*List of 4 G-tetrads*
 1 glyco-bond=---- sugar=---- groove=---- planarity=0.121 type=planar O+
nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other  O+
nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.091 type=planar O+
nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.121 type=planar O+
nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25


*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,
INTRA-molecular, with 1 stem*
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG
A.DG3,A.DG6,A.DG9,A.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG
A.DG4,A.DG7,A.DG10,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG
A.DG21,A.DG18,A.DG15,A.DG24
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG
A.DG22,A.DG19,A.DG16,A.DG25
  step#1  mp(<<,backward) area=11.87 rise=3.23 twist=-26.3
  step#2  mm(<>,outward)  area=28.76 rise=3.31 twist=-9.9
  step#3  pm(>>,forward)  area=8.87  rise=3.34 twist=32.5
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG
A.DG3,A.DG4,A.DG21,A.DG22
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG
A.DG6,A.DG7,A.DG18,A.DG19
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG
A.DG9,A.DG10,A.DG15,A.DG16
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG
A.DG12,A.DG1,A.DG24,A.DG25


*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-tetrads, 3 loops,
INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)*
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG
A.DG15,A.DG18,A.DG21,A.DG24
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG
A.DG16,A.DG19,A.DG22,A.DG25
  step#1  pm(>>,forward)  area=8.87  rise=3.34 twist=32.5
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG18,A.DG19
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG21,A.DG22
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG24,A.DG25
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT17
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT20
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT23

The algorithm and the website for "DSSR-enabled identification, annotation, and visualization of G-quadruplexes" (http://g4.x3dna.org/) have recently been updated and polished. In addition to the list of all G4s in the PDB ( http://g4.x3dna.org/DSSR-G4DB.html), the website also allows users to upload their own structures in PDB or mmCIF format for on-demand processing. As an example, see the output from DSSR on PDB entry 8taa ( http://g4.x3dna.org/pdb/8taa/index.html). ``` *List of 4 G-tetrads* 1 glyco-bond=---- sugar=---- groove=---- planarity=0.121 type=planar O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.091 type=planar O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 4 glyco-bond=---- sugar=---- groove=---- planarity=0.121 type=planar O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25 *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, INTRA-molecular, with 1 stem* 1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25 step#1 mp(<<,backward) area=11.87 rise=3.23 twist=-26.3 step#2 mm(<>,outward) area=28.76 rise=3.31 twist=-9.9 step#3 pm(>>,forward) area=8.87 rise=3.34 twist=32.5 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,A.DG21,A.DG22 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG7,A.DG18,A.DG19 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG9,A.DG10,A.DG15,A.DG16 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG12,A.DG1,A.DG24,A.DG25 *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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)* 1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25 step#1 pm(>>,forward) area=8.87 rise=3.34 twist=32.5 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG18,A.DG19 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG21,A.DG22 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG24,A.DG25 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT17 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT20 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT23 ``` -- Xiang-Jun Lu (Ph.D.) Director, X3DNA-DSSR NIGMS National Resource Email: xiangjun@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/