Summary information

PDB id
6gzn
Class
DNA
Method
NMR
Summary
Adenine-driven structural switch from two- to three-quartet DNA g-quadruplex
Reference
Lenarcic Zivkovic M, Rozman J, Plavec J (2018): "Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex." Angew. Chem. Int. Ed. Engl., 57, 15395-15399. doi: 10.1002/anie.201809328.
Abstract
G-rich sequence found in the regulatory region of RANKL gene associated with homeostasis of bone metabolism folds into a two-quartet basket-type G-quadruplex stabilized by A•G•A and G•G•G base-triads. Perusal of local structural features together with G/A-to-T modifications uncovered critical role of A5 for formation of distinct antiparallel two-quartet and not three-quartet topology that would be expected based on sequence with four GGG-tracts alone. Structural changes induced by A5-to-T5 modification include a switch in orientation and relative positions of G-strands that together with anti to syn reorientation of G12 provide insights into complexity of intricate interactions that influence folding process of G-rich DNA. Understanding the impact of loop residues for overall stability and formation of G-quadruplexes advances our knowledge and ability to predict structures adopted by G-rich sequences which are involved in regulatory mechanisms in cell and may also facilitate drug design driven by structural insights.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwD+Ln), basket(2+2), UDDU

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s--s groove=w-n- planarity=0.086 type=planar nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13
 2 glyco-bond=-ss- groove=w-n- planarity=0.129 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14
  step#1  mm(<>,outward)  area=16.89 rise=3.44 twist=16.6
  strand#1 DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s nts=2 GG A.DG7,A.DG6
  strand#3 DNA glyco-bond=-s nts=2 GG A.DG19,A.DG18
  strand#4 DNA glyco-bond=s- nts=2 GG A.DG13,A.DG14

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1 stacking diagram
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14
step#1 mm(<>,outward) area=16.89 rise=3.44 twist=16.6

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 2(-LwD+Ln), basket(2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14
  step#1  mm(<>,outward)  area=16.89 rise=3.44 twist=16.6
  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.DG19,A.DG18
  strand#4  U DNA glyco-bond=s- nts=2 GG A.DG13,A.DG14
  loop#1 type=lateral   strands=[#1,#2] nts=3 GTA A.DG3,A.DT4,A.DA5
  loop#2 type=diagonal  strands=[#2,#4] nts=5 GAGCG A.DG8,A.DA9,A.DG10,A.DC11,A.DG12
  loop#3 type=lateral   strands=[#4,#3] nts=3 AGA A.DA15,A.DG16,A.DA17

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