Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
2avj
Class
DNA
Method
X-ray (2.39 Å)
Summary
G4(br)uttg4 dimeric quadruplex
Reference
Hazel, P., Parkinson, G.N., Neidle, S.: (2006) "Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex." J.Am.Chem.Soc., 128, 5480-5487.
Abstract
The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K(+) ions between the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2(1) unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T(4) loops. A total of seven independent T(3) loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.
G4 notes
12 G-tetrads, 2 G4 helices, 3 G4 stems, 1 G4 coaxial stack · (2+2), UDDU; (2+2), UDUD; (2+2), UUDD · coaxial interfaces: mixed

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 12 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s-s- groove=wnwn planarity=0.452 type=bowl   nts=4 GGGG A.DG1,A.DG11,B.DG19,B.DG15
 2 glyco-bond=-s-s groove=wnwn planarity=0.343 type=other  nts=4 GGGG A.DG2,A.DG10,B.DG20,B.DG14
 3 glyco-bond=s-s- groove=wnwn planarity=0.282 type=other  nts=4 GGGG A.DG3,A.DG9,B.DG21,B.DG13
 4 glyco-bond=-s-s groove=wnwn planarity=0.411 type=bowl   nts=4 GGGG A.DG4,A.DG8,B.DG22,B.DG12
 5 glyco-bond=ss-- groove=-w-n planarity=0.131 type=planar nts=4 GGGG C.DG23,D.DG34,D.DG44,C.DG33
 6 glyco-bond=--ss groove=-w-n planarity=0.094 type=planar nts=4 GGGG C.DG24,D.DG35,D.DG43,C.DG32
 7 glyco-bond=ss-- groove=-w-n planarity=0.148 type=planar nts=4 GGGG C.DG25,D.DG36,D.DG42,C.DG31
 8 glyco-bond=--ss groove=-w-n planarity=0.245 type=bowl-2 nts=4 GGGG C.DG26,D.DG37,D.DG41,C.DG30
 9 glyco-bond=s--s groove=w-n- planarity=0.125 type=planar nts=4 GGGG E.DG45,E.DG55,F.DG66,F.DG56
10 glyco-bond=-ss- groove=w-n- planarity=0.084 type=planar nts=4 GGGG E.DG46,E.DG54,F.DG65,F.DG57
11 glyco-bond=s--s groove=w-n- planarity=0.120 type=planar nts=4 GGGG E.DG47,E.DG53,F.DG64,F.DG58
12 glyco-bond=-ss- groove=w-n- planarity=0.258 type=bowl   nts=4 GGGG E.DG48,E.DG52,F.DG63,F.DG59

List of 2 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

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-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG11,B.DG19,B.DG15
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG10,B.DG20,B.DG14
 3  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG9,B.DG21,B.DG13
 4  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG22,B.DG12
  step#1  mm(<>,outward)  area=14.79 rise=3.50 twist=17.7
  step#2  pp(><,inward)   area=20.47 rise=3.58 twist=36.1
  step#3  mm(<>,outward)  area=14.54 rise=3.54 twist=17.3
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG A.DG11,A.DG10,A.DG9,A.DG8
  strand#3 DNA glyco-bond=s-s- nts=4 GGGG B.DG19,B.DG20,B.DG21,B.DG22
  strand#4 DNA glyco-bond=-s-s nts=4 GGGG B.DG15,B.DG14,B.DG13,B.DG12

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3 stacking diagrams
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG11,B.DG19,B.DG15
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG10,B.DG20,B.DG14
step#1 mm(<>,outward) area=14.79 rise=3.50 twist=17.7

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 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG10,B.DG20,B.DG14
3 glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG9,B.DG21,B.DG13
step#2 pp(><,inward) area=20.47 rise=3.58 twist=36.1

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 3  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG9,B.DG21,B.DG13
4 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG22,B.DG12
step#3 mm(<>,outward) area=14.54 rise=3.54 twist=17.3

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Helix#2, 8 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG26,D.DG37,D.DG41,C.DG30
 2  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG25,D.DG36,D.DG42,C.DG31
 3  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG24,D.DG35,D.DG43,C.DG32
 4* glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG23,D.DG34,D.DG44,C.DG33
 5  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG66,E.DG55,E.DG45,F.DG56
 6  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG65,E.DG54,E.DG46,F.DG57
 7  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG64,E.DG53,E.DG47,F.DG58
 8  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG63,E.DG52,E.DG48,F.DG59
  step#1  mm(<>,outward)  area=13.50 rise=3.44 twist=18.8
  step#2  pp(><,inward)   area=20.94 rise=3.39 twist=38.2
  step#3  mm(<>,outward)  area=13.78 rise=3.46 twist=18.6
  step#4  pp(><,inward)   area=18.99 rise=3.32 twist=40.8
  step#5  mm(<>,outward)  area=11.97 rise=3.42 twist=19.7
  step#6  pp(><,inward)   area=19.22 rise=3.49 twist=38.1
  step#7  mm(<>,outward)  area=16.85 rise=3.49 twist=16.4
  strand#1 DNA glyco-bond=-s-s-s-s nts=8 GGGGGGGG C.DG26,C.DG25,C.DG24,C.DG23,F.DG66,F.DG65,F.DG64,F.DG63
  strand#2 DNA glyco-bond=-s-s-s-s nts=8 GGGGGGGG D.DG37,D.DG36,D.DG35,D.DG34,E.DG55,E.DG54,E.DG53,E.DG52
  strand#3 DNA glyco-bond=s-s-s-s- nts=8 GGGGGGGG D.DG41,D.DG42,D.DG43,D.DG44,E.DG45,E.DG46,E.DG47,E.DG48
  strand#4 DNA glyco-bond=s-s-s-s- nts=8 GGGGGGGG C.DG30,C.DG31,C.DG32,C.DG33,F.DG56,F.DG57,F.DG58,F.DG59

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7 stacking diagrams
 1  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG26,D.DG37,D.DG41,C.DG30
2 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG25,D.DG36,D.DG42,C.DG31
step#1 mm(<>,outward) area=13.50 rise=3.44 twist=18.8

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 2  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG25,D.DG36,D.DG42,C.DG31
3 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG24,D.DG35,D.DG43,C.DG32
step#2 pp(><,inward) area=20.94 rise=3.39 twist=38.2

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 3  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG24,D.DG35,D.DG43,C.DG32
4* glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG23,D.DG34,D.DG44,C.DG33
step#3 mm(<>,outward) area=13.78 rise=3.46 twist=18.6

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 4* glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG23,D.DG34,D.DG44,C.DG33
5 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG66,E.DG55,E.DG45,F.DG56
step#4 pp(><,inward) area=18.99 rise=3.32 twist=40.8

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 5  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG66,E.DG55,E.DG45,F.DG56
6 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG65,E.DG54,E.DG46,F.DG57
step#5 mm(<>,outward) area=11.97 rise=3.42 twist=19.7

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 6  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG65,E.DG54,E.DG46,F.DG57
7 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG64,E.DG53,E.DG47,F.DG58
step#6 pp(><,inward) area=19.22 rise=3.49 twist=38.1

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 7  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG F.DG64,E.DG53,E.DG47,F.DG58
8 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG F.DG63,E.DG52,E.DG48,F.DG59
step#7 mm(<>,outward) area=16.85 rise=3.49 twist=16.4

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List of 3 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

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-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG11,B.DG19,B.DG15
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG10,B.DG20,B.DG14
 3  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG9,B.DG21,B.DG13
 4  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG22,B.DG12
  step#1  mm(<>,outward)  area=14.79 rise=3.50 twist=17.7
  step#2  pp(><,inward)   area=20.47 rise=3.58 twist=36.1
  step#3  mm(<>,outward)  area=14.54 rise=3.54 twist=17.3
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG A.DG11,A.DG10,A.DG9,A.DG8
  strand#3  U DNA glyco-bond=s-s- nts=4 GGGG B.DG19,B.DG20,B.DG21,B.DG22
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG B.DG15,B.DG14,B.DG13,B.DG12
  loop#1 type=lateral   strands=[#1,#2] nts=3 uTT A.BRU5,A.DT6,A.DT7
  loop#2 type=lateral   strands=[#4,#3] nts=3 uTT B.BRU16,B.DT17,B.DT18

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

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG23,D.DG34,D.DG44,C.DG33
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG24,D.DG35,D.DG43,C.DG32
 3  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG C.DG25,D.DG36,D.DG42,C.DG31
 4  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG C.DG26,D.DG37,D.DG41,C.DG30
  step#1  mm(<>,outward)  area=13.78 rise=3.46 twist=18.6
  step#2  pp(><,inward)   area=20.94 rise=3.39 twist=38.2
  step#3  mm(<>,outward)  area=13.50 rise=3.44 twist=18.8
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG C.DG23,C.DG24,C.DG25,C.DG26
  strand#2  U DNA glyco-bond=s-s- nts=4 GGGG D.DG34,D.DG35,D.DG36,D.DG37
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG D.DG44,D.DG43,D.DG42,D.DG41
  strand#4  D DNA glyco-bond=-s-s nts=4 GGGG C.DG33,C.DG32,C.DG31,C.DG30
  loop#1 type=lateral   strands=[#1,#4] nts=3 uTT C.BRU27,C.DT28,C.DT29
  loop#2 type=lateral   strands=[#2,#3] nts=3 uTT D.BRU38,D.DT39,D.DT40

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Stem#3, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG45,E.DG55,F.DG66,F.DG56
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG46,E.DG54,F.DG65,F.DG57
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG47,E.DG53,F.DG64,F.DG58
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG48,E.DG52,F.DG63,F.DG59
  step#1  mm(<>,outward)  area=11.97 rise=3.42 twist=19.7
  step#2  pp(><,inward)   area=19.22 rise=3.49 twist=38.1
  step#3  mm(<>,outward)  area=16.85 rise=3.49 twist=16.4
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG E.DG45,E.DG46,E.DG47,E.DG48
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG E.DG55,E.DG54,E.DG53,E.DG52
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG F.DG66,F.DG65,F.DG64,F.DG63
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG F.DG56,F.DG57,F.DG58,F.DG59
  loop#1 type=lateral   strands=[#1,#2] nts=3 uTT E.BRU49,E.DT50,E.DT51
  loop#2 type=lateral   strands=[#4,#3] nts=3 uTT F.BRU60,F.DT61,F.DT62

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#2 contains 2 G4 stems: [#2,#3]  [mixed]

List of 0 non-stem G4-loops (including the two closing Gs)