DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 1emq
Class: DNA
Method: NMR
Summary: NMR observation of t-tetrads in a parallel stranded DNA quadruplex formed by saccharomyces cerevisiae telomere repeats
Reference: Patel PK, Hosur RV (1999): "NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats." Nucleic Acids Res., 27, 2457-2464. doi: 10.1093/nar/27.12.2457.
Abstract: We report here the NMR structure of the DNA sequence d-TGGTGGC containing two repeats of Saccharomyces cerevisiae telomere DNA which is unique in that it has a single thymine in the repeat sequence and the number of Gs can vary from one to three. The structure is a novel quadruplex incor-porating T-tetrads formed by symmetrical pairing of four Ts via O4-H3 H-bonds in a plane. This is in contrast to the previous results on other telomeric sequences which contained more than one T in the repeat sequences and they were seen mostly in the flexible regions of the structures. We observed that the T4-tetrad was nicely accommodated in the center of the G-quadruplex, but it caused a small underwinding of the right handed helix. The T tetrad stacked well on the adjacent G3-tetrad, but poorly on the G5 tetrad. Likewise, T1 also formed a stable T-tetrad at the 5' end of the quadruplex. To our knowledge, this is the first report of T-tetrad formation in DNA structures. These observations are of significance from the points of view of both structural diversity and specific recognitions.
G4 notes: 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, coaxial interfaces: 3'/5'

Cartoon-block schematics in six views (download the tarball)

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.147 type=planar -- nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.070 type=planar -- nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.192 type=bowl   -- nts=4 GGGG A.DG105,C.DG405,D.DG305,B.DG205
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.194 type=other  -- nts=4 GGGG A.DG106,C.DG406,D.DG306,B.DG206

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, 4 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202 2* glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203 3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG105,B.DG205,D.DG305,C.DG405 4 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG106,B.DG206,D.DG306,C.DG406 step#1 pm(>>,forward) area=12.06 rise=3.18 twist=29.9 step#2 pm(>>,forward) area=0.00 rise=6.76 twist=148.0 step#3 pm(>>,forward) area=15.73 rise=3.06 twist=24.0 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG102,A.DG103,A.DG105,A.DG106 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG402,C.DG403,B.DG205,B.DG206 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG302,D.DG303,D.DG305,D.DG306 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG202,B.DG203,C.DG405,C.DG406 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202 2* glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203 step#1 pm(>>,forward) area=12.06 rise=3.18 twist=29.9 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203 3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG105,B.DG205,D.DG305,C.DG405 step#2 pm(>>,forward) area=0.00 rise=6.76 twist=148.0 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG105,B.DG205,D.DG305,C.DG405 4 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG106,B.DG206,D.DG306,C.DG406 step#3 pm(>>,forward) area=15.73 rise=3.06 twist=24.0 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
  step#1  pm(>>,forward)  area=12.06 rise=3.18 twist=29.9
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG102,A.DG103
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG C.DG402,C.DG403
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG302,D.DG303
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG202,B.DG203

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 2 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG105,C.DG405,D.DG305,B.DG205
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG106,C.DG406,D.DG306,B.DG206
  step#1  pm(>>,forward)  area=15.73 rise=3.06 twist=24.0
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG105,A.DG106
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG C.DG405,C.DG406
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG305,D.DG306
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG205,B.DG206