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Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.

Martín-Pintado N, Yahyaee-Anzahaee M, Deleavey GF, Portella G, Orozco M, Damha MJ, González C
J Am Chem Soc 135 5344-7 (2013)
Cited: 29 times
EuropePMC logo PMID: 23521511

Abstract

Human telomeric DNA quadruplexes can adopt different conformations in solution. We have found that arabinose, 2'F-arabinose, and ribose substitutions stabilize the propeller parallel G-quadruplex form over competing conformers, allowing NMR structural determination of this particularly significant nucleic acid structure. 2'F-arabinose substitution provides the greatest stabilization as a result of electrostatic (F-CH---O4') and pseudo-hydrogen-bond (F---H8) stabilizing interactions. In contrast, 2'F-rG substitution provokes a dramatic destabilization of the quadruplex structure due to unfavorable electrostatic repulsion between the phosphate and the 2'-F.

Reviews citing this publication (2)

  1. Synthesis and biological applications of fluoro-modified nucleic acids. Guo F, Li Q, Zhou C. Org Biomol Chem 15 9552-9565 (2017)
  2. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? Sagi J. J Nucleic Acids 2017 1641845 (2017)

Articles citing this publication (27)

  1. Parmbsc1: a refined force field for DNA simulations. Ivani I, Dans PD, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí JL, González C, Vendruscolo M, Laughton CA, Harris SA, Case DA, Orozco M. Nat Methods 13 55-58 (2016)
  2. Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations. Dalvit C, Invernizzi C, Vulpetti A. Chemistry 20 11058-11068 (2014)
  3. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Biochemistry (Mosc) 81 1602-1649 (2016)
  4. NMR structure of a G-quadruplex formed by four d(G4C2) repeats: insights into structural polymorphism. Brcic J, Plavec J. Nucleic Acids Res 46 11605-11617 (2018)
  5. Stabilization of i-motif structures by 2'-β-fluorination of DNA. Assi HA, Harkness RW, Martin-Pintado N, Wilds CJ, Campos-Olivas R, Mittermaier AK, González C, Damha MJ. Nucleic Acids Res 44 4998-5009 (2016)
  6. Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G·G·X·O tetrad. Cheong VV, Heddi B, Lech CJ, Phan AT. Nucleic Acids Res 43 10506-10514 (2015)
  7. Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays. Lietard J, Abou Assi H, Gómez-Pinto I, González C, Somoza MM, Damha MJ. Nucleic Acids Res 45 1619-1632 (2017)
  8. PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs. Wang KB, Dickerhoff J, Wu G, Yang D. J Am Chem Soc 142 5204-5211 (2020)
  9. Photoswitching the cytotoxic properties of platinum(II) compounds. Presa A, Brissos RF, Caballero AB, Borilovic I, Korrodi-Gregório L, Pérez-Tomás R, Roubeau O, Gamez P. Angew Chem Int Ed Engl 54 4561-4565 (2015)
  10. Backbone FC-H···O hydrogen bonds in 2'F-substituted nucleic acids. Martin-Pintado N, Deleavey GF, Portella G, Campos-Olivas R, Orozco M, Damha MJ, González C. Angew Chem Int Ed Engl 52 12065-12068 (2013)
  11. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening. Dalvit C, Vulpetti A. Chemistry 22 7592-7601 (2016)
  12. Sugar-modified G-quadruplexes: effects of LNA-, 2'F-RNA- and 2'F-ANA-guanosine chemistries on G-quadruplex structure and stability. Li Z, Lech CJ, Phan AT. Nucleic Acids Res 42 4068-4079 (2014)
  13. Inverting the G-Tetrad Polarity of a G-Quadruplex by Using Xanthine and 8-Oxoguanine. Cheong VV, Lech CJ, Heddi B, Phan AT. Angew Chem Int Ed Engl 55 160-163 (2016)
  14. Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. Aviñó A, Portella G, Ferreira R, Gargallo R, Mazzini S, Gabelica V, Orozco M, Eritja R. FEBS J 281 1085-1099 (2014)
  15. 2'-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA. Abou Assi H, El-Khoury R, González C, Damha MJ. Nucleic Acids Res 45 11535-11546 (2017)
  16. Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway. Dickerhoff J, Weisz K. Chembiochem 19 927-930 (2018)
  17. Influence of Alcohol β-Fluorination on Hydrogen-Bond Acidity of Conformationally Flexible Substrates. Graton J, Compain G, Besseau F, Bogdan E, Watts JM, Mtashobya L, Wang Z, Weymouth-Wilson A, Galland N, Le Questel JY, Linclau B. Chemistry 23 2811-2819 (2017)
  18. The Folding Landscapes of Human Telomeric RNA and DNA G-Quadruplexes are Markedly Different. Müller D, Bessi I, Richter C, Schwalbe H. Angew Chem Int Ed Engl 60 10895-10901 (2021)
  19. Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops. Haase L, Dickerhoff J, Weisz K. Chemistry 26 524-533 (2020)
  20. Sugar-Edge Interactions in a DNA-RNA G-Quadruplex: Evidence of Sequential C-H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding. Dickerhoff J, Appel B, Müller S, Weisz K. Angew Chem Int Ed Engl 55 15162-15165 (2016)
  21. Synthesis and Antisense Properties of 2'β-F-Arabinouridine Modified Oligonucleotides with 4'-C-OMe Substituent. He XY, Wang J, Lu DD, Wang SQ. Molecules 23 E2374 (2018)
  22. Studying DNA G-Quadruplex Aptamer by 19F NMR. Ishizuka T, Yamashita A, Asada Y, Xu Y. ACS Omega 2 8843-8848 (2017)
  23. α-2'-Deoxyguanosine can switch DNA G-quadruplex topologies from antiparallel to parallel. Filitcheva J, Edwards PJB, Norris GE, Filichev VV. Org Biomol Chem 17 4031-4042 (2019)
  24. i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. El-Khoury R, Macaluso V, Hennecker C, Mittermaier AK, Orozco M, González C, Garavís M, Damha MJ. Commun Chem 6 31 (2023)
  25. Insights into protein-carbohydrate recognition: A novel binding mechanism for CBM family 43. Mompeán M, Villalba M, Bruix M, Zamora-Carreras H. J Mol Graph Model 73 152-156 (2017)
  26. Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes. Karg B, Weisz K. Chemistry 24 10246-10252 (2018)
  27. O4 -Alkylated-2-Deoxyuridine Repair by O6 -Alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification. Sacre L, O'Flaherty DK, Archambault P, Copp W, Peslherbe GH, Muchall HM, Wilds CJ. Chembiochem 19 575-582 (2018)


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