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

PDB-id
1evo
Class
DNA
Method
NMR
Summary
NMR observation of a novel c-tetrad
Reference
Patel, P.K., Bhavesh, N.S., Hosur, R.V.: (2000) "NMR observation of a novel C-tetrad in the structure of the SV40 repeat sequence GGGCGG." Biochem.Biophys.Res.Commun., 270, 967-971.
Abstract
We report the NMR structure of the DNA sequence d-TGGGCGGT in Na(+) solutions at neutral pH, containing a repeat sequence from SV40 viral genome. The structure is a novel quadruplex incorporating the C-tetrad formed by symmetrical pairing of four Cs via NH(2)&bond;O(2) H-bonds in a plane. The C-tetrad has a wider cavity compared to G-tetrads and stacks well over the adjacent G4-tetrad, but poorly on the G6 tetrad. The quadruplex helix is largely underwound by 8-10 degrees compared to B-DNA except at the C5-G6 step. To our knowledge this is the first report of C-tetrad formation in DNA structures, and would be of significance from the point of view of both structural diversity and specific recognition.
G4 notes
5 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 3'/5'

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

PyMOL session file PDB file View in 3Dmol.js

List of 5 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.409 type=other  nts=4 GGGG O.DG302,Q.DG202,P.DG102,R.DG402
 2 glyco-bond=---- groove=---- planarity=0.316 type=other  nts=4 GGGG O.DG303,Q.DG203,P.DG103,R.DG403
 3 glyco-bond=---- groove=---- planarity=0.190 type=other  nts=4 GGGG O.DG304,Q.DG204,P.DG104,R.DG404
 4 glyco-bond=---- groove=---- planarity=0.235 type=other  nts=4 GGGG O.DG306,Q.DG206,P.DG106,R.DG406
 5 glyco-bond=---- groove=---- planarity=0.210 type=other  nts=4 GGGG O.DG307,Q.DG207,P.DG107,R.DG407

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, 5 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG302,Q.DG202,P.DG102,R.DG402
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG303,Q.DG203,P.DG103,R.DG403
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG304,Q.DG204,P.DG104,R.DG404
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG O.DG306,R.DG406,P.DG106,Q.DG206
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG O.DG307,R.DG407,P.DG107,Q.DG207
  step#1  pm(>>,forward)  area=17.33 rise=3.19 twist=28.0
  step#2  pm(>>,forward)  area=15.73 rise=3.21 twist=26.1
  step#3  pm(>>,forward)  area=0.00  rise=6.45 twist=-35.6
  step#4  pm(>>,forward)  area=11.11 rise=3.20 twist=33.8
  strand#1 DNA glyco-bond=----- nts=5 GGGGG O.DG302,O.DG303,O.DG304,O.DG306,O.DG307
  strand#2 DNA glyco-bond=----- nts=5 GGGGG Q.DG202,Q.DG203,Q.DG204,R.DG406,R.DG407
  strand#3 DNA glyco-bond=----- nts=5 GGGGG P.DG102,P.DG103,P.DG104,P.DG106,P.DG107
  strand#4 DNA glyco-bond=----- nts=5 GGGGG R.DG402,R.DG403,R.DG404,Q.DG206,Q.DG207

Download PDB file
Interactive view in 3Dmol.js

4 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG302,Q.DG202,P.DG102,R.DG402
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG303,Q.DG203,P.DG103,R.DG403
step#1 pm(>>,forward) area=17.33 rise=3.19 twist=28.0

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG303,Q.DG203,P.DG103,R.DG403
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG304,Q.DG204,P.DG104,R.DG404
step#2 pm(>>,forward) area=15.73 rise=3.21 twist=26.1

Download PDB file
Interactive view in 3Dmol.js

 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG304,Q.DG204,P.DG104,R.DG404
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG O.DG306,R.DG406,P.DG106,Q.DG206
step#3 pm(>>,forward) area=0.00 rise=6.45 twist=-35.6

Download PDB file
Interactive view in 3Dmol.js

 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG O.DG306,R.DG406,P.DG106,Q.DG206
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG O.DG307,R.DG407,P.DG107,Q.DG207
step#4 pm(>>,forward) area=11.11 rise=3.20 twist=33.8

Download PDB file
Interactive view in 3Dmol.js

List of 2 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, 3 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG302,Q.DG202,P.DG102,R.DG402
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG303,Q.DG203,P.DG103,R.DG403
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG304,Q.DG204,P.DG104,R.DG404
  step#1  pm(>>,forward)  area=17.33 rise=3.19 twist=28.0
  step#2  pm(>>,forward)  area=15.73 rise=3.21 twist=26.1
  strand#1  U DNA glyco-bond=--- nts=3 GGG O.DG302,O.DG303,O.DG304
  strand#2  U DNA glyco-bond=--- nts=3 GGG Q.DG202,Q.DG203,Q.DG204
  strand#3  U DNA glyco-bond=--- nts=3 GGG P.DG102,P.DG103,P.DG104
  strand#4  U DNA glyco-bond=--- nts=3 GGG R.DG402,R.DG403,R.DG404

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG306,Q.DG206,P.DG106,R.DG406
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG O.DG307,Q.DG207,P.DG107,R.DG407
  step#1  pm(>>,forward)  area=11.11 rise=3.20 twist=33.8
  strand#1  U DNA glyco-bond=-- nts=2 GG O.DG306,O.DG307
  strand#2  U DNA glyco-bond=-- nts=2 GG Q.DG206,Q.DG207
  strand#3  U DNA glyco-bond=-- nts=2 GG P.DG106,P.DG107
  strand#4  U DNA glyco-bond=-- nts=2 GG R.DG406,R.DG407

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [3'/5']

List of 0 non-stem G4-loops (including the two closing Gs)