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

PDB-id
6kvb
Class
DNA
Method
NMR
Summary
Structure of an intra-locked G-quadruplex
Reference
Maity, A., Winnerdy, F.R., Chang, W.D., Chen, G., Phan, A.T.: (2020) "Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs." Nucleic Acids Res., 48, 3315-3327.
Abstract
G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
G4 notes
4 G-tetrads, 1 G4 helix

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--- groove=w--n planarity=0.044 type=planar nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6
 2 glyco-bond=s--- groove=w--n planarity=0.094 type=planar nts=4 GGGG A.DG3,A.DG23,A.DG20,A.DG17
 3 glyco-bond=---. groove=--.. planarity=0.075 type=planar nts=4 GGGG A.DG5,A.DG8,A.DG11,A.DG15
 4 glyco-bond=---s groove=--wn planarity=0.023 type=planar nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27

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, 4 G-tetrad layers, INTRA-molecular

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6
 2  glyco-bond=.--- groove=.--. Major-->WC nts=4 GGGG A.DG15,A.DG11,A.DG8,A.DG5
 3  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG3
 4  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27
  step#1  mp(<<,backward) area=8.89  rise=3.40 twist=32.9
  step#2  mm(<>,outward)  area=10.15 rise=3.92 twist=23.1
  step#3  pm(>>,forward)  area=8.09  rise=3.21 twist=32.2
  strand#1 DNA glyco-bond=s.-- nts=4 GGGG A.DG2,A.DG15,A.DG17,A.DG18
  strand#2 DNA glyco-bond=---- nts=4 GGGG A.DG12,A.DG11,A.DG20,A.DG21
  strand#3 DNA glyco-bond=---- nts=4 GGGG A.DG9,A.DG8,A.DG23,A.DG24
  strand#4 DNA glyco-bond=--ss nts=4 GGGG A.DG6,A.DG5,A.DG3,A.DG27

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3 stacking diagrams
 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6
2 glyco-bond=.--- groove=.--. Major-->WC nts=4 GGGG A.DG15,A.DG11,A.DG8,A.DG5
step#1 mp(<<,backward) area=8.89 rise=3.40 twist=32.9

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 2  glyco-bond=.--- groove=.--. Major-->WC nts=4 GGGG A.DG15,A.DG11,A.DG8,A.DG5
3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG3
step#2 mm(<>,outward) area=10.15 rise=3.92 twist=23.1

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 3  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG3
4 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27
step#3 pm(>>,forward) area=8.09 rise=3.21 twist=32.2

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List of 0 G4-stems [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.

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

List of 3 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=5 GGTGG A.DG2,A.DG3,A.DT4,A.DG5,A.DG6
 2* type=V-shaped  helix=#1 nts=5 GGTTG A.DG11,A.DG12,A.DT13,A.DT14,A.DG15
 3 type=lateral   helix=#1 nts=4 GTTG A.DG24,A.DT25,A.DT26,A.DG27