DSSR-derived G-quadruplex features in PDB entry 6t51
Poster "DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB" presented at the RNA2020 online meeting
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- NMR structure of kras22rt G-quadruplex forming within kras promoter region at physological temperature
- Marquevielle, J., Kumar, M.V.V., Mergny, J.L., Salgado, G.F.: (2018) "1H,13C, and15N chemical shift assignments of a G-quadruplex forming sequence within the KRAS proto-oncogene promoter region." Biomol.Nmr Assign., 12, 123-127.
- Single stranded guanine rich DNA (or RNA) sequences adopt noncanonical secondary structures called G-quadruplexes (G4). Functionally, quadruplexes control gene transcription and regulate activities such as replication, gene recombination or alternative splicing. Hence they are potential targets for cancer, neuronal, and viral related diseases. KRAS is one of the most mutated oncogenes in the genome of cancer cells and contains a nuclease hypersensitive element (NHE) sequence capable of forming G-quadruplexes via its six runs of guanines. In our work, we are interested in the NMR structure of the major G4 scaffold formed in the KRAS NHE region with a mutated sequence of 22 residues. Here, we report 1H, 13C and 15N chemical shift assignments the G4 formed within KRAS22RT sequence.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.186 type=other nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- groove=---- planarity=0.252 type=other nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- groove=---- planarity=0.163 type=other nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20