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

PDB-id
1fqp
Class
DNA
Method
NMR
Summary
Intramolecular quadruplex DNA with three gggg repeats, NMR, ph 6.7, 0.1 m na+ and 4 mm (strand concentration), 5 structures
Reference
Keniry, M.A., Strahan, G.D., Owen, E.A., Shafer, R.H.: (1995) "Solution structure of the Na+ form of the dimeric guanine quadruplex [d(G3T4G3)]2." Eur.J.Biochem., 233, 631-643.
Abstract
The solution structure of the DNA quadruplex formed by the association of two strands of the DNA oligonucleotide, d(G3T4G3), in NaCl solution has been determined by 1H two-dimensional NMR techniques, full relaxation matrix calculations and restrained molecular dynamics. The refined structure incorporates the sequences 5'-G1sG2AG3AT4AT5AT6AT7AG8sG9AG10A-3' and 5'-G11sG12AG13AT14AT15AT16AT17AG18sG19sG20A-3' (where S and A denote syn and anti, respectively) in a three-quartet, diagonal-looped structure that we [Strahan, G. D., Shafer, R. H. & Keniry, M. A. (1994) Nucleic Acids Res. 22, 5447-5455] and others [Smith, F. W., Lau, F. W. & Feigon, J. (1994) Proc. Natl. Acad. Sci. USA 91, 10546-10550] have described. The loop structure is compact and incorporates many of the features found in duplex hairpin loops including base stacking, intraloop hydrogen bonding and extensive van der Waals' interactions. The first and third loop thymines stack over the outermost G-quartet and are also associated by hydrogen bonding. The second and the fourth loop thymines fold inwards in order to enhance van der Waals' interactions. The unexpected sequential syn-syn deoxyguanosines in the quadruplex stem appear to be a direct consequence of the way DNA oligonucleotides fold and the subsequent search for the most stable loop structure. The implications of loop sequence and length on the structure of quadruplexes are discussed.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU

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

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--s groove=w-n- planarity=0.409 type=bowl   nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
 2 glyco-bond=s--s groove=w-n- planarity=0.158 type=planar nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
 3 glyco-bond=-ss- groove=w-n- planarity=0.243 type=other  nts=4 GGGG A.DG3,B.DG11,A.DG8,B.DG20

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, 3 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
 2  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
 3  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG3,B.DG11,A.DG8,B.DG20
  step#1  mp(<<,backward) area=15.83 rise=3.59 twist=18.6
  step#2  mm(<>,outward)  area=13.80 rise=3.51 twist=18.7
  strand#1 DNA glyco-bond=ss- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=--s nts=3 GGG B.DG13,B.DG12,B.DG11
  strand#3 DNA glyco-bond=--s nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#4 DNA glyco-bond=ss- nts=3 GGG B.DG18,B.DG19,B.DG20

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2 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
2 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
step#1 mp(<<,backward) area=15.83 rise=3.59 twist=18.6

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 2  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
3 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG3,B.DG11,A.DG8,B.DG20
step#2 mm(<>,outward) area=13.80 rise=3.51 twist=18.7

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List of 1 G4-stem [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, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
 2  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
 3  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG3,B.DG11,A.DG8,B.DG20
  step#1  mp(<<,backward) area=15.83 rise=3.59 twist=18.6
  step#2  mm(<>,outward)  area=13.80 rise=3.51 twist=18.7
  strand#1  U DNA glyco-bond=ss- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=--s nts=3 GGG B.DG13,B.DG12,B.DG11
  strand#3  D DNA glyco-bond=--s nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#4  U DNA glyco-bond=ss- nts=3 GGG B.DG18,B.DG19,B.DG20
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT4,A.DT5,A.DT6,A.DT7
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT14,B.DT15,B.DT16,B.DT17

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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)