Summary information

PDB id
1jjp
Class
DNA
Method
NMR
Summary
A(gggg) pentad-containing dimeric DNA quadruplex involving stacked g(anti)g(anti)g(anti)g(syn) tetrads
Reference
Zhang N, Gorin A, Majumdar A, Kettani A, Chernichenko N, Skripkin E, Patel DJ (2001): "V-shaped scaffold: a new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads." J.Mol.Biol., 311, 1063-1079. doi: 10.1006/jmbi.2001.4916.
Abstract
We report the results of an NMR study of unlabeled and uniformly (13)C,(15)N-labeled d(G(3)AG(2)T(3)G(3)AT) in 100 mM NaCl, conditions under which it forms a dimeric quadruplex containing several new topological features. The DNA oligomer chain in each symmetry-related monomer subunit undergoes three sharp turns to form a compact domain, with all the purine bases involved in pairing alignments. The first turn is of the double chain reversal type, the second is of the edgewise type, and the third represents a new alignment, the V-shaped type. Each monomer of the dimeric quadruplex contains two stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads, one of which forms a newly identified A x (G x G x G x G) pentad, through sheared G.A mismatch formation. There is a break in one of the four G-G columns that link adjacent G x G x G x G tetrads within each monomer. This architectural interruption is compensated by a new topological feature of quadruplex architecture, the V-shaped scaffold. The missing G-G column results in an opening that could facilitate insertion of planar ligands into the quadruplex. The dimeric interface contains stacked A.(G.G.G.G) pentads, with each pentad containing four bases from one monomer and a syn G1 from the partner monomer. Several potential ligand-binding pockets, positioned towards either end of the folded architecture, were identifiable in a surface view of the solution structure of the dimeric d(G(3)AG(2)T(3)G(3)AT) quadruplex.
G4 notes
4 G-tetrads, 1 G4 helix

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=.3-- groove=---- planarity=0.151 type=planar nts=4 GGGG A.DG1,B.DG11,B.DG2,B.DG5
 2 glyco-bond=---- sugar=--.3 groove=---- planarity=0.150 type=planar nts=4 GGGG A.DG2,A.DG5,B.DG1,A.DG11
 3 glyco-bond=--s- sugar=-.3- groove=-wn- planarity=0.191 type=other  nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG12
 4 glyco-bond=--s- sugar=-.3- groove=-wn- planarity=0.191 type=other  nts=4 GGGG B.DG3,B.DG6,B.DG10,B.DG12

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, 4 G-tetrad layers, inter-molecular

 1  glyco-bond=--s- sugar=-.3- groove=-wn- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG12
 2  glyco-bond=---- sugar=--.3 groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,B.DG1,A.DG11
 3  glyco-bond=---- sugar=.--3 groove=---- Major-->WC nts=4 GGGG A.DG1,B.DG5,B.DG2,B.DG11
 4  glyco-bond=s--- sugar=3.-- groove=w--n Major-->WC nts=4 GGGG B.DG10,B.DG6,B.DG3,B.DG12
  step#1  mp(<<,backward) area=8.92  rise=3.00 twist=36.7
  step#2  mm(<>,outward)  area=10.19 rise=3.09 twist=21.9
  step#3  pm(>>,forward)  area=8.92  rise=2.99 twist=36.7
  strand#1 DNA glyco-bond=---s sugar=--.3 nts=4 GGGG A.DG3,A.DG2,A.DG1,B.DG10
  strand#2 DNA glyco-bond=---- sugar=.--. nts=4 GGGG A.DG6,A.DG5,B.DG5,B.DG6
  strand#3 DNA glyco-bond=s--- sugar=3.-- nts=4 GGGG A.DG10,B.DG1,B.DG2,B.DG3
  strand#4 DNA glyco-bond=---- sugar=-33- nts=4 GGGG A.DG12,A.DG11,B.DG11,B.DG12

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3 stacking diagrams 
 1  glyco-bond=--s- sugar=-.3- groove=-wn- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG12
 2  glyco-bond=---- sugar=--.3 groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,B.DG1,A.DG11
  step#1  mp(<<,backward) area=8.92  rise=3.00 twist=36.7

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Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=--.3 groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,B.DG1,A.DG11
 3  glyco-bond=---- sugar=.--3 groove=---- Major-->WC nts=4 GGGG A.DG1,B.DG5,B.DG2,B.DG11
  step#2  mm(<>,outward)  area=10.19 rise=3.09 twist=21.9

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 3  glyco-bond=---- sugar=.--3 groove=---- Major-->WC nts=4 GGGG A.DG1,B.DG5,B.DG2,B.DG11
 4  glyco-bond=s--- sugar=3.-- groove=w--n Major-->WC nts=4 GGGG B.DG10,B.DG6,B.DG3,B.DG12
  step#3  pm(>>,forward)  area=8.92  rise=2.99 twist=36.7

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List of 4 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=5 GTTTG A.DG6,A.DT7,A.DT8,A.DT9,A.DG10
 2 type=V-shaped  helix=#1 nts=3 GGG A.DG10,A.DG11,A.DG12
 3 type=lateral   helix=#1 nts=5 GTTTG B.DG6,B.DT7,B.DT8,B.DT9,B.DG10
 4 type=V-shaped  helix=#1 nts=3 GGG B.DG10,B.DG11,B.DG12