Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations

  • Carolyn L. Mazzitelli
  • Junmei Wang
  • Suncerae I. Smith
  • Jennifer S. Brodbelt


The relative gas-phase stabilities of seven quadruplex DNA structures, [d(TG4T)]4, [d(T2G3T)]4, [d(G4T4G4)]2, [d(T2AG3)2]2, d(T2AG3)4, d(T2G4)4, and d(G2T4)4, were investigated using molecular dynamics simulations and electrospray ionization mass spectrometry (ESI-MS). MD simulations revealed that the G-quadruplexes maintained their structures in the gas phase although the G-quartets were distorted to some degree and ammonium ions, retained by [d(TG4T)]4 and [d(T2G3T)]4, played a key role in stabilizing the tetrad structure. Energy-variable collisional activated dissociation was used to assess the relative stabilities of each quadruplex based on E1/2 values, and the resulting order of relative stabilities was found to be [d(TG4T)]4≫d(T2AG3)4∼d(T2G4)4 > [d(T2G3T)]4>[d(T2AG3)2]2∼d(G2T4)4∼[d(G4T4G4)]2. The stabilities from the E1/2 values generally paralleled the RMSD and relative free energies of the quadruplexes based on the MD energy analysis. One exception to the general agreement is [d(G4T4G4)]2, which had the lowest E1/2 value, but was determined to be the most stable quadruplex according to the free-energy analysis and ranked fourth based on the RMSD comparison. This discrepancy is attributed to differences in the fragmentation pathway of the quadruplex.

Supplementary material

13361_2011_181001760_MOESM1_ESM.doc (763 kb)
Supplementary material, approximately 781 KB.
13361_2011_181001760_MOESM2_ESM.doc (763 kb)
Supplementary material, approximately 781 KB.
13361_2011_181001760_MOESM3_ESM.doc (763 kb)
Supplementary material, approximately 781 KB.
13361_2011_181001760_MOESM4_ESM.doc (763 kb)
Supplementary material, approximately 781 KB.
13361_2011_181001760_MOESM5_ESM.doc (763 kb)
Supplementary material, approximately 781 KB.


  1. 1.
    Rezler, E. M.; Bearss, D. J.; Hurley, L. H. Telomeres and Telomerases as Drug Targets. Curr. Opin. Pharmacol. 2002, 2, 415–423.CrossRefGoogle Scholar
  2. 2.
    Bearss, D. J.; Hurley, L. H.; Von Hoff, D. D. Telomere Maintenance Mechanisms as a Target for Drug Development. Oncogene 2000, 19, 6632–6641.CrossRefGoogle Scholar
  3. 3.
    Rezler, E. M.; Bearss, D. J.; Hurley, L. H. Telomere inhibition and telomere disruption as processes for drug targeting. Annu. Rev. Pharmacol. Toxicol. 2003, 43, 359–379.CrossRefGoogle Scholar
  4. 4.
    Wellinger, R. J.; Sen, D. The DNA Structures at the Ends of Eukaryotic Chromosomes. Eur. J. Cancer 1997, 33, 735–749.CrossRefGoogle Scholar
  5. 5.
    Harley, C. B.; Futcher, A. B.; Greider, C. W. Telomeres Shorten During Aging of Human Fibroblasts. Nature 1990, 345, 458–460.CrossRefGoogle Scholar
  6. 6.
    Kim, N. W.; Piatyszek, M. A.; Prowse, K. R.; Harley, C. B.; West, M. D.; Ho, P. L. C.; Coviello, G. M.; Wright, W. E.; Weinrich, S. L.; Shay, J. W. Specific Association of Human Telomerase Activity with Immortal Cells and Cancer. Science 1994, 266, 2011–2015.CrossRefGoogle Scholar
  7. 7.
    Nakamura, T. M.; Morin, G. B.; Chapman, K. B.; Weinrich, S. L.; Andrews, W. H.; Lingner, J.; Harley, C. B.; Cech, T. R. Telomerase Catalytic Subunit Homologs from Fission Yeast and Human. Science 1997, 277, 955–959.CrossRefGoogle Scholar
  8. 8.
    Moyzis, R. K.; Buckingham, J. M.; Cram, L. S.; Dani, M.; Deaven, L. L.; Jones, M. D.; Meyne, J.; Ratliff, R. L.; Wu, J. R. A Highly Conserved Repetitive DNA Sequence, (TTAGGG)n, Present at the Telomeres of Human Chromosomes. Proc. Natl. Acad. Sci. U S A. 1988, 85, 6622–6626.CrossRefGoogle Scholar
  9. 9.
    Blackburn, E. H.; Gall, J. G. Tandemly Repeated Sequence at Termini of Extrachromosomal Ribosomal RNA Genes in Tetrahymena. J. Mol. Biol. 1978, 120, 33–53.CrossRefGoogle Scholar
  10. 10.
    Haider, S.; Parkinson, G. N.; Neidle, S. Crystal Structure of the Potassium Form of an Oxytricha nova G-quadruplex. J. Mol. Biol. 2002, 320, 189–200.CrossRefGoogle Scholar
  11. 11.
    Tohl, J.; Eimer, W. Interaction of a G-DNA Quadruplex with Mono- and Divalent Cations—A Force Field Calculation. Biophys. Chem. 1997, 67, 177–186.CrossRefGoogle Scholar
  12. 12.
    Kerwin, S. M. G-quadruplex DNA as a Target for Drug Design. Curr. Pharm. Des. 2000, 6, 441–471.CrossRefGoogle Scholar
  13. 13.
    Mergny, J. L.; Mailliet, P.; Lavelle, F.; Riou, J.. F.; Laoui, A.; Helene, C. The Development of Telomerase Inhibitors: The G-quartet Approach. Anticancer Drug Des. 1999, 14, 327–339.Google Scholar
  14. 14.
    Hurley, L. H.; Wheelhouse, R. T.; Sun, D.; Kerwin, S. M.; Salazar, M.; Fedoroff, O. Y.; Han, F. X.; Han, H. Y.; Izbicka, E.; Von Hoff, D. D. G-quadruplexes as Targets for Drug Design. Pharmacol. Ther. 2000, 85, 141–158.CrossRefGoogle Scholar
  15. 15.
    Han, H. Y.; Hurley, L. H. G-quadruplex DNA: A Potential Target for Anticancer Drug Design. Trends Pharmacol. Sci. 2000, 21, 136–142.CrossRefGoogle Scholar
  16. 16.
    David, W. M.; Brodbelt, J.; Kerwin, S. M.; Thomas, P. W. Investigation of Quadruplex Oligonucleotide-Drug Interactions by Electrospray Ionization Mass Spectrometry. Anal. Chem. 2002, 74, 2029–2033.CrossRefGoogle Scholar
  17. 17.
    Mazzitelli, C. L.; Kern, J. T.; Rodriguez, M.; Brodbelt, J. S.; Kerwin, S. M. Evaluation of Binding of Perylene Diimide and Benzannulated Perylene Diimide Ligands to DNA by Electrospray Ionization Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2006, 17, 593–604.CrossRefGoogle Scholar
  18. 18.
    Baker, E. S.; Lee, J. T.; Sessler, J. L.; Bowers, M. T. Cyclo[n]pyrroles: Size and Site-Specific Binding to G-quadruplexes. J. Am. Chem. Soc. 2006, 128, 2641–2648.CrossRefGoogle Scholar
  19. 19.
    Rosu, F.; De Pauw, E.; Guittat, L.; Alberti, P.; Lacroix, L.; Mailliet, P.; Riou, J. F.; Mergny, J. L. Selective Interaction of Ethidium Derivatives with Quadruplexes: An Equilibrium Dialysis and Electrospray Ionization Mass Spectrometry Analysis. Biochemistry 2003, 42, 10361–10371.CrossRefGoogle Scholar
  20. 20.
    Guittat, L.; Alberti, P.; Rosu, F.; Van Miert, S.; Thetiot, E.; Pieters, L.; Gabelica, V.; De Pauw, E.; Ottaviani, A.; Riou, J. F. Interactions of Cryptolepine and Neocryptolepine with Unusual DNA Structures. Biochimie 2005, 85, 535–547.CrossRefGoogle Scholar
  21. 21.
    Guittat, L.; De Cian, A.; Rosu, F.; Gabelica, V.; De Pauw, E.; Delfourne, E.; Mergny, J. L. Ascididemin and Meridine stabilize G-quadruplexes and Inhibit Telomerase in vitro. Biochim. Biophys. Acta 2005, 1724, 375–384.CrossRefGoogle Scholar
  22. 22.
    Carrasco, C.; Rosu, F.; Gabelica, V.; Houssier, C.; De Pauw, E.; Garbay-Jaureguiberry, C.; Roques, B.; Wilson, W. D.; Chaires, J. B.; Waring, M. J.; Bailly, C. Tight Binding of the Antitumor Drug Ditercalinium to Quadruplex DNA. Chem. Biochem. 2002, 3, 1235–1241.Google Scholar
  23. 23.
    Rosu, F.; Gabelica, V.; Shin-ya, K.; De Pauw, E. Telomestatin-Induced Stabilization of the Human Telomeric DNA Quadruplex Monitored by Electrospray Mass Spectrometry. Chem. Commun. 2003, 21, 2702–2703.CrossRefGoogle Scholar
  24. 24.
    Gabelica, V.; Shammel-Baker, E.; Teulade-Fichou, M. P.; De Pauw, E.; Bowers, M. T. Stabilization and Structure of Telomeric and c-myc Region Intramolecular G-quadruplexes: The Role of Central Cations and Small Planar Ligands. J. Am. Chem. Soc. 2007, 129, 895–904.CrossRefGoogle Scholar
  25. 25.
    Gidden, J.; Ferzoco, A.; Shammel-Baker, E.; Bowers, M. T. Duplex Formation and the Onset of Helicity in Poly d(CG) (n)Oligonucleotides in a Solvent-Free Environment. J. Am. Chem. Soc. 2004, 126, 15132–15140.CrossRefGoogle Scholar
  26. 26.
    Gabelica, V.; De Pauw, E. Collision-Induced Dissociation of 16-mer DNA Duplexes with Various Sequences: Evidence for Conservation of the Double Helix Conformation in the Gas Phase. Int. J. Mass Spectrom. 2002, 219, 151–159.CrossRefGoogle Scholar
  27. 27.
    Pan, S.; Sun, X. J.; Lee, J. K. Stability of Complementary and Mismatched DNA Duplexes: Comparison and Contrast in Gas Versus Solution Phases. Int. J. Mass Spectrom. 2006, 253, 238–248.CrossRefGoogle Scholar
  28. 28.
    Guo, X. H.; Bruist, M. F.; Davis, D. L.; Bentzley, C. M. Secondary Structural Characterization of Oligonucleotide Strands Using Electrospray Ionization Mass Spectrometry. Nucleic Acids Res. 2005, 33, 3659–3666.CrossRefGoogle Scholar
  29. 29.
    Guo, X. H.; Liu, Z. Q.; Liu, S. Y.; Bentzley, C. M.; Bruist, M. F. Structural Features of the L-Argininamide-Binding DNA Aptamer Studied with ESI-FTMS. Anal. Chem. 2006, 78, 7259–7266.CrossRefGoogle Scholar
  30. 30.
    Wan, K. X.; Gross, M. L.; Shibue, T. Gas-Phase Stability of Double-Stranded Oligodeoxynucleotides and Their Noncovalent Complexes with DNA-Binding Drugs as Revealed by Collisional Activation in an Ion Trap. J. Am. Soc. Mass Spectrom. 2000, 11, 450–457.CrossRefGoogle Scholar
  31. 31.
    Gabelica, V.; De Pauw, E. Comparison Between Solution-Phase Stability and Gas-Phase Kinetic Stability of Oligodeoxynucleotide Duplexes. J. Mass Spectrom. 2001, 36, 397–402.CrossRefGoogle Scholar
  32. 32.
    Rosu, F.; Gabelica, V.; Houssier, C.; Colson, P.; De Pauw, E. Triplex and Quadruplex DNA Structures Studied by Electrospray Mass Spectrometry. Rapid Commun. Mass Spectrom. 2002, 16, 1729–1736.CrossRefGoogle Scholar
  33. 33.
    Baker, E. S.; Bernstein, S. L.; Gabelica, V.; De Pauw, E.; Bowers, M. T. G-quadruplexes in Telomeric Repeats are Conserved in a Solvent-Free Environment. Int. J. Mass Spectrom. 2006, 253, 225–237.CrossRefGoogle Scholar
  34. 34.
    Rueda, M.; Kalko, S. G.; Luque, F. J.; Orozco, M. The Structure and Dynamics of DNA in the Gas Phase. J. Am. Chem. Soc. 2003, 125, 8007–8014.CrossRefGoogle Scholar
  35. 35.
    Rueda, M.; Luque, F. J.; Orozco, M. Nature of Minor-Groove Binders-DNA Complexes in the Gas Phase. J. Am. Chem. Soc. 2005, 127, 11690–11698.CrossRefGoogle Scholar
  36. 36.
    Rueda, M.; Luque, F. J.; Orozco, M. G-quadruplexes Can Maintain Their Structure in the Gas Phase. J. Am. Chem. Soc. 2006, 128, 3608–3619.CrossRefGoogle Scholar
  37. 37.
    Gros, J.; Rosu, F.; Amrane, S.; De Cian, A.; Gabelica, V.; Lacroix, L.; Mergny, J.-L. Guanines are a Quartet’s Best Friend: Impact of Base Substitutions on the Kinetics and Stability of Tetramolecular Quadruplexes. Nucleic Acids Res. 2007, 35, 3064–3075.CrossRefGoogle Scholar
  38. 38.
    Kerwin, S. M.; Chen, G.; Kern, J. T.; Thomas, P. W. Perylene Diimide G-quadruplex DNA Binding Selectivity is Mediated by Ligand Aggregation. Bioorg. Med. Chem. Lett. 2002, 12, 447–450.CrossRefGoogle Scholar
  39. 39.
    Caceres, C.; Wright, G.; Gouyette, C.; Parkinson, G.; Subirana, J. A. A Thymine Tetrad in d(TGGGGT) Quadruplexes Stabilized with Tl+/Na+ Ions. Nucleic Acids Res. 2004, 32, 1097–1102.CrossRefGoogle Scholar
  40. 40.
    Horvath, M. P.; Schultz, S. C. DNA G-quartets in a 1.86 Angstrom Resolution Structure of an Oxytricha nova Telomeric Protein-DNA Complex. J. Mol. Biol. 2001, 310, 367–377.CrossRefGoogle Scholar
  41. 41.
    Muller, S.; Diederichs, K.; Breed, J.; Kissmehl, R.; Hauser, K.; Plattner, H.; Welte, W. Crystal Structure Analysis of the Exocytosis-Sensitive Phosphoprotein, pp63/Parafusin (Phosphoglucomutase), from Paramecium Reveals Significant Conformational Variability. J. Mol. Biol. 2002, 315, 141–153.CrossRefGoogle Scholar
  42. 42.
    Wang, Y.; Patel, D. J. Solution Structure of the Human Telomeric Repeat d[(AG3T2AG3)3] G-Tetraplex. Structure 1993, 1, 263–282.CrossRefGoogle Scholar
  43. 43.
    Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Duke, R. E.; Crowley, M.; Brozell, S.; Luo, R.; Tsui, V.; Gohlke, H.; Morgan, J.; Hornak, V.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8, University of California, San Francisco, 2005.Google Scholar
  44. 44.
    Wang, J. M.; Cieplak, P.; Kollman, P. A. How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?. J. Comput. Chem. 2000, 21, 1049–1074.CrossRefGoogle Scholar
  45. 45.
    Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81, 3684–3690.CrossRefGoogle Scholar
  46. 46.
    Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of Cartesian Equations of Motion of a System with Constraints-Molecular-Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23, 327–341.CrossRefGoogle Scholar
  47. 47.
    Gabb, H. A.; Sanghani, S. R.; Robert, C. H.; Prévost, C. Finding and Visualizing Nucleic Acid Base Stacking. J. Mol. Graphics 1996, 14, 6–11.CrossRefGoogle Scholar
  48. 48.
    Keller, K. M.; Zhang, J. M.; Oehlers, L.; Brodbelt, J. S. Influence of Initial Charge State on Fragmentation Patterns for Noncovalent Drug/DNA Duplex Complexes. J. Mass Spectrom. 2005, 40, 1362–1371.CrossRefGoogle Scholar
  49. 49.
    Gabelica, V.; De Pauw, E. Comparison of the Collision-Induced Dissociation of Duplex DNA at Different Collision Regimes: Evidence for a Multistep Dissociation Mechanism. J. Am. Soc. Mass Spectrom. 2002, 13, 91–98.CrossRefGoogle Scholar
  50. 50.
    Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of a, g conformers. Biophys. J. 2007, 92, 3817–3829.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2007

Authors and Affiliations

  • Carolyn L. Mazzitelli
    • 1
  • Junmei Wang
    • 2
  • Suncerae I. Smith
    • 1
  • Jennifer S. Brodbelt
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of Texas at AustinAustinUSA
  2. 2.Encysive Pharmaceuticals Inc.HoustonUSA

Personalised recommendations