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

PDB-id
2m53
Class
DNA
Method
NMR
Summary
G-rich vegf aptamer with lna modifications
Reference
Marusic, M., Veedu, R.N., Wengel, J., Plavec, J.: (2013) "G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold." Nucleic Acids Res.
Abstract
The formation of a single G-quadruplex structure adopted by a promising 25 nt G-rich vascular endothelial growth factor aptamer in a K(+) rich environment was facilitated by locked nucleic acid modifications. An unprecedented all parallel-stranded monomeric G-quadruplex with three G-quartet planes exhibits several unique structural features. Five consecutive guanine residues are all involved in G-quartet formation and occupy positions in adjacent DNA strands, which are bridged with a no-residue propeller-type loop. A two-residue D-shaped loop facilitates inclusion of an isolated guanine residue into the vacant spot within the G-quartet. The remaining two G-rich tracts of three residues each adopt parallel orientation and are linked with edgewise and propeller loops. Both 5' with 3 nt and 3' with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology. Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex. Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-P-P-P), parallel(4+0), UUUU

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=---- groove=---- planarity=0.352 type=other  nts=4 GGGG A.DG4,A.DG11,A.DG14,A.DG19
 2 glyco-bond=---- groove=---- planarity=0.174 type=other  nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20
 3 glyco-bond=---- groove=---- planarity=0.200 type=other  nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21

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=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG14,A.DG19
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21
  step#1  pm(>>,forward)  area=24.23 rise=3.66 twist=11.9
  step#2  pm(>>,forward)  area=13.48 rise=3.32 twist=26.7
  strand#1 DNA glyco-bond=--- nts=3 GgG A.DG4,A.LCG5,A.DG6
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG7,A.DG8
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4 DNA glyco-bond=--- nts=3 GGg A.DG19,A.DG20,A.LCG21

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG14,A.DG19
2 glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20
step#1 pm(>>,forward) area=24.23 rise=3.66 twist=11.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21
step#2 pm(>>,forward) area=13.48 rise=3.32 twist=26.7

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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, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21
  step#1  pm(>>,forward)  area=13.48 rise=3.32 twist=26.7
  strand#1  U DNA glyco-bond=-- nts=2 gG A.LCG5,A.DG6
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG15,A.DG16
  strand#4  U DNA glyco-bond=-- nts=2 Gg A.DG20,A.LCG21
  loop#1 type=propeller strands=[#1,#2] nts=0
  loop#2 type=propeller strands=[#2,#3] nts=6 TGGACG A.DT9,A.DG10,A.DG11,A.DA12,A.DC13,A.DG14
  loop#3 type=propeller strands=[#3,#4] nts=3 CCG A.DC17,A.DC18,A.DG19

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

List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=lateral   helix=#1 nts=4 GACG A.DG11,A.DA12,A.DC13,A.DG14