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

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.
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 · 3(-PD+Lw), U3D(3+1), UUUD

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

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=---s groove=--wn planarity=0.243 type=other  nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16
 2 glyco-bond=---s groove=--wn planarity=0.253 type=other  nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3 glyco-bond=---s groove=--wn planarity=0.342 type=bowl-2 nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14

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, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3  glyco-bond=---s groove=--wn WC-->Major 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=--- nts=3 GGG A.G1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 D+R glyco-bond=--- nts=3 GGG A.G20,A.DG21,A.DG22
  strand#4 DNA glyco-bond=sss nts=3 GGG A.DG16,A.DG15,A.DG14

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2 stacking diagrams
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
step#1 pm(>>,forward) area=17.44 rise=3.46 twist=20.4

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 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14
step#2 pm(>>,forward) area=11.35 rise=3.43 twist=30.1

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List of 1 G4-stem [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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, anti-parallel, 3(-PD+Lw), U3D(3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3  glyco-bond=---s groove=--wn WC-->Major 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=--- nts=3 GGG A.G1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3  U D+R glyco-bond=--- nts=3 GGG A.G20,A.DG21,A.DG22
  strand#4  D DNA glyco-bond=sss 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

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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