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

PDB-id
1myq
Class
DNA
Method
NMR
Summary
An intramolecular quadruplex of (gga)(4) triplet repeat DNA with a g:g:g:g tetrad and a g(:a):g(:a):g(:a):g heptad, and its dimeric interaction
Reference
Matsugami, A., Ouhashi, K., Kanagawa, M., Liu, H., Kanagawa, S., Uesugi, S., Katahira, M.: (2001) "An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction." J.Mol.Biol., 313, 255-269.
Abstract
The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K(+) conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 2(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.409 type=other  nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- groove=---- planarity=0.505 type=other  nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11
 3 glyco-bond=---- groove=---- planarity=0.454 type=other  nts=4 GGGG B.DG13,B.DG16,B.DG19,B.DG22
 4 glyco-bond=---- groove=---- planarity=0.348 type=other  nts=4 GGGG B.DG14,B.DG17,B.DG20,B.DG23

List of 1 G4-helix [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 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11
 2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG13
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG23,B.DG20,B.DG17,B.DG14
  step#1  mp(<<,backward) area=7.61  rise=3.21 twist=31.4
  step#2  mm(<>,outward)  area=23.82 rise=3.34 twist=-3.7
  step#3  pm(>>,forward)  area=7.55  rise=3.20 twist=32.8
  strand#1 DNA glyco-bond=---- nts=4 GGGG A.DG2,A.DG1,B.DG22,B.DG23
  strand#2 DNA glyco-bond=---- nts=4 GGGG A.DG5,A.DG4,B.DG19,B.DG20
  strand#3 DNA glyco-bond=---- nts=4 GGGG A.DG8,A.DG7,B.DG16,B.DG17
  strand#4 DNA glyco-bond=---- nts=4 GGGG A.DG11,A.DG10,B.DG13,B.DG14

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11
2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
step#1 mp(<<,backward) area=7.61 rise=3.21 twist=31.4

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 2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG13
step#2 mm(<>,outward) area=23.82 rise=3.34 twist=-3.7

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 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG13
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG23,B.DG20,B.DG17,B.DG14
step#3 pm(>>,forward) area=7.55 rise=3.20 twist=32.8

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11
  step#1  pm(>>,forward)  area=7.61  rise=3.21 twist=31.4
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG1,A.DG2
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG4,A.DG5
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG7,A.DG8
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG10,A.DG11
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA3
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA6
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA9

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG13,B.DG16,B.DG19,B.DG22
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG14,B.DG17,B.DG20,B.DG23
  step#1  pm(>>,forward)  area=7.55  rise=3.20 twist=32.8
  strand#1  U DNA glyco-bond=-- nts=2 GG B.DG13,B.DG14
  strand#2  U DNA glyco-bond=-- nts=2 GG B.DG16,B.DG17
  strand#3  U DNA glyco-bond=-- nts=2 GG B.DG19,B.DG20
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG22,B.DG23
  loop#1 type=propeller strands=[#1,#2] nts=1 A B.DA15
  loop#2 type=propeller strands=[#2,#3] nts=1 A B.DA18
  loop#3 type=propeller strands=[#3,#4] nts=1 A B.DA21

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

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

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