DSSR-enabled G4 identification/annotation: PDB entry 2lee
Summary information and primary citation
- PDB-id
- 2lee
- Class
- DNA
- Method
- NMR
- Summary
- Unique structural features of interconverting monomeric and dimeric g-quadruplexes adopted by a sequence from intron of n-myc gene
- Reference
- Trajkovski M, Webba da Silva M, Plavec J (2012): "Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene." J.Am.Chem.Soc., 134, 4132-4141. doi: 10.1021/ja208483v.
- Abstract
- A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K(+), NH(4)(+), and Na(+) ions. A monomeric G-quadruplex formed in K(+) ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K(+) ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.291 type=other O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- planarity=0.329 type=bowl O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 3 glyco-bond=---- sugar=---- groove=---- planarity=0.219 type=other O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
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, 3 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17 step#1 pm(>>,forward) area=11.76 rise=3.34 twist=28.5 step#2 pm(>>,forward) area=10.46 rise=3.36 twist=30.9 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17 |
| 2 stacking diagrams | |
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 |
List of 1 G4-stem
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, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17 step#1 pm(>>,forward) area=11.76 rise=3.34 twist=28.5 step#2 pm(>>,forward) area=10.46 rise=3.36 twist=30.9 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17 loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC6 loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA10 loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA14 |