Summary information and primary citation

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 MA, Strahan GD, Owen EA, Shafer RH (1995): "Solution structure of the Na+ form of the dimeric guanine quadruplex [d(G3T4G3)]2." Eur.J.Biochem., 233, 631-643. doi: 10.1111/j.1432-1033.1995.631_2.x.
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, UDDU, anti-parallel:basket, 2+2

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List of 3 G-tetrads

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

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, 3 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
 2  glyco-bond=s--s sugar=.--- groove=w-n- Major-->WC -- nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
 3  glyco-bond=-ss- sugar=---- 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- sugar=-.- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=--s sugar=--- nts=3 GGG B.DG13,B.DG12,B.DG11
  strand#3 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#4 DNA glyco-bond=ss- sugar=--- nts=3 GGG B.DG18,B.DG19,B.DG20

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2 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
 2  glyco-bond=s--s sugar=.--- 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 sugar=.--- groove=w-n- Major-->WC -- nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
 3  glyco-bond=-ss- sugar=---- 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

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-tetrads, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG A.DG1,B.DG13,A.DG10,B.DG18
 2  glyco-bond=s--s sugar=.--- groove=w-n- Major-->WC -- nts=4 GGGG A.DG2,B.DG12,A.DG9,B.DG19
 3  glyco-bond=-ss- sugar=---- 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- sugar=-.- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=--s sugar=--- nts=3 GGG B.DG13,B.DG12,B.DG11
  strand#3  D DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#4  U DNA glyco-bond=ss- sugar=--- 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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