DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 7xdh
Class: DNA
Method: X-ray (1.83 Å)
Summary: Crystal structure of a dimeric interlocked parallel g-quadruplex
Reference: Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT (2022): "Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A.G.G.G.G pentad in an interlocked G-quadruplex." Biochem.Biophys.Res.Commun., 613, 153-158. doi: 10.1016/j.bbrc.2022.04.020.
Abstract: 93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K<sub>+</sub> solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A•G•G•G•G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 2(-P-P-P), coaxial interfaces: 5'/5'-SEPARATED

Cartoon-block schematics in six views (download the tarball)

List of 6 G-tetrads

 1 glyco-bond=s--- sugar=---. groove=w--n planarity=0.093 type=planar -- nts=4 GGGG 1:A.DG1,1:B.DG6,1:B.DG2,1:B.DG13
 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.127 type=planar -- nts=4 GGGG 1:A.DG2,1:A.DG6,1:B.DG1,1:A.DG13
 3 glyco-bond=---- sugar=.-3- groove=---- planarity=0.086 type=planar O+ nts=4 GGGG 1:A.DG3,1:A.DG7,1:A.DG10,1:A.DG14
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.238 type=other  O+ nts=4 GGGG 1:A.DG4,1:A.DG8,1:A.DG11,1:A.DG15
 5 glyco-bond=---- sugar=3-.- groove=---- planarity=0.082 type=planar O+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG10,1:B.DG14
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.208 type=other  O+ nts=4 GGGG 1:B.DG4,1:B.DG8,1:B.DG11,1:B.DG15

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, 6 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG8,1:A.DG11,1:A.DG15 2 glyco-bond=---- sugar=.-3- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG7,1:A.DG10,1:A.DG14 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG2,1:A.DG6,1:B.DG1,1:A.DG13 4 glyco-bond=s--- sugar=---. groove=w--n Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG6,1:B.DG2,1:B.DG13 5 glyco-bond=---- sugar=.-3- groove=---- Major-->WC O+ nts=4 GGGG 1:B.DG10,1:B.DG7,1:B.DG3,1:B.DG14 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:B.DG11,1:B.DG8,1:B.DG4,1:B.DG15 step#1 mp(<<,backward) area=10.52 rise=3.42 twist=30.1 step#2 mp(<<,backward) area=9.59 rise=3.34 twist=32.0 step#3 mm(<>,outward) area=11.70 rise=3.45 twist=21.4 step#4 pm(>>,forward) area=9.73 rise=3.36 twist=32.4 step#5 pm(>>,forward) area=11.17 rise=3.44 twist=29.6 strand#1 DNA glyco-bond=---s-- sugar=-.--.- nts=6 GGGGGG 1:A.DG4,1:A.DG3,1:A.DG2,1:A.DG1,1:B.DG10,1:B.DG11 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG 1:A.DG8,1:A.DG7,1:A.DG6,1:B.DG6,1:B.DG7,1:B.DG8 strand#3 DNA glyco-bond=--s--- sugar=-3--3- nts=6 GGGGGG 1:A.DG11,1:A.DG10,1:B.DG1,1:B.DG2,1:B.DG3,1:B.DG4 strand#4 DNA glyco-bond=------ sugar=---.-- nts=6 GGGGGG 1:A.DG15,1:A.DG14,1:A.DG13,1:B.DG13,1:B.DG14,1:B.DG15 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG8,1:A.DG11,1:A.DG15 2 glyco-bond=---- sugar=.-3- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG7,1:A.DG10,1:A.DG14 step#1 mp(<<,backward) area=10.52 rise=3.42 twist=30.1 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=.-3- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG7,1:A.DG10,1:A.DG14 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG2,1:A.DG6,1:B.DG1,1:A.DG13 step#2 mp(<<,backward) area=9.59 rise=3.34 twist=32.0 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG2,1:A.DG6,1:B.DG1,1:A.DG13 4 glyco-bond=s--- sugar=---. groove=w--n Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG6,1:B.DG2,1:B.DG13 step#3 mm(<>,outward) area=11.70 rise=3.45 twist=21.4 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=s--- sugar=---. groove=w--n Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG6,1:B.DG2,1:B.DG13 5 glyco-bond=---- sugar=.-3- groove=---- Major-->WC O+ nts=4 GGGG 1:B.DG10,1:B.DG7,1:B.DG3,1:B.DG14 step#4 pm(>>,forward) area=9.73 rise=3.36 twist=32.4 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=.-3- groove=---- Major-->WC O+ nts=4 GGGG 1:B.DG10,1:B.DG7,1:B.DG3,1:B.DG14 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:B.DG11,1:B.DG8,1:B.DG4,1:B.DG15 step#5 pm(>>,forward) area=11.17 rise=3.44 twist=29.6 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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

 1  glyco-bond=---- sugar=.-3- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG7,1:A.DG10,1:A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG8,1:A.DG11,1:A.DG15
  step#1  pm(>>,forward)  area=10.52 rise=3.42 twist=30.1
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG 1:A.DG3,1:A.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG7,1:A.DG8
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 GG 1:A.DG10,1:A.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG14,1:A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG 1:A.DT5,1:A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A 1:A.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 AG 1:A.DA12,1:A.DG13

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Interactive view in 3Dmol.js

Stem#2, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)

 1  glyco-bond=---- sugar=3-.- groove=---- WC-->Major O+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG10,1:B.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:B.DG4,1:B.DG8,1:B.DG11,1:B.DG15
  step#1  pm(>>,forward)  area=11.17 rise=3.44 twist=29.6
  strand#1  U DNA glyco-bond=-- sugar=3- nts=2 GG 1:B.DG3,1:B.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:B.DG7,1:B.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG 1:B.DG10,1:B.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:B.DG14,1:B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG 1:B.DT5,1:B.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A 1:B.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 AG 1:B.DA12,1:B.DG13