Summary information

PDB id
6rs3
Class
DNA
Method
NMR
Summary
2'-f-riboguanosine modified g-quadruplex with v-loop
Reference
Haase L, Dickerhoff J, Weisz K (2020): "Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops." Chemistry, 26, 524-533. doi: 10.1002/chem.201904044.
Abstract
A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2'-deoxy-2'-fluoro-riboguanosine (FrG) analogs. The two substitutions promoted a structural rearrangement to a topology with the 5'-terminal G residue located in the central tetrad and the two modified residues linked by a V-shaped zero-nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the FrG analog preceding the V-loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3'-endo sugar pucker within the V-loop architecture outweighs the propensity of the FrG analog to adopt an anti glycosidic conformation. Refolding into a V-loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2'-F-arabinoguanosine analogs with their favored south-east sugar conformation do not support formation of the V-loop topology. Examination of known G-quadruplexes with a V-shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwX+P), UD3(1+3), UDDD

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.407 type=bowl-2 nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 2 glyco-bond=-ss- sugar=---. groove=w-n- planarity=0.364 type=saddle nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15
 3 glyco-bond=-s-- sugar=-3-- groove=wn-- planarity=0.354 type=other  nts=4 GgGG A.DG8,A.GF2/14,A.DG17,A.DG22

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 3  glyco-bond=s--- sugar=3--- groove=w--n Major-->WC nts=4 gGGG A.GF2/14,A.DG8,A.DG22,A.DG17
  step#1  mm(<>,outward)  area=13.48 rise=3.43 twist=19.5
  step#2  pm(>>,forward)  area=9.12  rise=3.46 twist=31.5
  strand#1 DNA glyco-bond=-ss sugar=--3 nts=3 GGg A.DG2,A.DG1,A.GF2/14
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#4 DNA glyco-bond=--- sugar=.-- nts=3 gGG A.GF2/15,A.DG16,A.DG17

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2 stacking diagrams 
 1  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
  step#1  mm(<>,outward)  area=13.48 rise=3.43 twist=19.5

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 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 3  glyco-bond=s--- sugar=3--- groove=w--n Major-->WC nts=4 gGGG A.GF2/14,A.DG8,A.DG22,A.DG17
  step#2  pm(>>,forward)  area=9.12  rise=3.46 twist=31.5

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(-LwX+P), UD3(1+3)

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 2  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15
  step#1  mm(<>,outward)  area=13.48 rise=3.43 twist=19.5
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG7,A.DG6
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG21,A.DG20
  strand#4  D DNA glyco-bond=-- sugar=-. nts=2 Gg A.DG16,A.GF2/15
  loop#1 type=lateral   strands=[#1,#2] nts=3 GAT A.DG3,A.DA4,A.DT5
  loop#2 type=diag-prop strands=[#2,#4] nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GF2/14
  loop#3 type=propeller strands=[#4,#3] nts=3 GAC A.DG17,A.DA18,A.DC19

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GF2/14
 2 type=V-shaped  helix=#1 nts=4 ggGG A.GF2/14,A.GF2/15,A.DG16,A.DG17