DSSR-enabled G4 identification/annotation: PDB entry 1myq
Summary information and primary citation
- 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. doi: 10.1006/jmbi.2001.5047.
- 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, UUUU, parallel, 4+0, 2(-P-P-P), coaxial interfaces: 5'/5'
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=-..- groove=---- planarity=0.409 type=other O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=---. groove=---- planarity=0.505 type=other O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 3 glyco-bond=---- sugar=-... groove=---- planarity=0.454 type=other O+ nts=4 GGGG B.DG13,B.DG16,B.DG19,B.DG22 4 glyco-bond=---- sugar=---. groove=---- planarity=0.348 type=other O+ nts=4 GGGG B.DG14,B.DG17,B.DG20,B.DG23
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, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 2* glyco-bond=---- sugar=-..- groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 3 glyco-bond=---- sugar=...- groove=---- Major-->WC O+ nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG13 4 glyco-bond=---- sugar=.--- groove=---- Major-->WC O+ 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=---- sugar=--.. nts=4 GGGG A.DG2,A.DG1,B.DG22,B.DG23 strand#2 DNA glyco-bond=---- sugar=-..- nts=4 GGGG A.DG5,A.DG4,B.DG19,B.DG20 strand#3 DNA glyco-bond=---- sugar=-..- nts=4 GGGG A.DG8,A.DG7,B.DG16,B.DG17 strand#4 DNA glyco-bond=---- sugar=.--- nts=4 GGGG A.DG11,A.DG10,B.DG13,B.DG14 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 |
|
2* glyco-bond=---- sugar=-..- groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 |
|
3 glyco-bond=---- sugar=...- groove=---- Major-->WC O+ nts=4 GGGG B.DG22,B.DG19,B.DG16,B.DG13 |
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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=-..- groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ 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=-- sugar=-- nts=2 GG A.DG1,A.DG2 strand#2 U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG4,A.DG5 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.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 |
Stem#2, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=-... groove=---- WC-->Major O+ nts=4 GGGG B.DG13,B.DG16,B.DG19,B.DG22 2 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ 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=-- sugar=-- nts=2 GG B.DG13,B.DG14 strand#2 U DNA glyco-bond=-- sugar=.- nts=2 GG B.DG16,B.DG17 strand#3 U DNA glyco-bond=-- sugar=.- nts=2 GG B.DG19,B.DG20 strand#4 U DNA glyco-bond=-- sugar=.. 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 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']