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

PDB-id
6tzq*
Class
DNA
Method
X-ray (2.29 Å)
Summary
A DNA G-quadruplex-i-motif hybrid
Reference
Chu, B., Zhang, D., Paukstelis, P.J.: (2019) "A DNA G-quadruplex/i-motif hybrid." Nucleic Acids Res., 47, 11921-11930.
Abstract
DNA can form many structures beyond the canonical Watson-Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal structure of the DNA oligonucleotide, d(CCAGGCTGCAA), that self-associates to form a quadruplex structure containing two central antiparallel G-tetrads and six i-motif C-C+ base pairs. Solution studies suggest a robust structural motif capable of assembling as a tetramer of individual strands or as a dimer when composed of tandem repeats. This hybrid structure highlights the growing structural diversity of DNA and suggests that biological systems may harbor many functionally important non-duplex structures.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDUD

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=0.289 type=other  nts=4 GGGG 1:A.DG4,2:B.DG5,1:B.DG4,2:A.DG5
 2 glyco-bond=-s-s groove=wnwn planarity=0.289 type=other  nts=4 GGGG 1:A.DG5,2:B.DG4,1:B.DG5,2:A.DG4

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, inter-molecular, with 1 stem

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG 1:A.DG4,2:B.DG5,1:B.DG4,2:A.DG5
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG 1:A.DG5,2:B.DG4,1:B.DG5,2:A.DG4
  step#1  mm(<>,outward)  area=14.32 rise=3.50 twist=16.3
  strand#1 DNA glyco-bond=s- nts=2 GG 1:A.DG4,1:A.DG5
  strand#2 DNA glyco-bond=-s nts=2 GG 2:B.DG5,2:B.DG4
  strand#3 DNA glyco-bond=s- nts=2 GG 1:B.DG4,1:B.DG5
  strand#4 DNA glyco-bond=-s nts=2 GG 2:A.DG5,2:A.DG4

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Interactive view in 3Dmol.js

1 stacking diagram
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG 1:A.DG4,2:B.DG5,1:B.DG4,2:A.DG5
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG 1:A.DG5,2:B.DG4,1:B.DG5,2:A.DG4
step#1 mm(<>,outward) area=14.32 rise=3.50 twist=16.3

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Interactive view in 3Dmol.js

List of 1 G4-stem [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.

Stem#1, 2 G-tetrad layers, 0 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG 1:A.DG4,2:B.DG5,1:B.DG4,2:A.DG5
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG 1:A.DG5,2:B.DG4,1:B.DG5,2:A.DG4
  step#1  mm(<>,outward)  area=14.32 rise=3.50 twist=16.3
  strand#1  U DNA glyco-bond=s- nts=2 GG 1:A.DG4,1:A.DG5
  strand#2  D DNA glyco-bond=-s nts=2 GG 2:B.DG5,2:B.DG4
  strand#3  U DNA glyco-bond=s- nts=2 GG 1:B.DG4,1:B.DG5
  strand#4  D DNA glyco-bond=-s nts=2 GG 2:A.DG5,2:A.DG4

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

List of 0 non-stem G4-loops (including the two closing Gs)