Summary information

PDB id
7d5d
Class
DNA
Method
X-ray (1.18 Å)
Summary
Left-handed g-quadruplex containing one bulge
Reference
Das P, Ngo KH, Winnerdy FR, Maity A, Bakalar B, Mechulam Y, Schmitt E, Phan AT (2021): "Bulges in left-handed G-quadruplexes." Nucleic Acids Res., 49, 1724-1736. doi: 10.1093/nar/gkaa1259.
Abstract
G-quadruplex (G4) DNA structures with a left-handed backbone progression have unique and conserved structural features. Studies on sequence dependency of the structures revealed the prerequisites and some minimal motifs required for left-handed G4 formation. To extend the boundaries, we explore the adaptability of left-handed G4s towards the existence of bulges. Here we present two X-ray crystal structures and an NMR solution structure of left-handed G4s accommodating one, two and three bulges. Bulges in left-handed G4s show distinct characteristics as compared to those in right-handed G4s. The elucidation of intricate structural details will help in understanding the possible roles and limitations of these unique structures.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+P+P+P), parallel(4+0), UUUU, negative twist

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.144 type=planar nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.039 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.155 type=planar nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25

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, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25
  step#1  mp(<<,backward) area=10.83 rise=3.29 twist=-29.3
  step#2  mm(<>,outward)  area=29.28 rise=3.29 twist=-10.7
  step#3  pm(>>,forward)  area=12.29 rise=3.33 twist=-25.7
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG23,A.DG22
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG4,A.DG6,A.DG20,A.DG19
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG9,A.DG17,A.DG16
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG11,A.DG12,A.DG14,A.DG25

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12
  step#1  mp(<<,backward) area=10.83 rise=3.29 twist=-29.3

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14
  step#2  mm(<>,outward)  area=29.28 rise=3.29 twist=-10.7

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 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25
  step#3  pm(>>,forward)  area=12.29 rise=3.33 twist=-25.7

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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, 3 loops, INTRA-molecular, UUUU, parallel, 2(+P+P+P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG11,A.DG8,A.DG4
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6
  step#1  mp(<<,backward) area=10.83 rise=3.29 twist=-29.3
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG12
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9
  strand#4* U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG4,A.DG6 bulged-nts=1 T A.DT5
  loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT3
  loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT7
  loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT10

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=4 GTGG A.DG14,A.DT15,A.DG16,A.DG17
 2* type=V-shaped  helix=#1 nts=4 GGTG A.DG22,A.DG23,A.DT24,A.DG25