Summary information

PDB id
7dfy
Class
DNA
Method
X-ray (1.69 Å)
Summary
Novel motif for left-handed g-quadruplex formation
Reference
Das P, Winnerdy FR, Maity A, Mechulam Y, Phan AT (2021): "A novel minimal motif for left-handed G-quadruplex formation." Chem.Commun.(Camb.), 57, 2527-2530. doi: 10.1039/d0cc08146a.
Abstract
A recent study on the left-handed G-quadruplex (LHG4) DNA revealed a 12-nt minimal motif GTGGTGGTGGTG with the ability to independently form an LHG4 and to drive an adjacent sequence to LHG4 formation. Here we have identified a second LHG4-forming motif, GGTGGTGGTGTG, and determined the X-ray crystal structure of an LHG4 involving this motif. Our structural analysis indicated the role of split guanines and single thymine loops in promoting LHG4 formation.
G4 notes
8 G-tetrads, 2 G4 helices, 4 G4 stems, 2 G4 coaxial stacks, 2(+P+P+P), parallel(4+0), UUUU, coaxial interfaces: 3'/3', negative twist

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 8 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.224 type=other  nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.096 type=planar nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.204 type=other  nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.086 type=planar nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG26
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.246 type=other  nts=4 GGGG B.DG1,B.DG4,B.DG7,B.DG10
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.147 type=planar nts=4 GGGG B.DG2,B.DG5,B.DG8,B.DG12
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.181 type=other  nts=4 GGGG B.DG15,B.DG18,B.DG21,B.DG24
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.100 type=planar nts=4 GGGG B.DG16,B.DG19,B.DG22,B.DG26

List of 2 G4-helices

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-tetrad layers, INTRA-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG26
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24
  step#1  mp(<<,backward) area=11.66 rise=3.32 twist=-26.2
  step#2  mm(<>,outward)  area=30.06 rise=3.36 twist=-12.0
  step#3  pm(>>,forward)  area=11.84 rise=3.32 twist=-25.5
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG22,A.DG21
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG19,A.DG18
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG7,A.DG8,A.DG16,A.DG15
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG10,A.DG12,A.DG26,A.DG24

Download PDB file
Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12
  step#1  mp(<<,backward) area=11.66 rise=3.32 twist=-26.2

Download PDB file
Interactive view in 3Dmol.js

 
 2* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG26
  step#2  mm(<>,outward)  area=30.06 rise=3.36 twist=-12.0

Download PDB file
Interactive view in 3Dmol.js

 
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG26
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24
  step#3  pm(>>,forward)  area=11.84 rise=3.32 twist=-25.5

Download PDB file
Interactive view in 3Dmol.js

Helix#2, 4 G-tetrad layers, INTRA-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG4,B.DG7,B.DG10
 2* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG5,B.DG8,B.DG12
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG26
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG21,B.DG18,B.DG15,B.DG24
  step#1  mp(<<,backward) area=12.80 rise=3.20 twist=-26.9
  step#2  mm(<>,outward)  area=29.25 rise=3.31 twist=-11.4
  step#3  pm(>>,forward)  area=12.41 rise=3.31 twist=-26.0
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG1,B.DG2,B.DG22,B.DG21
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG4,B.DG5,B.DG19,B.DG18
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG7,B.DG8,B.DG16,B.DG15
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG10,B.DG12,B.DG26,B.DG24

Download PDB file
Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG4,B.DG7,B.DG10
 2* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG5,B.DG8,B.DG12
  step#1  mp(<<,backward) area=12.80 rise=3.20 twist=-26.9

Download PDB file
Interactive view in 3Dmol.js

 
 2* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG5,B.DG8,B.DG12
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG26
  step#2  mm(<>,outward)  area=29.25 rise=3.31 twist=-11.4

Download PDB file
Interactive view in 3Dmol.js

 
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG26
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG21,B.DG18,B.DG15,B.DG24
  step#3  pm(>>,forward)  area=12.41 rise=3.31 twist=-26.0

Download PDB file
Interactive view in 3Dmol.js

List of 4 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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(+P+P+P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG10,A.DG7,A.DG4
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG2,A.DG12,A.DG8,A.DG5
  step#1  mp(<<,backward) area=11.66 rise=3.32 twist=-26.2
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2* U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG10,A.DG12 bulged-nts=1 T A.DT11
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG4,A.DG5
  loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT3
  loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT6
  loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT9

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(+P+P+P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG15,A.DG24,A.DG21,A.DG18
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG16,A.DG26,A.DG22,A.DG19
  step#1  mp(<<,backward) area=11.84 rise=3.32 twist=-25.5
  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.DG24,A.DG26 bulged-nts=1 T A.DT25
  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.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT17
  loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT20
  loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT23

Download PDB file
Interactive view in 3Dmol.js

Stem#3, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(+P+P+P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG1,B.DG10,B.DG7,B.DG4
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG12,B.DG8,B.DG5
  step#1  mp(<<,backward) area=12.80 rise=3.20 twist=-26.9
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2* U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG10,B.DG12 bulged-nts=1 T B.DT11
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG7,B.DG8
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG4,B.DG5
  loop#1 type=propeller strands=[#1,#4] nts=1 T B.DT3
  loop#2 type=propeller strands=[#4,#3] nts=1 T B.DT6
  loop#3 type=propeller strands=[#3,#2] nts=1 T B.DT9

Download PDB file
Interactive view in 3Dmol.js

Stem#4, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(+P+P+P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG15,B.DG24,B.DG21,B.DG18
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG16,B.DG26,B.DG22,B.DG19
  step#1  mp(<<,backward) area=12.41 rise=3.31 twist=-26.0
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG15,B.DG16
  strand#2* U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG24,B.DG26 bulged-nts=1 T B.DT25
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG21,B.DG22
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG18,B.DG19
  loop#1 type=propeller strands=[#1,#4] nts=1 T B.DT17
  loop#2 type=propeller strands=[#4,#3] nts=1 T B.DT20
  loop#3 type=propeller strands=[#3,#2] nts=1 T B.DT23

Download PDB file
Interactive view in 3Dmol.js

List of 2 G4 coaxial stacks

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [3'/3']
 2 G4 helix#2 contains 2 G4 stems: [#3,#4]  [3'/3']