Addition of bases to the 5′-end of human telomeric DNA: Influences on thermal stability and energetics of unfolding

Molecules

Volumn 19, Issue 2, 2014, Pages 2286-2298

  Hayden, Katherine L ^a   Graves, David E ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

Circular dichroism (CD); Differential scanning calorimetry (DSC); G quadruplex; Osmolyte perturbation; Pressure perturbation calorimetry (PPC); Stability; Telomere

Indexed keywords

DNA; GUANINE; GUANINE QUADRUPLEX;

ARTICLE; CHEMISTRY; CHROMOSOME; CIRCULAR DICHROISM; CONFORMATION; GENETICS; HUMAN; TANDEM REPEAT; TELOMERE; THERMODYNAMICS;

CHROMOSOMES; CIRCULAR DICHROISM; DNA; G-QUADRUPLEXES; GUANINE; HUMANS; NUCLEIC ACID CONFORMATION; TANDEM REPEAT SEQUENCES; TELOMERE; THERMODYNAMICS;

EID: 84894618623     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules19022286     Document Type: Article

References (29)

1. Petraccone, L.; Spink, C.; Trent, J.O.; Garbett, N.C.; Mekmaysy, C.S.; Giancola, C.; Chaires, J.B. Structure and stability of higher-order human telomeric quadruplexes. J. Am. Chem. Soc. 2011, 133, 20951-20961.
2. Parkinson, G.N.; Lee, M.P.; Neidle, S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 2002, 417, 876-880.
3. Luu, K.N.; Phan, A.T.; Kuryavyi, V.; Lacroix, L.; Patel, D.J. Structure of the human telomere in K+ solution: An intramolecular (3 + 1) G-quadruplex scaffold. J. Am. Chem. Soc. 2006, 128, 9963-9970.
4. Lim, K.W.; Amrane, S.; Bouaziz, S.; Xu, W.; Mu, Y.; Patel, D.J.; Luu, K.N.; Phan, A.T. Structure of the human telomere in K+ solution: A stable basket-type G-quadruplex with only two G-tetrad layers. J. Am. Chem. Soc. 2009, 131, 4301-4309.
5. Gray, R.D.; Chaires, J.B. Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures. Nucl. Acid. Res. 2008, 36, 4191-4203.
6. Gray, R.D.; Li, J.; Chaires, J.B. Energetics and kinetics of a conformational switch in G-quadruplex DNA. J. Phys. Chem. B 2009, 113, 2676-2683.
7. Wang, Y.; Patel, D.J. Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1993, 1, 263-282.
8. Wang, Y.; Patel, D.J. Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex. J. Mol. Biol. 1995, 251, 76-94.
9. Gray, D.M.; Wen, J.D.; Gray, C.W.; Repges, R.; Repges, C.; Raabe, G.; Fleischhauer, J. Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities. Chirality 2008, 20, 431-440.
10. Gottarelli, G.; Lena, S.; Masiero, S.; Pieraccini, S.; Spada, G.P. The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: An overview. Chirality 2008, 20, 471-485.
11. Karsisiotis, A.I.; Hessari, N.M.; Novellino, E.; Spada, G.P.; Randazzo, A.; Webba da Silva, M. Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism. Angew. Chem. 2011, 50, 10645-10648.
12. Parsegian, V.A.; Rand, R.P.; Rau, D.C. Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives. Proc. Natl. Acad. Sci. USA 2000, 97, 3987-3992.
13. Spink, C.H.; Garbett, N.; Chaires, J.B. Enthalpies of DNA melting in the presence of osmolytes. Biophys. Chem. 2007, 126, 176-185.
14. Qu, X.; Chaires, J.B. Hydration changes for DNA intercalation reactions. J. Am. Chem. Soc. 2001, 123, 1-7.
15. Kiser, J.R.; Monk, R.W.; Smalls, R.L.; Petty, J.T. Hydration changes in the association of Hoechst 33258 with DNA. Biochemistry 2005, 44, 16988-16997.
16. Nakano, S.; Yamaguchi, D.; Tateishi-Karimata, H.; Miyoshi, D.; Sugimoto, N. Hydration changes upon DNA folding studied by osmotic stress experiments. Biophys. J. 2012, 102, 2808-2817.
17. Cantor, C.R.; Warshaw, M.M.; Shapiro, H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 1970, 9, 1059-1077.
18. Olsen, C.M.; Gmeiner, W.H.; Marky, L.A. Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking. J. Phys. Chem. B 2006, 110, 6962-6969.
19. Miyoshi, D.; Karimata, H.; Sugimoto, N. Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. J. Am. Chem. Soc. 2006, 128, 7957-7963.
20. Miller, M.C.; Buscaglia, R.; Chaires, J.B.; Lane, A.N.; Trent, J.O. Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 3' sequence of d(AG3(TTAG3)3). J. Am. Chem. Soc.2010, 132, 17105-17107.
21. Spink, C.H.; Chaires, J.B. Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA. Biochemistry 1999, 38, 496-508.
22. Lin, L.N.; Brandts, J.F.; Brandts, J.M.; Plotnikov, V. Determination of the volumetric properties of proteins and other solutes using pressure perturbation calorimetry. Anal. Biochem. 2002, 302, 144-160.
23. Fan, H.Y.; Shek, Y.L.; Amiri, A.; Dubins, D.N.; Heerklotz, H.; Macgregor, R.B., Jr.; Chalikian, T.V. Volumetric characterization of sodium-induced G-quadruplex formation. J. Am. Chem. Soc. 2011, 133, 4518-4526.
24. Chalikian, T.V.; Breslauer, K.J. Volumetric properties of nucleic acids. Biopolymers 1998, 48, 264-280.
25. Schweiker, K.L.; Makhatadze, G.I. Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins. Meth. Enzymol. 2009, 466, 527-547.
26. Wu, J.Q.; Macgregor, R.B., Jr. Pressure dependence of the melting temperature of dA·dT polymers. Biochemistry 1993, 32, 12531-12537.
27. Case, D.A.; Darden, T.A.; Cheatham, T.E.; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Walker, R.C.; Zhang, W.; Merz, K.M.; et al. AMBER 12; University of California: San Francisco, CA, USA, 2012.
28. Freier, S.M.; Alkema, D.; Sinclair, A.; Neilson, T.; Turner, D.H. Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry 1985, 24, 4533-4539.
29. Freier, S.M.; Albergo, D.D.; Turner, D.H. Solvent effects on the dynamics of (dG-dC)3. Biopolymers 1983, 22, 1107-1131.