Summary information

PDB id
7vf1
Class
DNA
Method
NMR
Summary
Solution structure of a duplex-quadruplex hybrid formed by d[g4c2] repeats
Reference
Maity A, Lim KW, Shneider NA, Chen G, Phan AT: "A duplex-quadruplex hybrid formed by d[G4C2] repeats."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UUDD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=ss-- sugar=---. groove=-w-n planarity=0.097 type=planar nts=4 GGGG A.DG1,B.DG9,A.DG10,B.DG2
 2 glyco-bond=--ss sugar=.--- groove=-w-n planarity=0.097 type=planar nts=4 GGGG A.DG2,B.DG10,A.DG9,B.DG1

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, inter-molecular, with 1 stem

 1  glyco-bond=ss-- sugar=---. groove=-w-n Major-->WC nts=4 GGGG A.DG1,B.DG9,A.DG10,B.DG2
 2  glyco-bond=--ss sugar=.--- groove=-w-n WC-->Major nts=4 GGGG A.DG2,B.DG10,A.DG9,B.DG1
  step#1  mm(<>,outward)  area=11.75 rise=3.90 twist=19.8
  strand#1 DNA glyco-bond=s- sugar=-. nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG9,B.DG10
  strand#3 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9
  strand#4 DNA glyco-bond=-s sugar=.- nts=2 GG B.DG2,B.DG1

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1 stacking diagram 
 1  glyco-bond=ss-- sugar=---. groove=-w-n Major-->WC nts=4 GGGG A.DG1,B.DG9,A.DG10,B.DG2
 2  glyco-bond=--ss sugar=.--- groove=-w-n WC-->Major nts=4 GGGG A.DG2,B.DG10,A.DG9,B.DG1
  step#1  mm(<>,outward)  area=11.75 rise=3.90 twist=19.8

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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-tetrad layers, 2 loops, inter-molecular, UUDD, anti-parallel, (2+2)

 1  glyco-bond=ss-- sugar=---. groove=-w-n Major-->WC nts=4 GGGG A.DG1,B.DG9,A.DG10,B.DG2
 2  glyco-bond=--ss sugar=.--- groove=-w-n WC-->Major nts=4 GGGG A.DG2,B.DG10,A.DG9,B.DG1
  step#1  mm(<>,outward)  area=11.75 rise=3.90 twist=19.8
  strand#1  U DNA glyco-bond=s- sugar=-. nts=2 GG A.DG1,A.DG2
  strand#2  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG9,B.DG10
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9
  strand#4  D DNA glyco-bond=-s sugar=.- nts=2 GG B.DG2,B.DG1
  loop#1 type=diagonal  strands=[#1,#3] nts=6 GGCCGG A.DG3,A.DG4,A.DC5,A.DC6,A.DG7,A.DG8
  loop#2 type=diagonal  strands=[#4,#2] nts=6 GGCCGG B.DG3,B.DG4,B.DC5,B.DC6,B.DG7,B.DG8

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