007. doi: 10.1126/sciadv.aat3007.
Abstract
The main challenge in DNA quadruplex design is to encode a three-dimensional structure into the primary sequence, despite its multiple, repetitive guanine segments. We identify and detail structural elements describing all 14 feasible canonical quadruplex scaffolds and demonstrate their use in control of design. This work outlines a new roadmap for implementation of targeted design of quadruplexes for material, biotechnological, and therapeutic applications.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2, 2(-LwD+Ln)

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s--s sugar=---. groove=w-n- planarity=0.073 type=planar N- nts=4 GGGG A.DG1,A.DG7,A.DG18,A.DG12
 2 glyco-bond=-ss- sugar=...- groove=w-n- planarity=0.087 type=planar N+ nts=4 GGGG A.DG2,A.DG6,A.DG17,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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s--s sugar=---. groove=w-n- Major-->WC N- nts=4 GGGG A.DG1,A.DG7,A.DG18,A.DG12
 2  glyco-bond=-ss- sugar=...- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG2,A.DG6,A.DG17,A.DG13
  step#1  mm(<>,outward)  area=12.60 rise=3.06 twist=18.5
  strand#1 DNA glyco-bond=s- sugar=-. nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-. nts=2 GG A.DG7,A.DG6
  strand#3 DNA glyco-bond=-s sugar=-. nts=2 GG A.DG18,A.DG17
  strand#4 DNA glyco-bond=s- sugar=.- nts=2 GG A.DG12,A.DG13

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=s--s sugar=---. groove=w-n- Major-->WC N- nts=4 GGGG A.DG1,A.DG7,A.DG18,A.DG12
 2  glyco-bond=-ss- sugar=...- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG2,A.DG6,A.DG17,A.DG13
  step#1  mm(<>,outward)  area=12.60 rise=3.06 twist=18.5

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4-stem

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

Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UDDU, anti-parallel:basket, 2+2, 2(-LwD+Ln)
 1  glyco-bond=s--s sugar=---. groove=w-n- Major-->WC N- nts=4 GGGG A.DG1,A.DG7,A.DG18,A.DG12
 2  glyco-bond=-ss- sugar=...- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG2,A.DG6,A.DG17,A.DG13
  step#1  mm(<>,outward)  area=12.60 rise=3.06 twist=18.5
  strand#1  U DNA glyco-bond=s- sugar=-. nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-. nts=2 GG A.DG7,A.DG6
  strand#3  D DNA glyco-bond=-s sugar=-. nts=2 GG A.DG18,A.DG17
  strand#4  U DNA glyco-bond=s- sugar=.- nts=2 GG A.DG12,A.DG13
  loop#1 type=lateral   strands=[#1,#2] nts=3 TTT A.DT3,A.DT4,A.DT5
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT A.DT8,A.DT9,A.DT10,A.DT11
  loop#3 type=lateral   strands=[#4,#3] nts=3 TTT A.DT14,A.DT15,A.DT16

Download PDB file
Interactive view in 3Dmol.js