Summary information and primary citation

PDB-id
6ftu
Class
DNA
Method
X-ray (2.95 Å)
Summary
Structure of a quadruplex forming sequence from d. discoideum
Reference
Guedin A, Lin LY, Armane S, Lacroix L, Mergny JL, Thore S, Yatsunyk LA (2018): "Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome." Nucleic Acids Res., 46, 5297-5307. doi: 10.1093/nar/gky290.
Abstract
Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UUDD, anti-parallel:basket2, 2+2, 4(+LnD-Lw)

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List of 4 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.227 type=other  N+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG26,1:A.DG10
 2 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.140 type=planar N- nts=4 GGGG 1:A.DG2,1:A.DG16,1:A.DG25,1:A.DG9
 3 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.143 type=planar N+ nts=4 GGGG 1:A.DG3,1:A.DG17,1:A.DG24,1:A.DG8
 4 glyco-bond=--ss sugar=3--- groove=-w-n planarity=0.207 type=other  N- nts=4 GGGG 1:A.DG4,1:A.DG18,1:A.DG23,1:A.DG7

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, 4 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG26,1:A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG2,1:A.DG16,1:A.DG25,1:A.DG9
 3  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG3,1:A.DG17,1:A.DG24,1:A.DG8
 4  glyco-bond=--ss sugar=3--- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG4,1:A.DG18,1:A.DG23,1:A.DG7
  step#1  mm(<>,outward)  area=14.53 rise=3.48 twist=18.1
  step#2  pp(><,inward)   area=18.75 rise=3.50 twist=37.0
  step#3  mm(<>,outward)  area=15.07 rise=3.43 twist=17.5
  strand#1 DNA glyco-bond=s-s- sugar=---3 nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG15,1:A.DG16,1:A.DG17,1:A.DG18
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG26,1:A.DG25,1:A.DG24,1:A.DG23
  strand#4 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG10,1:A.DG9,1:A.DG8,1:A.DG7

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3 stacking diagrams 
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG26,1:A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG2,1:A.DG16,1:A.DG25,1:A.DG9
  step#1  mm(<>,outward)  area=14.53 rise=3.48 twist=18.1

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 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG2,1:A.DG16,1:A.DG25,1:A.DG9
 3  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG3,1:A.DG17,1:A.DG24,1:A.DG8
  step#2  pp(><,inward)   area=18.75 rise=3.50 twist=37.0

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 3  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG3,1:A.DG17,1:A.DG24,1:A.DG8
 4  glyco-bond=--ss sugar=3--- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG4,1:A.DG18,1:A.DG23,1:A.DG7
  step#3  mm(<>,outward)  area=15.07 rise=3.43 twist=17.5

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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, 4 G-tetrads, 3 loops, INTRA-molecular, UUDD, anti-parallel:basket2, 2+2, 4(+LnD-Lw)
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG26,1:A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG2,1:A.DG16,1:A.DG25,1:A.DG9
 3  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG 1:A.DG3,1:A.DG17,1:A.DG24,1:A.DG8
 4  glyco-bond=--ss sugar=3--- groove=-w-n WC-->Major N- nts=4 GGGG 1:A.DG4,1:A.DG18,1:A.DG23,1:A.DG7
  step#1  mm(<>,outward)  area=14.53 rise=3.48 twist=18.1
  step#2  pp(><,inward)   area=18.75 rise=3.50 twist=37.0
  step#3  mm(<>,outward)  area=15.07 rise=3.43 twist=17.5
  strand#1  U DNA glyco-bond=s-s- sugar=---3 nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG15,1:A.DG16,1:A.DG17,1:A.DG18
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG26,1:A.DG25,1:A.DG24,1:A.DG23
  strand#4  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG10,1:A.DG9,1:A.DG8,1:A.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=2 GA 1:A.DG5,1:A.DA6
  loop#2 type=diagonal  strands=[#4,#2] nts=4 TACA 1:A.DT11,1:A.DA12,1:A.DC13,1:A.DA14
  loop#3 type=lateral   strands=[#2,#3] nts=4 TACA 1:A.DT19,1:A.DA20,1:A.DC21,1:A.DA22

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