Summary information

PDB id
1d59
Class
DNA
Method
X-ray (2.3 Å)
Summary
Crystal structure of 4-stranded oxytricha telomeric DNA
Reference
Kang C, Zhang X, Ratliff R, Moyzis R, Rich A (1992): "Crystal structure of four-stranded Oxytricha telomeric DNA." Nature, 356, 126-131. doi: 10.1038/356126a0.
Abstract
The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.
G4 notes
8 G-tetrads, 2 G4 helices, 2 G4 stems, (2+2), UDUD

Base-block schematics in six views

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List of 8 G-tetrads

 1 glyco-bond=--s- sugar=-.-- groove=-wn- planarity=0.244 type=other  nts=4 GGGG A.DG1,B.DG16,B.DG21,A.DG12
 2 glyco-bond=-s-s sugar=33.. groove=wnwn planarity=0.284 type=other  nts=4 GGGG A.DG2,A.DG11,B.DG22,B.DG15
 3 glyco-bond=--s- sugar=.-3- groove=-wn- planarity=0.425 type=other  nts=4 GGGG A.DG3,B.DG14,B.DG23,A.DG10
 4 glyco-bond=-s-s sugar=-.3- groove=wnwn planarity=0.374 type=other  nts=4 GGGG A.DG4,A.DG9,B.DG24,B.DG13
 5 glyco-bond=s-s- sugar=-3-3 groove=wnwn planarity=0.320 type=other  nts=4 GGGG C.DG25,C.DG36,D.DG45,D.DG40
 6 glyco-bond=-s-s sugar=-3.3 groove=wnwn planarity=0.323 type=other  nts=4 GGGG C.DG26,C.DG35,D.DG46,D.DG39
 7 glyco-bond=s-s- sugar=--33 groove=wnwn planarity=0.441 type=bowl   nts=4 GGGG C.DG27,C.DG34,D.DG47,D.DG38
 8 glyco-bond=-s-s sugar=.--- groove=wnwn planarity=0.373 type=other  nts=4 GGGG C.DG28,C.DG33,D.DG48,D.DG37

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, inter-molecular, with 1 stem

 1  glyco-bond=--s- sugar=-.-- groove=-wn- WC-->Major nts=4 GGGG A.DG1,B.DG16,B.DG21,A.DG12
 2  glyco-bond=-s-s sugar=3..3 groove=nwnw Major-->WC nts=4 GGGG A.DG2,B.DG15,B.DG22,A.DG11
 3  glyco-bond=--s- sugar=.-3- groove=-wn- WC-->Major nts=4 GGGG A.DG3,B.DG14,B.DG23,A.DG10
 4  glyco-bond=-s-s sugar=--3. groove=nwnw Major-->WC nts=4 GGGG A.DG4,B.DG13,B.DG24,A.DG9
  step#1  mm(<>,outward)  area=9.62  rise=3.46 twist=28.8
  step#2  pp(><,inward)   area=25.87 rise=3.47 twist=28.0
  step#3  mm(<>,outward)  area=16.06 rise=3.48 twist=32.3
  strand#1 DNA glyco-bond=---- sugar=-3.- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s sugar=..-- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13
  strand#3 DNA glyco-bond=s-s- sugar=-.33 nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24
  strand#4 DNA glyco-bond=-s-s sugar=-3-. nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9

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3 stacking diagrams 
 1  glyco-bond=--s- sugar=-.-- groove=-wn- WC-->Major nts=4 GGGG A.DG1,B.DG16,B.DG21,A.DG12
 2  glyco-bond=-s-s sugar=3..3 groove=nwnw Major-->WC nts=4 GGGG A.DG2,B.DG15,B.DG22,A.DG11
  step#1  mm(<>,outward)  area=9.62  rise=3.46 twist=28.8

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 2  glyco-bond=-s-s sugar=3..3 groove=nwnw Major-->WC nts=4 GGGG A.DG2,B.DG15,B.DG22,A.DG11
 3  glyco-bond=--s- sugar=.-3- groove=-wn- WC-->Major nts=4 GGGG A.DG3,B.DG14,B.DG23,A.DG10
  step#2  pp(><,inward)   area=25.87 rise=3.47 twist=28.0

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 3  glyco-bond=--s- sugar=.-3- groove=-wn- WC-->Major nts=4 GGGG A.DG3,B.DG14,B.DG23,A.DG10
 4  glyco-bond=-s-s sugar=--3. groove=nwnw Major-->WC nts=4 GGGG A.DG4,B.DG13,B.DG24,A.DG9
  step#3  mm(<>,outward)  area=16.06 rise=3.48 twist=32.3

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Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC nts=4 GGGG C.DG25,C.DG36,D.DG45,D.DG40
 2  glyco-bond=-s-s sugar=-3.3 groove=wnwn WC-->Major nts=4 GGGG C.DG26,C.DG35,D.DG46,D.DG39
 3  glyco-bond=s-s- sugar=--33 groove=wnwn Major-->WC nts=4 GGGG C.DG27,C.DG34,D.DG47,D.DG38
 4  glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG C.DG28,C.DG33,D.DG48,D.DG37
  step#1  mm(<>,outward)  area=9.77  rise=3.45 twist=27.3
  step#2  pp(><,inward)   area=21.62 rise=3.43 twist=31.0
  step#3  mm(<>,outward)  area=12.13 rise=3.40 twist=28.6
  strand#1 DNA glyco-bond=s-s- sugar=---. nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28
  strand#2 DNA glyco-bond=-s-s sugar=33-- nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33
  strand#3 DNA glyco-bond=s-s- sugar=-.3- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48
  strand#4 DNA glyco-bond=-s-s sugar=333- nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37

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3 stacking diagrams 
 1  glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC nts=4 GGGG C.DG25,C.DG36,D.DG45,D.DG40
 2  glyco-bond=-s-s sugar=-3.3 groove=wnwn WC-->Major nts=4 GGGG C.DG26,C.DG35,D.DG46,D.DG39
  step#1  mm(<>,outward)  area=9.77  rise=3.45 twist=27.3

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 2  glyco-bond=-s-s sugar=-3.3 groove=wnwn WC-->Major nts=4 GGGG C.DG26,C.DG35,D.DG46,D.DG39
 3  glyco-bond=s-s- sugar=--33 groove=wnwn Major-->WC nts=4 GGGG C.DG27,C.DG34,D.DG47,D.DG38
  step#2  pp(><,inward)   area=21.62 rise=3.43 twist=31.0

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 3  glyco-bond=s-s- sugar=--33 groove=wnwn Major-->WC nts=4 GGGG C.DG27,C.DG34,D.DG47,D.DG38
 4  glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG C.DG28,C.DG33,D.DG48,D.DG37
  step#3  mm(<>,outward)  area=12.13 rise=3.40 twist=28.6

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

 1  glyco-bond=--s- sugar=---. groove=-nw- Major-->WC nts=4 GGGG A.DG1,A.DG12,B.DG21,B.DG16
 2  glyco-bond=-s-s sugar=33.. groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG11,B.DG22,B.DG15
 3  glyco-bond=--s- sugar=.-3- groove=-nw- Major-->WC nts=4 GGGG A.DG3,A.DG10,B.DG23,B.DG14
 4  glyco-bond=-s-s sugar=-.3- groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG9,B.DG24,B.DG13
  step#1  mm(<>,outward)  area=9.62  rise=3.46 twist=28.8
  step#2  pp(><,inward)   area=25.87 rise=3.47 twist=28.0
  step#3  mm(<>,outward)  area=16.06 rise=3.48 twist=32.3
  strand#1  U DNA glyco-bond=---- sugar=-3.- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=-3-. nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#3  U DNA glyco-bond=s-s- sugar=-.33 nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24
  strand#4  D DNA glyco-bond=-s-s sugar=..-- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13
  loop#1 type=lateral   strands=[#1,#2] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=lateral   strands=[#4,#3] nts=4 TTTT B.DT17,B.DT18,B.DT19,B.DT20

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Stem#2, 4 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC nts=4 GGGG C.DG25,C.DG36,D.DG45,D.DG40
 2  glyco-bond=-s-s sugar=-3.3 groove=wnwn WC-->Major nts=4 GGGG C.DG26,C.DG35,D.DG46,D.DG39
 3  glyco-bond=s-s- sugar=--33 groove=wnwn Major-->WC nts=4 GGGG C.DG27,C.DG34,D.DG47,D.DG38
 4  glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG C.DG28,C.DG33,D.DG48,D.DG37
  step#1  mm(<>,outward)  area=9.77  rise=3.45 twist=27.3
  step#2  pp(><,inward)   area=21.62 rise=3.43 twist=31.0
  step#3  mm(<>,outward)  area=12.13 rise=3.40 twist=28.6
  strand#1  U DNA glyco-bond=s-s- sugar=---. nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28
  strand#2  D DNA glyco-bond=-s-s sugar=33-- nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33
  strand#3  U DNA glyco-bond=s-s- sugar=-.3- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48
  strand#4  D DNA glyco-bond=-s-s sugar=333- nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37
  loop#1 type=lateral   strands=[#1,#2] nts=4 TTTT C.DT29,C.DT30,C.DT31,C.DT32
  loop#2 type=lateral   strands=[#4,#3] nts=4 TTTT D.DT41,D.DT42,D.DT43,D.DT44

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