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

PDB-id
6ycv
Class
DNA
Method
NMR
Summary
2'-f-riboguanosine and lna modified hybrid type G-quadruplex with v-loop
Reference
Haase, L., Weisz, K.: (2020) "Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design." Nucleic Acids Res.
Abstract
A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2'-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5'-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3'-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-LwX+P), UD3(1+3), UDDD

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=w--n planarity=0.322 type=bowl   nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 2 glyco-bond=-ss- groove=w-n- planarity=0.264 type=other  nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15
 3 glyco-bond=-s-- groove=wn-- planarity=0.252 type=other  nts=4 GgGG A.DG8,A.GF2/14,A.DG17,A.DG22

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=-ss- groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15
 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.GF2/14,A.DG8,A.DG22,A.DG17
  step#1  mm(<>,outward)  area=9.39  rise=3.42 twist=23.3
  step#2  pm(>>,forward)  area=8.82  rise=3.40 twist=33.6
  strand#1 DNA glyco-bond=-ss nts=3 GGg A.DG2,A.DG1,A.GF2/14
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#4 DNA glyco-bond=--- nts=3 gGG A.LCG15,A.DG16,A.DG17

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2 stacking diagrams
 1  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15
2 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
step#1 mm(<>,outward) area=9.39 rise=3.42 twist=23.3

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 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
3 glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.GF2/14,A.DG8,A.DG22,A.DG17
step#2 pm(>>,forward) area=8.82 rise=3.40 twist=33.6

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

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15
  step#1  mm(<>,outward)  area=9.39  rise=3.42 twist=23.3
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG A.DG7,A.DG6
  strand#3  D DNA glyco-bond=-s nts=2 GG A.DG21,A.DG20
  strand#4  D DNA glyco-bond=-- nts=2 Gg A.DG16,A.LCG15
  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 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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.LCG15,A.DG16,A.DG17