Detailed DSSR results for the G-quadruplex: PDB entry 8twh
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 8twh
- Class
- DNA
- Method
- X-ray (2.47 Å)
- Summary
- Crystal structure of (gggtt)3ggg g-quadruplex in complex with small molecule ligand rhps4
- Reference
- Lam G, Martin KN, Yatsunyk LA: "Crystal structure of (GGGTT)3GGG G-quadruplex in complex with small molecule ligand RHPS4."
- Abstract
- G4 notes
- 30 G-tetrads, 5 G4 helices, 10 G4 stems, 5 G4 coaxial stacks, 3(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'
Base-block schematics in six views
List of 30 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.071 type=planar nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16 2 glyco-bond=---- sugar=---- groove=---- planarity=0.080 type=planar nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17 3 glyco-bond=---- sugar=---- groove=---- planarity=0.274 type=bowl nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18 4 glyco-bond=---- sugar=---- groove=---- planarity=0.085 type=planar nts=4 GGGG B.DG1,B.DG6,B.DG11,B.DG16 5 glyco-bond=---- sugar=---- groove=---- planarity=0.107 type=planar nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17 6 glyco-bond=---- sugar=---- groove=---- planarity=0.269 type=bowl nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18 7 glyco-bond=---- sugar=-.-- groove=---- planarity=0.129 type=planar nts=4 GGGG C.DG1,C.DG6,C.DG11,C.DG16 8 glyco-bond=---- sugar=---- groove=---- planarity=0.141 type=planar nts=4 GGGG C.DG2,C.DG7,C.DG12,C.DG17 9 glyco-bond=---- sugar=---- groove=---- planarity=0.236 type=bowl nts=4 GGGG C.DG3,C.DG8,C.DG13,C.DG18 10 glyco-bond=---- sugar=---- groove=---- planarity=0.112 type=planar nts=4 GGGG D.DG1,D.DG6,D.DG11,D.DG16 11 glyco-bond=---- sugar=---- groove=---- planarity=0.091 type=planar nts=4 GGGG D.DG2,D.DG7,D.DG12,D.DG17 12 glyco-bond=---- sugar=---- groove=---- planarity=0.362 type=bowl nts=4 GGGG D.DG3,D.DG8,D.DG13,D.DG18 13 glyco-bond=---- sugar=---- groove=---- planarity=0.058 type=planar nts=4 GGGG E.DG1,E.DG6,E.DG11,E.DG16 14 glyco-bond=---- sugar=---- groove=---- planarity=0.105 type=planar nts=4 GGGG E.DG2,E.DG7,E.DG12,E.DG17 15 glyco-bond=---- sugar=---- groove=---- planarity=0.209 type=other nts=4 GGGG E.DG3,E.DG8,E.DG13,E.DG18 16 glyco-bond=---- sugar=---- groove=---- planarity=0.083 type=planar nts=4 GGGG F.DG1,F.DG6,F.DG11,F.DG16 17 glyco-bond=---- sugar=---- groove=---- planarity=0.067 type=planar nts=4 GGGG F.DG2,F.DG7,F.DG12,F.DG17 18 glyco-bond=---- sugar=---- groove=---- planarity=0.298 type=bowl nts=4 GGGG F.DG3,F.DG8,F.DG13,F.DG18 19 glyco-bond=---- sugar=---- groove=---- planarity=0.099 type=planar nts=4 GGGG G.DG1,G.DG6,G.DG11,G.DG16 20 glyco-bond=---- sugar=---- groove=---- planarity=0.139 type=planar nts=4 GGGG G.DG2,G.DG7,G.DG12,G.DG17 21 glyco-bond=---- sugar=---- groove=---- planarity=0.294 type=bowl nts=4 GGGG G.DG3,G.DG8,G.DG13,G.DG18 22 glyco-bond=---- sugar=---. groove=---- planarity=0.070 type=planar nts=4 GGGG H.DG1,H.DG6,H.DG11,H.DG16 23 glyco-bond=---- sugar=---- groove=---- planarity=0.074 type=planar nts=4 GGGG H.DG2,H.DG7,H.DG12,H.DG17 24 glyco-bond=---- sugar=---- groove=---- planarity=0.264 type=bowl nts=4 GGGG H.DG3,H.DG8,H.DG13,H.DG18 25 glyco-bond=---- sugar=---- groove=---- planarity=0.089 type=planar nts=4 GGGG I.DG1,I.DG6,I.DG11,I.DG16 26 glyco-bond=---- sugar=---- groove=---- planarity=0.167 type=other nts=4 GGGG I.DG2,I.DG7,I.DG12,I.DG17 27 glyco-bond=---- sugar=---- groove=---- planarity=0.215 type=other nts=4 GGGG I.DG3,I.DG8,I.DG13,I.DG18 28 glyco-bond=---- sugar=---- groove=---- planarity=0.042 type=planar nts=4 GGGG J.DG1,J.DG6,J.DG11,J.DG16 29 glyco-bond=---- sugar=---- groove=---- planarity=0.071 type=planar nts=4 GGGG J.DG2,J.DG7,J.DG12,J.DG17 30 glyco-bond=---- sugar=---- groove=---- planarity=0.324 type=bowl nts=4 GGGG J.DG3,J.DG8,J.DG13,J.DG18
List of 5 G4-helices
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-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG1,B.DG16,B.DG11,B.DG6 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG17,B.DG12,B.DG7 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG3,B.DG18,B.DG13,B.DG8 step#1 mp(<<,backward) area=17.95 rise=3.48 twist=22.4 step#2 mp(<<,backward) area=8.36 rise=3.27 twist=34.1 step#3 mm(<>,outward) area=27.65 rise=3.33 twist=-8.5 step#4 pm(>>,forward) area=9.23 rise=3.27 twist=33.4 step#5 pm(>>,forward) area=14.03 rise=3.53 twist=23.6 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG3,A.DG2,A.DG1,B.DG1,B.DG2,B.DG3 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG8,A.DG7,A.DG6,B.DG16,B.DG17,B.DG18 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG13,A.DG12,A.DG11,B.DG11,B.DG12,B.DG13 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG18,A.DG17,A.DG16,B.DG6,B.DG7,B.DG8 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17 |
 |
3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16 |
 |
4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG1,B.DG16,B.DG11,B.DG6 |
 |
5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG17,B.DG12,B.DG7 |
Helix#2, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG8,C.DG13,C.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG7,C.DG12,C.DG17 3* glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG6,C.DG11,C.DG16 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG1,D.DG16,D.DG11,D.DG6 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG2,D.DG17,D.DG12,D.DG7 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG3,D.DG18,D.DG13,D.DG8 step#1 mp(<<,backward) area=16.88 rise=3.50 twist=22.8 step#2 mp(<<,backward) area=9.15 rise=3.19 twist=33.7 step#3 mm(<>,outward) area=27.26 rise=3.41 twist=-7.1 step#4 pm(>>,forward) area=10.15 rise=3.33 twist=32.1 step#5 pm(>>,forward) area=13.50 rise=3.56 twist=22.4 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG C.DG3,C.DG2,C.DG1,D.DG1,D.DG2,D.DG3 strand#2 DNA glyco-bond=------ sugar=--.--- nts=6 GGGGGG C.DG8,C.DG7,C.DG6,D.DG16,D.DG17,D.DG18 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG C.DG13,C.DG12,C.DG11,D.DG11,D.DG12,D.DG13 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG C.DG18,C.DG17,C.DG16,D.DG6,D.DG7,D.DG8 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG8,C.DG13,C.DG18 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG7,C.DG12,C.DG17 |
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3* glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG6,C.DG11,C.DG16 |
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4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG1,D.DG16,D.DG11,D.DG6 |
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5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG2,D.DG17,D.DG12,D.DG7 |
Helix#3, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG8,E.DG13,E.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG7,E.DG12,E.DG17 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG1,E.DG6,E.DG11,E.DG16 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG1,F.DG16,F.DG11,F.DG6 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG2,F.DG17,F.DG12,F.DG7 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG3,F.DG18,F.DG13,F.DG8 step#1 mp(<<,backward) area=18.71 rise=3.49 twist=21.8 step#2 mp(<<,backward) area=7.77 rise=3.21 twist=35.6 step#3 mm(<>,outward) area=27.59 rise=3.34 twist=-8.2 step#4 pm(>>,forward) area=10.21 rise=3.27 twist=33.2 step#5 pm(>>,forward) area=14.55 rise=3.55 twist=23.1 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG E.DG3,E.DG2,E.DG1,F.DG1,F.DG2,F.DG3 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG E.DG8,E.DG7,E.DG6,F.DG16,F.DG17,F.DG18 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG E.DG13,E.DG12,E.DG11,F.DG11,F.DG12,F.DG13 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG E.DG18,E.DG17,E.DG16,F.DG6,F.DG7,F.DG8 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG8,E.DG13,E.DG18 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG7,E.DG12,E.DG17 |
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3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG1,E.DG6,E.DG11,E.DG16 |
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4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG1,F.DG16,F.DG11,F.DG6 |
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5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG2,F.DG17,F.DG12,F.DG7 |
Helix#4, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG3,G.DG8,G.DG13,G.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG2,G.DG7,G.DG12,G.DG17 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG1,G.DG6,G.DG11,G.DG16 4 glyco-bond=---- sugar=-.-- groove=---- Major-->WC nts=4 GGGG H.DG1,H.DG16,H.DG11,H.DG6 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG2,H.DG17,H.DG12,H.DG7 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG3,H.DG18,H.DG13,H.DG8 step#1 mp(<<,backward) area=14.18 rise=3.54 twist=24.1 step#2 mp(<<,backward) area=7.64 rise=3.25 twist=33.7 step#3 mm(<>,outward) area=27.32 rise=3.39 twist=-8.5 step#4 pm(>>,forward) area=8.91 rise=3.25 twist=33.9 step#5 pm(>>,forward) area=17.27 rise=3.55 twist=21.9 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG G.DG3,G.DG2,G.DG1,H.DG1,H.DG2,H.DG3 strand#2 DNA glyco-bond=------ sugar=---.-- nts=6 GGGGGG G.DG8,G.DG7,G.DG6,H.DG16,H.DG17,H.DG18 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG G.DG13,G.DG12,G.DG11,H.DG11,H.DG12,H.DG13 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG G.DG18,G.DG17,G.DG16,H.DG6,H.DG7,H.DG8 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG3,G.DG8,G.DG13,G.DG18 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG2,G.DG7,G.DG12,G.DG17 |
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3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG1,G.DG6,G.DG11,G.DG16 |
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4 glyco-bond=---- sugar=-.-- groove=---- Major-->WC nts=4 GGGG H.DG1,H.DG16,H.DG11,H.DG6 |
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5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG2,H.DG17,H.DG12,H.DG7 |
Helix#5, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG3,I.DG8,I.DG13,I.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG2,I.DG7,I.DG12,I.DG17 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG1,I.DG6,I.DG11,I.DG16 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG J.DG1,J.DG16,J.DG11,J.DG6 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG J.DG2,J.DG17,J.DG12,J.DG7 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG J.DG3,J.DG18,J.DG13,J.DG8 step#1 mp(<<,backward) area=17.51 rise=3.49 twist=21.8 step#2 mp(<<,backward) area=8.60 rise=3.27 twist=34.8 step#3 mm(<>,outward) area=27.15 rise=3.36 twist=-7.8 step#4 pm(>>,forward) area=8.80 rise=3.27 twist=32.9 step#5 pm(>>,forward) area=13.41 rise=3.54 twist=24.3 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG I.DG3,I.DG2,I.DG1,J.DG1,J.DG2,J.DG3 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG I.DG8,I.DG7,I.DG6,J.DG16,J.DG17,J.DG18 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG I.DG13,I.DG12,I.DG11,J.DG11,J.DG12,J.DG13 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG I.DG18,I.DG17,I.DG16,J.DG6,J.DG7,J.DG8 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG3,I.DG8,I.DG13,I.DG18 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG2,I.DG7,I.DG12,I.DG17 |
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3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG1,I.DG6,I.DG11,I.DG16 |
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4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG J.DG1,J.DG16,J.DG11,J.DG6 |
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5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG J.DG2,J.DG17,J.DG12,J.DG7 |
List of 10 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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18 step#1 pm(>>,forward) area=8.36 rise=3.27 twist=34.1 step#2 pm(>>,forward) area=17.95 rise=3.48 twist=22.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT4,A.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT9,A.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT14,A.DT15 1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG J.DG1,J.DG6,J.DG11,J.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG J.DG2,J.DG7,J.DG12,J.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG J.DG3,J.DG8,J.DG13,J.DG18 step#1 pm(>>,forward) area=8.80 rise=3.27 twist=32.9 step#2 pm(>>,forward) area=13.41 rise=3.54 twist=24.3 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG1,J.DG2,J.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG6,J.DG7,J.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG11,J.DG12,J.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG16,J.DG17,J.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT J.DT4,J.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT J.DT9,J.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT J.DT14,J.DT15 |
Stem#2, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG6,B.DG11,B.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18 step#1 pm(>>,forward) area=9.23 rise=3.27 twist=33.4 step#2 pm(>>,forward) area=14.03 rise=3.53 twist=23.6 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG1,B.DG2,B.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG6,B.DG7,B.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG16,B.DG17,B.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT B.DT4,B.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT B.DT9,B.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT B.DT14,B.DT15 |
Stem#3, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG6,C.DG11,C.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG7,C.DG12,C.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG8,C.DG13,C.DG18 step#1 pm(>>,forward) area=9.15 rise=3.19 twist=33.7 step#2 pm(>>,forward) area=16.88 rise=3.50 twist=22.8 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1,C.DG2,C.DG3 strand#2 U DNA glyco-bond=--- sugar=.-- nts=3 GGG C.DG6,C.DG7,C.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG11,C.DG12,C.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG16,C.DG17,C.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT C.DT4,C.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT C.DT9,C.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT C.DT14,C.DT15 |
Stem#4, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG1,D.DG6,D.DG11,D.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG2,D.DG7,D.DG12,D.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG3,D.DG8,D.DG13,D.DG18 step#1 pm(>>,forward) area=10.15 rise=3.33 twist=32.1 step#2 pm(>>,forward) area=13.50 rise=3.56 twist=22.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1,D.DG2,D.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG6,D.DG7,D.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG11,D.DG12,D.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG16,D.DG17,D.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT D.DT4,D.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT D.DT9,D.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT D.DT14,D.DT15 |
Stem#5, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG1,E.DG6,E.DG11,E.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG7,E.DG12,E.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG8,E.DG13,E.DG18 step#1 pm(>>,forward) area=7.77 rise=3.21 twist=35.6 step#2 pm(>>,forward) area=18.71 rise=3.49 twist=21.8 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG E.DG1,E.DG2,E.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG E.DG6,E.DG7,E.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG E.DG11,E.DG12,E.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG E.DG16,E.DG17,E.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT E.DT4,E.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT E.DT9,E.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT E.DT14,E.DT15 |
Stem#6, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG F.DG1,F.DG6,F.DG11,F.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG F.DG2,F.DG7,F.DG12,F.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG F.DG3,F.DG8,F.DG13,F.DG18 step#1 pm(>>,forward) area=10.21 rise=3.27 twist=33.2 step#2 pm(>>,forward) area=14.55 rise=3.55 twist=23.1 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG F.DG1,F.DG2,F.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG F.DG6,F.DG7,F.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG F.DG11,F.DG12,F.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG F.DG16,F.DG17,F.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT F.DT4,F.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT F.DT9,F.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT F.DT14,F.DT15 |
Stem#7, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG1,G.DG6,G.DG11,G.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG2,G.DG7,G.DG12,G.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG G.DG3,G.DG8,G.DG13,G.DG18 step#1 pm(>>,forward) area=7.64 rise=3.25 twist=33.7 step#2 pm(>>,forward) area=14.18 rise=3.54 twist=24.1 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG G.DG1,G.DG2,G.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG G.DG6,G.DG7,G.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG G.DG11,G.DG12,G.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG G.DG16,G.DG17,G.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT G.DT4,G.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT G.DT9,G.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT G.DT14,G.DT15 |
Stem#8, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG H.DG1,H.DG6,H.DG11,H.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG H.DG2,H.DG7,H.DG12,H.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG H.DG3,H.DG8,H.DG13,H.DG18 step#1 pm(>>,forward) area=8.91 rise=3.25 twist=33.9 step#2 pm(>>,forward) area=17.27 rise=3.55 twist=21.9 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG H.DG1,H.DG2,H.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG H.DG6,H.DG7,H.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG H.DG11,H.DG12,H.DG13 strand#4 U DNA glyco-bond=--- sugar=.-- nts=3 GGG H.DG16,H.DG17,H.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT H.DT4,H.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT H.DT9,H.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT H.DT14,H.DT15 |
Stem#9, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG1,I.DG6,I.DG11,I.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG2,I.DG7,I.DG12,I.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG3,I.DG8,I.DG13,I.DG18 step#1 pm(>>,forward) area=8.60 rise=3.27 twist=34.8 step#2 pm(>>,forward) area=17.51 rise=3.49 twist=21.8 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG I.DG1,I.DG2,I.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG I.DG6,I.DG7,I.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG I.DG11,I.DG12,I.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG I.DG16,I.DG17,I.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT I.DT4,I.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT I.DT9,I.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT I.DT14,I.DT15 |
Stem#10, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG J.DG1,J.DG6,J.DG11,J.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG J.DG2,J.DG7,J.DG12,J.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG J.DG3,J.DG8,J.DG13,J.DG18 step#1 pm(>>,forward) area=8.80 rise=3.27 twist=32.9 step#2 pm(>>,forward) area=13.41 rise=3.54 twist=24.3 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG1,J.DG2,J.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG6,J.DG7,J.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG11,J.DG12,J.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG J.DG16,J.DG17,J.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT J.DT4,J.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT J.DT9,J.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT J.DT14,J.DT15 |
List of 5 G4 coaxial stacks
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5'] 2 G4 helix#2 contains 2 G4 stems: [#3,#4] [5'/5'] 3 G4 helix#3 contains 2 G4 stems: [#5,#6] [5'/5'] 4 G4 helix#4 contains 2 G4 stems: [#7,#8] [5'/5'] 5 G4 helix#5 contains 2 G4 stems: [#9,#10] [5'/5']