Biomolecular NMR Assignments

, Volume 12, Issue 1, pp 123–127 | Cite as

1H, 13C, and 15N chemical shift assignments of a G-quadruplex forming sequence within the KRAS proto-oncogene promoter region

  • Julien Marquevielle
  • M. V. Vasantha Kumar
  • Jean-Louis Mergny
  • Gilmar F. Salgado
Article
  • 163 Downloads

Abstract

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.

Keywords

KRAS oncogene Promoter region G-quadruplex Structure resonance assignments 

Notes

Acknowledgements

This work was possible thanks to financial supports from the IR-RMN THC Fr3050 CNRS facilities from Bordeaux (UMS3033/US001) and Gif-sur-Yvette. This work was also supported by iNEXT, Project Number 653706, funded by the Horizon 2020 from the European Union (Brno; Czech Republic). We are particularly grateful to R. Fiala from CEITEC for his help and his advices. Funds for conducting the research were also available from La Ligue contre le Cancer which we gratefully acknowledge. We also thank B. Vialet for synthesis of isotopically labeled oligonucleotides and our team for useful discussions.

References

  1. Adrian M, Heddi B, Phan AT (2012) NMR spectroscopy of G-quadruplexes. Methods 57, 11–24CrossRefGoogle Scholar
  2. Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A et al (2004) “The cosmic (catalogue of somatic mutations in cancer) database and website”. Br J Cancer 91(2):355–358CrossRefGoogle Scholar
  3. Bedrat A, Lacroix L, Mergny JL (2016) “Re-evaluation of g-quadruplex propensity with G4 hunter”. Nucleic Acids Res 44(4):1746–1759CrossRefGoogle Scholar
  4. Bochman ML, Paeschke K, Zakian VA (2012) “DNA secondary structures: stability and function of G-quadruplex structures”. Nat Rev Genet 13(11):770–780CrossRefGoogle Scholar
  5. Brito H, Martins AC, Lavrado J, Mendes E, Francisco AP, Santos SA, Ohnmacht SA et al (2015) “Targeting kras oncogene in colon cancer cells with 7-carboxylate indolo [3,2-B] quinoline tri-alkylamine derivatives”. PLoS ONE 10(5):e0126891CrossRefGoogle Scholar
  6. Eddy J, Maizels N (2006) “Gene function correlates with potential for G4 DNA formation in the human genome”. Nucleic Acids Res 34(14):3887–3896CrossRefGoogle Scholar
  7. Hansel-Hertsch R, Di Antonio M, Balasubramanian S (2017) “DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential”. Nat Rev Mol Cell Biol 18(5):279 –284CrossRefGoogle Scholar
  8. Henderson A, Wu Y, Huang YC, Chavez EA, Platt J, Johnson FB, Brosh RM Jr, Sen D, Lansdorp (2013) “Detection of G-quadruplex DNA in mammalian cells”. Nucleic Acids Res 42(2):860–869CrossRefGoogle Scholar
  9. Huppert JL, Balasubramanian S (2007) “G-quadruplexes in promoters throughout the human genome”. Nucleic Acids Res 35(2):406–413CrossRefGoogle Scholar
  10. 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(19):8082–8091CrossRefGoogle Scholar
  11. Largy E, Mergny JL, Gabelica V (2016) “Role of alkali metal ions in G-quadruplex nucleic acid structure and stability.” Met Ions Life Sci 16:203–258CrossRefGoogle Scholar
  12. Lavrado J, Brito H, Borralho PM, Ohnmacht SA, Kim NS, Leitao C, Pisco S et al (2015) “Kras oncogene repression in colon cancer cell lines by G-quadruplex binding indolo [3,2-C] quinolines”. Sci Rep 5:9696CrossRefGoogle Scholar
  13. McCormick F (2015) “Kras as a therapeutic target”. Clin Cancer Res 21(8):1797–1801CrossRefGoogle Scholar
  14. Qin Y, Hurley LH (2008) “Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions.” Biochimie 90(8):1149–1171CrossRefGoogle Scholar
  15. Sen D, Gilbert W (1988) “Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and Its implications for meiosis”. Nature 334(6180):364–366ADSCrossRefGoogle Scholar
  16. Stegle O, Payet L, Mergny JL, MacKay DJ, Leon JH (2009) “Predicting and understanding the stability of G-quadruplexes”. Bioinformatics 25(12):i374–i382CrossRefGoogle Scholar
  17. Wlodarczyk A, Grzybowski P, Patkowski A, Dobek A (2005) Effect of ions on the polymorphism, effective charge, and stability of human telomeric DNA. Photon correlation spectroscopy and circular dichroism studies. J Phys Chem B 109(8):3594–3605CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  1. 1.ARNA Laboratory, European Institute of Chemistry and Biology (IECB)Université de Bordeaux, Inserm U1212 – CNRS UMR 5320PessacFrance

Personalised recommendations