DSSR-enabled G4 identification/annotation: PDB entry 6ffr
Summary information and primary citation
- PDB-id
- 6ffr
- Class
- DNA-RNA hybrid
- Method
- NMR
- Summary
- DNA-RNA hybrid quadruplex with flipped tetrad
- Reference
- Haase L, Dickerhoff J, Weisz K (2018): "DNA-RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies." Chemistry, 24, 15365-15371. doi: 10.1002/chem.201803367.
- Abstract
- A DNA G-quadruplex adopting a (3+1)-hybrid structure was substituted at its 5'-tetrad by riboguanosine (rG) analogs. Incorporation of anti-favoring rG at appropriate syn-positions of the 5'-outer tetrad induced conformational rearrangements to yield a quadruplex featuring a 5'-tetrad with reversed polarity. A high-resolution structure of a disubstituted quadruplex variant as well as direct NMR experimental evidence reveals a non-conventional C-H⋅⋅⋅O hydrogen bond in a medium groove between the 2'-OH of an rG residue adopting a C2'-endo sugar pucker and H8 of a 3'-neighboring anti-G residue. In contrast, a C3'-endo sugar conformation for another guanine ribonucleotide prevents formation of a corresponding hydrogen bond but relocates its 2'-OH substituent from the quadruplex narrow groove into a medium groove. Both the formation of favorable CHO hydrogen bridges and unfavorable interactions of the 2'-hydroxyl group in a narrow groove will promote RNA folding into a parallel topology featuring all-anti core residues and four grooves of medium size.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 3(-PD+Lw)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---s sugar=3--- groove=--wn planarity=0.243 type=other N+ nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.253 type=other N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.342 type=bowl-2 N+ nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14
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
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1 glyco-bond=---s sugar=3--- groove=--wn WC-->Major N+ nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14 step#1 pm(>>,forward) area=17.44 rise=3.46 twist=20.4 step#2 pm(>>,forward) area=11.35 rise=3.43 twist=30.1 strand#1 D+R glyco-bond=--- sugar=3-- nts=3 GGG A.G1,A.DG2,A.DG3 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3 D+R glyco-bond=--- sugar=--- nts=3 GGG A.G20,A.DG21,A.DG22 strand#4 DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG16,A.DG15,A.DG14 |
| 2 stacking diagrams | |
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1 glyco-bond=---s sugar=3--- groove=--wn WC-->Major N+ nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16 |
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2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 |
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, UUUD, hybrid2, 3+1, 3(-PD+Lw)
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1 glyco-bond=---s sugar=3--- groove=--wn WC-->Major N+ nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14 step#1 pm(>>,forward) area=17.44 rise=3.46 twist=20.4 step#2 pm(>>,forward) area=11.35 rise=3.43 twist=30.1 strand#1 U D+R glyco-bond=--- sugar=3-- nts=3 GGG A.G1,A.DG2,A.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3 U D+R glyco-bond=--- sugar=--- nts=3 GGG A.G20,A.DG21,A.DG22 strand#4 D DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG16,A.DG15,A.DG14 loop#1 type=propeller strands=[#1,#2] nts=2 AT A.DA4,A.DT5 loop#2 type=diagonal strands=[#2,#4] nts=5 ACACA A.DA9,A.DC10,A.DA11,A.DC12,A.DA13 loop#3 type=lateral strands=[#4,#3] nts=3 GAC A.DG17,A.DA18,A.DC19 |