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

PDB-id
6ftu
Class
DNA
Method
X-ray (2.95 Å)
Summary
Structure of a quadruplex forming sequence from d. discoideum
Reference
Guedin, A., Lin, L.Y., Armane, S., Lacroix, L., Mergny, J.L., Thore, S., Yatsunyk, L.A.: (2018) "Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome." Nucleic Acids Res., 46, 5297-5307.
Abstract
Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.
G4 notes
28 G-tetrads, 7 G4 helices, 7 G4 stems · 4(+Ln-Lw), (2+2), UUDD; 4(+LnD), basket(2+2), UUDD; 4(+LnD-Lw), basket(2+2), UUDD

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

PyMOL session file PDB file View in 3Dmol.js

List of 28 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ss-- groove=-w-n planarity=0.227 type=other  nts=4 GGGG A.DG1,A.DG15,A.DG26,A.DG10
 2 glyco-bond=--ss groove=-w-n planarity=0.140 type=planar nts=4 GGGG A.DG2,A.DG16,A.DG25,A.DG9
 3 glyco-bond=ss-- groove=-w-n planarity=0.143 type=planar nts=4 GGGG A.DG3,A.DG17,A.DG24,A.DG8
 4 glyco-bond=--ss groove=-w-n planarity=0.207 type=other  nts=4 GGGG A.DG4,A.DG18,A.DG23,A.DG7
 5 glyco-bond=ss-- groove=-w-n planarity=0.328 type=bowl   nts=4 GGGG B.DG1,B.DG15,B.DG26,B.DG10
 6 glyco-bond=--ss groove=-w-n planarity=0.137 type=planar nts=4 GGGG B.DG2,B.DG16,B.DG25,B.DG9
 7 glyco-bond=ss-- groove=-w-n planarity=0.099 type=planar nts=4 GGGG B.DG3,B.DG17,B.DG24,B.DG8
 8 glyco-bond=--ss groove=-w-n planarity=0.192 type=other  nts=4 GGGG B.DG4,B.DG18,B.DG23,B.DG7
 9 glyco-bond=ss-- groove=-w-n planarity=0.257 type=other  nts=4 GGGG C.DG1,C.DG15,C.DG26,C.DG10
10 glyco-bond=--ss groove=-w-n planarity=0.134 type=planar nts=4 GGGG C.DG2,C.DG16,C.DG25,C.DG9
11 glyco-bond=ss-- groove=-w-n planarity=0.132 type=planar nts=4 GGGG C.DG3,C.DG17,C.DG24,C.DG8
12 glyco-bond=--ss groove=-w-n planarity=0.200 type=other  nts=4 GGGG C.DG4,C.DG18,C.DG23,C.DG7
13 glyco-bond=ss-- groove=-w-n planarity=0.425 type=bowl   nts=4 GGGG D.DG1,D.DG15,D.DG26,D.DG10
14 glyco-bond=--ss groove=-w-n planarity=0.235 type=other  nts=4 GGGG D.DG2,D.DG16,D.DG25,D.DG9
15 glyco-bond=ss-- groove=-w-n planarity=0.147 type=planar nts=4 GGGG D.DG3,D.DG17,D.DG24,D.DG8
16 glyco-bond=--ss groove=-w-n planarity=0.247 type=other  nts=4 GGGG D.DG4,D.DG18,D.DG23,D.DG7
17 glyco-bond=ss-- groove=-w-n planarity=0.407 type=bowl   nts=4 GGGG E.DG1,E.DG15,E.DG26,E.DG10
18 glyco-bond=--ss groove=-w-n planarity=0.219 type=other  nts=4 GGGG E.DG2,E.DG16,E.DG25,E.DG9
19 glyco-bond=ss-- groove=-w-n planarity=0.146 type=planar nts=4 GGGG E.DG3,E.DG17,E.DG24,E.DG8
20 glyco-bond=--ss groove=-w-n planarity=0.201 type=other  nts=4 GGGG E.DG4,E.DG18,E.DG23,E.DG7
21 glyco-bond=ss-- groove=-w-n planarity=0.248 type=bowl   nts=4 GGGG F.DG1,F.DG15,F.DG26,F.DG10
22 glyco-bond=--ss groove=-w-n planarity=0.130 type=planar nts=4 GGGG F.DG2,F.DG16,F.DG25,F.DG9
23 glyco-bond=ss-- groove=-w-n planarity=0.111 type=planar nts=4 GGGG F.DG3,F.DG17,F.DG24,F.DG8
24 glyco-bond=--ss groove=-w-n planarity=0.196 type=other  nts=4 GGGG F.DG4,F.DG18,F.DG23,F.DG7
25 glyco-bond=ss-- groove=-w-n planarity=0.497 type=bowl   nts=4 GGGG Z.DG1,Z.DG15,Z.DG26,Z.DG10
26 glyco-bond=--ss groove=-w-n planarity=0.303 type=other  nts=4 GGGG Z.DG2,Z.DG16,Z.DG25,Z.DG9
27 glyco-bond=ss-- groove=-w-n planarity=0.169 type=other  nts=4 GGGG Z.DG3,Z.DG17,Z.DG24,Z.DG8
28 glyco-bond=--ss groove=-w-n planarity=0.250 type=other  nts=4 GGGG Z.DG4,Z.DG18,Z.DG23,Z.DG7

List of 7 G4-helices [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, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG26,A.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG2,A.DG16,A.DG25,A.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG17,A.DG24,A.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG18,A.DG23,A.DG7
  step#1  mm(<>,outward)  area=14.53 rise=3.48 twist=18.1
  step#2  pp(><,inward)   area=18.75 rise=3.50 twist=37.0
  step#3  mm(<>,outward)  area=15.07 rise=3.43 twist=17.5
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG A.DG15,A.DG16,A.DG17,A.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG26,A.DG25,A.DG24,A.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG A.DG10,A.DG9,A.DG8,A.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG26,A.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG2,A.DG16,A.DG25,A.DG9
step#1 mm(<>,outward) area=14.53 rise=3.48 twist=18.1

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG2,A.DG16,A.DG25,A.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG17,A.DG24,A.DG8
step#2 pp(><,inward) area=18.75 rise=3.50 twist=37.0

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG17,A.DG24,A.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG18,A.DG23,A.DG7
step#3 mm(<>,outward) area=15.07 rise=3.43 twist=17.5

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Helix#2, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG26,B.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG2,B.DG16,B.DG25,B.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG3,B.DG17,B.DG24,B.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG4,B.DG18,B.DG23,B.DG7
  step#1  mm(<>,outward)  area=13.55 rise=3.55 twist=18.2
  step#2  pp(><,inward)   area=18.16 rise=3.48 twist=35.9
  step#3  mm(<>,outward)  area=17.33 rise=3.50 twist=17.9
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG B.DG1,B.DG2,B.DG3,B.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG B.DG15,B.DG16,B.DG17,B.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG B.DG26,B.DG25,B.DG24,B.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG B.DG10,B.DG9,B.DG8,B.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG26,B.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG2,B.DG16,B.DG25,B.DG9
step#1 mm(<>,outward) area=13.55 rise=3.55 twist=18.2

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG2,B.DG16,B.DG25,B.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG3,B.DG17,B.DG24,B.DG8
step#2 pp(><,inward) area=18.16 rise=3.48 twist=35.9

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG3,B.DG17,B.DG24,B.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG4,B.DG18,B.DG23,B.DG7
step#3 mm(<>,outward) area=17.33 rise=3.50 twist=17.9

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Helix#3, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG26,C.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG2,C.DG16,C.DG25,C.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG3,C.DG17,C.DG24,C.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG4,C.DG18,C.DG23,C.DG7
  step#1  mm(<>,outward)  area=14.77 rise=3.44 twist=18.4
  step#2  pp(><,inward)   area=18.55 rise=3.50 twist=36.0
  step#3  mm(<>,outward)  area=12.77 rise=3.48 twist=19.7
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG C.DG1,C.DG2,C.DG3,C.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG C.DG15,C.DG16,C.DG17,C.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG C.DG26,C.DG25,C.DG24,C.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG C.DG10,C.DG9,C.DG8,C.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG26,C.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG2,C.DG16,C.DG25,C.DG9
step#1 mm(<>,outward) area=14.77 rise=3.44 twist=18.4

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG2,C.DG16,C.DG25,C.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG3,C.DG17,C.DG24,C.DG8
step#2 pp(><,inward) area=18.55 rise=3.50 twist=36.0

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG3,C.DG17,C.DG24,C.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG4,C.DG18,C.DG23,C.DG7
step#3 mm(<>,outward) area=12.77 rise=3.48 twist=19.7

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Helix#4, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG26,D.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG2,D.DG16,D.DG25,D.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG3,D.DG17,D.DG24,D.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG4,D.DG18,D.DG23,D.DG7
  step#1  mm(<>,outward)  area=13.12 rise=3.58 twist=18.1
  step#2  pp(><,inward)   area=15.96 rise=3.55 twist=35.6
  step#3  mm(<>,outward)  area=16.80 rise=3.50 twist=18.6
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG D.DG1,D.DG2,D.DG3,D.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG D.DG15,D.DG16,D.DG17,D.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG D.DG26,D.DG25,D.DG24,D.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG D.DG10,D.DG9,D.DG8,D.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG26,D.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG2,D.DG16,D.DG25,D.DG9
step#1 mm(<>,outward) area=13.12 rise=3.58 twist=18.1

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG2,D.DG16,D.DG25,D.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG3,D.DG17,D.DG24,D.DG8
step#2 pp(><,inward) area=15.96 rise=3.55 twist=35.6

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG3,D.DG17,D.DG24,D.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG4,D.DG18,D.DG23,D.DG7
step#3 mm(<>,outward) area=16.80 rise=3.50 twist=18.6

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Helix#5, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG26,E.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG2,E.DG16,E.DG25,E.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG3,E.DG17,E.DG24,E.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG4,E.DG18,E.DG23,E.DG7
  step#1  mm(<>,outward)  area=16.21 rise=3.56 twist=15.6
  step#2  pp(><,inward)   area=20.88 rise=3.48 twist=35.7
  step#3  mm(<>,outward)  area=14.68 rise=3.45 twist=18.0
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG E.DG1,E.DG2,E.DG3,E.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG E.DG15,E.DG16,E.DG17,E.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG E.DG26,E.DG25,E.DG24,E.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG E.DG10,E.DG9,E.DG8,E.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG26,E.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG2,E.DG16,E.DG25,E.DG9
step#1 mm(<>,outward) area=16.21 rise=3.56 twist=15.6

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG2,E.DG16,E.DG25,E.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG3,E.DG17,E.DG24,E.DG8
step#2 pp(><,inward) area=20.88 rise=3.48 twist=35.7

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG3,E.DG17,E.DG24,E.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG4,E.DG18,E.DG23,E.DG7
step#3 mm(<>,outward) area=14.68 rise=3.45 twist=18.0

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Helix#6, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG1,F.DG15,F.DG26,F.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG2,F.DG16,F.DG25,F.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG3,F.DG17,F.DG24,F.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG4,F.DG18,F.DG23,F.DG7
  step#1  mm(<>,outward)  area=15.26 rise=3.47 twist=18.9
  step#2  pp(><,inward)   area=19.31 rise=3.47 twist=35.9
  step#3  mm(<>,outward)  area=13.54 rise=3.44 twist=19.8
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG F.DG1,F.DG2,F.DG3,F.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG F.DG15,F.DG16,F.DG17,F.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG F.DG26,F.DG25,F.DG24,F.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG F.DG10,F.DG9,F.DG8,F.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG1,F.DG15,F.DG26,F.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG2,F.DG16,F.DG25,F.DG9
step#1 mm(<>,outward) area=15.26 rise=3.47 twist=18.9

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG2,F.DG16,F.DG25,F.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG3,F.DG17,F.DG24,F.DG8
step#2 pp(><,inward) area=19.31 rise=3.47 twist=35.9

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG3,F.DG17,F.DG24,F.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG4,F.DG18,F.DG23,F.DG7
step#3 mm(<>,outward) area=13.54 rise=3.44 twist=19.8

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Helix#7, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG1,Z.DG15,Z.DG26,Z.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG2,Z.DG16,Z.DG25,Z.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG3,Z.DG17,Z.DG24,Z.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG4,Z.DG18,Z.DG23,Z.DG7
  step#1  mm(<>,outward)  area=15.91 rise=3.80 twist=18.3
  step#2  pp(><,inward)   area=15.68 rise=3.54 twist=36.8
  step#3  mm(<>,outward)  area=16.21 rise=3.45 twist=17.2
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG Z.DG1,Z.DG2,Z.DG3,Z.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG Z.DG15,Z.DG16,Z.DG17,Z.DG18
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG Z.DG26,Z.DG25,Z.DG24,Z.DG23
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG Z.DG10,Z.DG9,Z.DG8,Z.DG7

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3 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG1,Z.DG15,Z.DG26,Z.DG10
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG2,Z.DG16,Z.DG25,Z.DG9
step#1 mm(<>,outward) area=15.91 rise=3.80 twist=18.3

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG2,Z.DG16,Z.DG25,Z.DG9
3 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG3,Z.DG17,Z.DG24,Z.DG8
step#2 pp(><,inward) area=15.68 rise=3.54 twist=36.8

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 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG3,Z.DG17,Z.DG24,Z.DG8
4 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG4,Z.DG18,Z.DG23,Z.DG7
step#3 mm(<>,outward) area=16.21 rise=3.45 twist=17.2

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List of 7 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.

Stem#1, 4 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 4(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG26,A.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG2,A.DG16,A.DG25,A.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG17,A.DG24,A.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG18,A.DG23,A.DG7
  step#1  mm(<>,outward)  area=14.53 rise=3.48 twist=18.1
  step#2  pp(><,inward)   area=18.75 rise=3.50 twist=37.0
  step#3  mm(<>,outward)  area=15.07 rise=3.43 twist=17.5
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG A.DG15,A.DG16,A.DG17,A.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG A.DG26,A.DG25,A.DG24,A.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG A.DG10,A.DG9,A.DG8,A.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA A.DG5,A.DA6
  loop#2 type=diagonal  strands=[#4,#2] nts=4 TACA A.DT11,A.DA12,A.DC13,A.DA14
  loop#3 type=lateral   strands=[#2,#3] nts=4 TACA A.DT19,A.DA20,A.DC21,A.DA22

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Stem#2, 4 G-tetrad layers, 2 loops, INTRA-molecular, UUDD, anti-parallel, 4(+LnD), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG26,B.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG2,B.DG16,B.DG25,B.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG B.DG3,B.DG17,B.DG24,B.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG B.DG4,B.DG18,B.DG23,B.DG7
  step#1  mm(<>,outward)  area=13.55 rise=3.55 twist=18.2
  step#2  pp(><,inward)   area=18.16 rise=3.48 twist=35.9
  step#3  mm(<>,outward)  area=17.33 rise=3.50 twist=17.9
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG B.DG1,B.DG2,B.DG3,B.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG B.DG15,B.DG16,B.DG17,B.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG B.DG26,B.DG25,B.DG24,B.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG B.DG10,B.DG9,B.DG8,B.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA B.DG5,B.DA6
  loop#2 type=diagonal  strands=[#4,#2] nts=4 TACA B.DT11,B.DA12,B.DC13,B.DA14

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Stem#3, 4 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 4(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG26,C.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG2,C.DG16,C.DG25,C.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG3,C.DG17,C.DG24,C.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG4,C.DG18,C.DG23,C.DG7
  step#1  mm(<>,outward)  area=14.77 rise=3.44 twist=18.4
  step#2  pp(><,inward)   area=18.55 rise=3.50 twist=36.0
  step#3  mm(<>,outward)  area=12.77 rise=3.48 twist=19.7
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG C.DG1,C.DG2,C.DG3,C.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG C.DG15,C.DG16,C.DG17,C.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG C.DG26,C.DG25,C.DG24,C.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG C.DG10,C.DG9,C.DG8,C.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA C.DG5,C.DA6
  loop#2 type=diagonal  strands=[#4,#2] nts=4 TACA C.DT11,C.DA12,C.DC13,C.DA14
  loop#3 type=lateral   strands=[#2,#3] nts=4 TACA C.DT19,C.DA20,C.DC21,C.DA22

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Stem#4, 4 G-tetrad layers, 2 loops, INTRA-molecular, UUDD, anti-parallel, 4(+Ln-Lw), (2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG26,D.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG2,D.DG16,D.DG25,D.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG D.DG3,D.DG17,D.DG24,D.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG D.DG4,D.DG18,D.DG23,D.DG7
  step#1  mm(<>,outward)  area=13.12 rise=3.58 twist=18.1
  step#2  pp(><,inward)   area=15.96 rise=3.55 twist=35.6
  step#3  mm(<>,outward)  area=16.80 rise=3.50 twist=18.6
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG D.DG1,D.DG2,D.DG3,D.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG D.DG15,D.DG16,D.DG17,D.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG D.DG26,D.DG25,D.DG24,D.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG D.DG10,D.DG9,D.DG8,D.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA D.DG5,D.DA6
  loop#2 type=lateral   strands=[#2,#3] nts=4 TACA D.DT19,D.DA20,D.DC21,D.DA22

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Stem#5, 4 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 4(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG26,E.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG2,E.DG16,E.DG25,E.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG E.DG3,E.DG17,E.DG24,E.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG E.DG4,E.DG18,E.DG23,E.DG7
  step#1  mm(<>,outward)  area=16.21 rise=3.56 twist=15.6
  step#2  pp(><,inward)   area=20.88 rise=3.48 twist=35.7
  step#3  mm(<>,outward)  area=14.68 rise=3.45 twist=18.0
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG E.DG1,E.DG2,E.DG3,E.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG E.DG15,E.DG16,E.DG17,E.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG E.DG26,E.DG25,E.DG24,E.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG E.DG10,E.DG9,E.DG8,E.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA E.DG5,E.DA6
  loop#2 type=diagonal  strands=[#4,#2] nts=4 TACA E.DT11,E.DA12,E.DC13,E.DA14
  loop#3 type=lateral   strands=[#2,#3] nts=4 TACA E.DT19,E.DA20,E.DC21,E.DA22

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Stem#6, 4 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 4(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG1,F.DG15,F.DG26,F.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG2,F.DG16,F.DG25,F.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG3,F.DG17,F.DG24,F.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG4,F.DG18,F.DG23,F.DG7
  step#1  mm(<>,outward)  area=15.26 rise=3.47 twist=18.9
  step#2  pp(><,inward)   area=19.31 rise=3.47 twist=35.9
  step#3  mm(<>,outward)  area=13.54 rise=3.44 twist=19.8
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG F.DG1,F.DG2,F.DG3,F.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG F.DG15,F.DG16,F.DG17,F.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG F.DG26,F.DG25,F.DG24,F.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG F.DG10,F.DG9,F.DG8,F.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA F.DG5,F.DA6
  loop#2 type=diagonal  strands=[#4,#2] nts=4 TACA F.DT11,F.DA12,F.DC13,F.DA14
  loop#3 type=lateral   strands=[#2,#3] nts=4 TACA F.DT19,F.DA20,F.DC21,F.DA22

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Stem#7, 4 G-tetrad layers, 2 loops, INTRA-molecular, UUDD, anti-parallel, 4(+Ln-Lw), (2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG1,Z.DG15,Z.DG26,Z.DG10
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG2,Z.DG16,Z.DG25,Z.DG9
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG Z.DG3,Z.DG17,Z.DG24,Z.DG8
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG Z.DG4,Z.DG18,Z.DG23,Z.DG7
  step#1  mm(<>,outward)  area=15.91 rise=3.80 twist=18.3
  step#2  pp(><,inward)   area=15.68 rise=3.54 twist=36.8
  step#3  mm(<>,outward)  area=16.21 rise=3.45 twist=17.2
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG Z.DG1,Z.DG2,Z.DG3,Z.DG4
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG Z.DG15,Z.DG16,Z.DG17,Z.DG18
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG Z.DG26,Z.DG25,Z.DG24,Z.DG23
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG Z.DG10,Z.DG9,Z.DG8,Z.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA Z.DG5,Z.DA6
  loop#2 type=lateral   strands=[#2,#3] nts=4 TACA Z.DT19,Z.DA20,Z.DC21,Z.DA22

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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)