Summary information

PDB id
6yep
Class
DNA
Method
NMR
Summary
Lna modified g-quadruplex with flipped g-tract and central tetrad
Reference
Haase L, Weisz K (2020): "Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design." Nucleic Acids Res., 48, 10555-10566. doi: 10.1093/nar/gkaa720.
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, 3(+LnD-Lw), basket(2+2), UUDD

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.293 type=bowl   nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2 glyco-bond=--ss sugar=-3-- groove=-w-n planarity=0.193 type=other  nts=4 GgGG A.DG2,A.LCG15,A.DG21,A.DG7
 3 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.238 type=other  nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6

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 Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2  glyco-bond=--ss sugar=-3-- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.LCG15,A.DG21,A.DG7
 3  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
  step#1  mm(<>,outward)  area=11.41 rise=3.51 twist=20.8
  step#2  pm(>>,forward)  area=15.86 rise=3.51 twist=22.6
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- sugar=-3- nts=3 GgG A.DG14,A.LCG15,A.DG16
  strand#3 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG22,A.DG21,A.DG20
  strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG8,A.DG7,A.DG6

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2 stacking diagrams 
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2  glyco-bond=--ss sugar=-3-- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.LCG15,A.DG21,A.DG7
  step#1  mm(<>,outward)  area=11.41 rise=3.51 twist=20.8

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 2  glyco-bond=--ss sugar=-3-- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.LCG15,A.DG21,A.DG7
 3  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
  step#2  pm(>>,forward)  area=15.86 rise=3.51 twist=22.6

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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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 3(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2  glyco-bond=--ss sugar=-3-- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.LCG15,A.DG21,A.DG7
 3  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
  step#1  mm(<>,outward)  area=11.41 rise=3.51 twist=20.8
  step#2  pm(>>,forward)  area=15.86 rise=3.51 twist=22.6
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- sugar=-3- nts=3 GgG A.DG14,A.LCG15,A.DG16
  strand#3  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG22,A.DG21,A.DG20
  strand#4  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG8,A.DG7,A.DG6
  loop#1 type=lateral   strands=[#1,#4] nts=2 AT A.DA4,A.DT5
  loop#2 type=diagonal  strands=[#4,#2] nts=5 ACACA A.DA9,A.DC10,A.DA11,A.DC12,A.DA13
  loop#3 type=lateral   strands=[#2,#3] nts=3 GAC A.DG17,A.DA18,A.DC19

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