Summary information

PDB id
1f3s
Class
DNA
Method
NMR
Summary
Solution structure of DNA sequence gggttcagg forms gggg tetrade and g(c-a) triad.
Reference
Kettani A, Basu G, Gorin A, Majumdar A, Skripkin E, Patel DJ (2000): "A two-stranded template-based approach to G.(C-A) triad formation: designing novel structural elements into an existing DNA framework." J.Mol.Biol., 301, 129-146. doi: 10.1006/jmbi.2000.3932.
Abstract
We have designed a DNA sequence, d(G-G-G-T-T-C-A-G-G), which dimerizes to form a 2-fold symmetric G-quadruplex in which G(syn). G(anti).G(syn).G(anti) tetrads are sandwiched between all trans G. (C-A) triads. The NMR-based solution structural analysis was greatly aided by monitoring hydrogen bond alignments across N-H...N and N-H...O==C hydrogen bonds within the triad and tetrad, in a uniformly ((13)C,(15)N)-labeled sample of the d(G-G-G-T-T-C-A-G-G) sequence. The solution structure establishes that the guanine base-pairs with the cytosine through Watson-Crick G.C pair formation and with adenine through sheared G.A mismatch formation within the G.(C-A) triad. A model of triad DNA was constructed that contains the experimentally determined G.(C-A) triad alignment as the repeating stacked unit.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDUD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.138 type=planar nts=4 GGGG A.DG1,A.DG9,B.DG8,B.DG2
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.141 type=planar nts=4 GGGG A.DG2,A.DG8,B.DG9,B.DG1

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

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG8,B.DG2
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG9,B.DG1
  step#1  mm(<>,outward)  area=12.48 rise=3.23 twist=19.7
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG9,A.DG8
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG8,B.DG9
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG2,B.DG1

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG8,B.DG2
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG9,B.DG1
  step#1  mm(<>,outward)  area=12.48 rise=3.23 twist=19.7

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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, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG8,B.DG2
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG9,B.DG1
  step#1  mm(<>,outward)  area=12.48 rise=3.23 twist=19.7
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG9,A.DG8
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG8,B.DG9
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG2,B.DG1
  loop#1 type=lateral   strands=[#1,#2] nts=5 GTTCA A.DG3,A.DT4,A.DT5,A.DC6,A.DA7
  loop#2 type=lateral   strands=[#4,#3] nts=5 GTTCA B.DG3,B.DT4,B.DT5,B.DC6,B.DA7

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