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

PDB-id
6a7y
Class
DNA
Method
NMR
Summary
Solution structure of an intermolecular leaped v-shape G-quadruplex
Reference
Wan, C., Fu, W., Jing, H., Zhang, N.: (2019) "NMR solution structure of an asymmetric intermolecular leaped V-shape G-quadruplex: selective recognition of the d(G2NG3NG4) sequence motif by a short linear G-rich DNA probe." Nucleic Acids Res., 47, 1544-1556.
Abstract
Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itself distinctive and thus an essentially more accessible target. As an alternative to the conventional antisense method using a complementary chain, forming an intermolecular G-quadruplex from two different oligomers, in which the longer one as the target is captured by a short G-rich fragment, could be helpful for recognizing G-rich sequences and structural motifs. However, such an intermolecular leaped V-shape G-quadruplex consisting of DNA oligomers of quite different lengths has not been evaluated. Here, we present the first nuclear magnetic resonance (NMR) study of an asymmetric intermolecular leaped V-shape G-quadruplex assembled between an Oxytricha nova telomeric sequence d(G2T4G4T4G4) and a single G-tract fragment d(TG4A). Furthermore, we explored the selectivity of this short fragment as a potential probe, examined the kinetic discrimination for probing a specific mutant, and proposed the key sequence motif d(G2NG3NG4) essential for building the leaped V-shape G-quadruplexes.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · (1+3), UDDD

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

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

 1 glyco-bond=s--- groove=w--n planarity=0.243 type=other  nts=4 GGGG A.DG1,A.DG9,B.DG22,A.DG17
 2 glyco-bond=-sss groove=w--n planarity=0.334 type=other  nts=4 GGGG A.DG2,A.DG8,B.DG21,A.DG16
 3 glyco-bond=-s-- groove=wn-- planarity=0.322 type=other  nts=4 GGGG A.DG10,A.DG15,A.DG18,B.DG23

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, inter-molecular, with 1 stem

 1  glyco-bond=-sss groove=w--n WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG21,A.DG16
 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG22,A.DG17
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG15,A.DG10,B.DG23,A.DG18
  step#1  mm(<>,outward)  area=14.09 rise=3.70 twist=21.2
  step#2  pm(>>,forward)  area=11.58 rise=3.60 twist=26.9
  strand#1 DNA glyco-bond=-ss nts=3 GGG A.DG2,A.DG1,A.DG15
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=s-- nts=3 GGG B.DG21,B.DG22,B.DG23
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG16,A.DG17,A.DG18

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2 stacking diagrams
 1  glyco-bond=-sss groove=w--n WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG21,A.DG16
2 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG22,A.DG17
step#1 mm(<>,outward) area=14.09 rise=3.70 twist=21.2

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 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG22,A.DG17
3 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG15,A.DG10,B.DG23,A.DG18
step#2 pm(>>,forward) area=11.58 rise=3.60 twist=26.9

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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, 2 loops, inter-molecular, UDDD, hybrid-(mixed), (1+3)

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,B.DG22,A.DG17
 2  glyco-bond=-sss groove=w--n WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG21,A.DG16
  step#1  mm(<>,outward)  area=14.09 rise=3.70 twist=21.2
  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.DG9,A.DG8
  strand#3  D DNA glyco-bond=-s nts=2 GG B.DG22,B.DG21
  strand#4  D DNA glyco-bond=-s nts=2 GG A.DG17,A.DG16
  loop#1 type=lateral   strands=[#1,#2] nts=5 TTTTG A.DT3,A.DT4,A.DT5,A.DT6,A.DG7
  loop#2 type=diag-prop strands=[#2,#4] nts=6 GTTTTG A.DG10,A.DT11,A.DT12,A.DT13,A.DT14,A.DG15

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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=6 GTTTTG A.DG10,A.DT11,A.DT12,A.DT13,A.DT14,A.DG15
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG15,A.DG16,A.DG17,A.DG18