DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 5i2v
Class: DNA
Method: NMR
Summary: NMR structure of a new g-quadruplex forming sequence within the kras proto-oncogene promoter region
Reference: Kerkour A, Marquevielle J, Ivashchenko S, Yatsunyk LA, Mergny JL, Salgado GF (2017): "High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation." J. Biol. Chem., 292, 8082-8091. doi: 10.1074/jbc.M117.781906.
Abstract: Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element located upstream of the major transcription start site. The KRAS nuclease-hypersensitive element (NHE) region contains a G-rich element (22RT; 5'-AGGGCGGTGTGGGAATAGGGAA-3') and encompasses a Myc-associated zinc finger-binding site that regulates KRAS transcription. The NEH region therefore has been proposed as a target for new drugs that control KRAS transcription, which requires detailed knowledge of the NHE structure. In this study, we report a high-resolution NMR structure of the G-rich element within the KRAS NHE. We found that the G-rich element forms a parallel structure with three G-quartets connected by a four-nucleotide loop and two short one-nucleotide double-chain reversal loops. In addition, a thymine bulge is found between G8 and G9. The loops of different lengths and the presence of a bulge between the G-quartets are structural elements that potentially can be targeted by small chemical ligands that would further stabilize the structure and interfere or block transcriptional regulators such as Myc-associated zinc finger from accessing their binding sites on the KRAS promoter. In conclusion, our work suggests a possible new route for the development of anticancer agents that could suppress KRAS expression.
G4 notes: 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)

Cartoon-block schematics in six views (download the tarball)

List of 3 G-tetrads

 1 glyco-bond=---- sugar=---. groove=---- planarity=0.172 type=other  O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2 glyco-bond=---- sugar=-3-- groove=---- planarity=0.253 type=other  O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.260 type=other  O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20

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-tetrads, INTRA-molecular, with 1 stem

	1 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 step#1 pm(>>,forward) area=10.75 rise=3.42 twist=27.8 step#2 pm(>>,forward) area=11.91 rise=3.44 twist=30.0 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG6,A.DG7,A.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG18,A.DG19,A.DG20 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 step#1 pm(>>,forward) area=10.75 rise=3.42 twist=27.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 step#2 pm(>>,forward) area=11.91 rise=3.44 twist=30.0 Download PDB file Interactive view in 3Dmol.js

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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)

 1  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2  glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
  step#1  pm(>>,forward)  area=10.75 rise=3.42 twist=27.8
  step#2  pm(>>,forward)  area=11.91 rise=3.44 twist=30.0
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2* U DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG6,A.DG7,A.DG9 bulged-nts=1 T A.DT8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG18,A.DG19,A.DG20
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC5
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT10
  loop#3 type=propeller strands=[#3,#4] nts=4 AATA A.DA14,A.DA15,A.DT16,A.DA17

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Interactive view in 3Dmol.js

DSSR-enabled G4 identification/annotation: PDB entry 5i2v