Determination of nucleic acid hydration using osmotic stress

Current Protocols in Nucleic Acid Chemistry

Volumn , Issue SUPPL.43, 2010, Pages

  Rozners, Eriks ^a  

^a BINGHAMTON UNIVERSITY   (United States)

Author keywords

Hydration; Nucleic acids; Osmotic stress; Thermodynamics

Indexed keywords

BIOPOLYMER; NUCLEIC ACID; SINGLE STRANDED DNA; WATER;

ARTICLE; CHEMICAL MODIFICATION; CONFORMATION; DNA HELIX; HYDRATION; MELTING POINT; MOLECULAR MODEL; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; OSMOTIC STRESS; PRIORITY JOURNAL; TEMPERATURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 79953285351     PISSN: 19349270     EISSN: 19349289     Source Type: Journal    
DOI: 10.1002/0471142700.nc0714s43     Document Type: Article

References (17)

1. Bewington, P.R. and Robinson, D.K. 1992. Data reduction and error analysis for the physical sciences. McGraw Hill, New York.
2. Breslauer, K.J. 1995. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods Enzymol. 259:221-242.
3. Courtenay, E.S., Capp, M.W., Anderson, C.F., and Record, M.T. Jr. 2000. Vapor pressure osmometry studies of osmolyte-protein interactions: Implications for the action of osmoprotectants in vivo and for the interpretation of "Osmotic Stress" experiments in vitro. Biochemistry 39:4455-4471.
4. Hwang, G.T., Hari, Y., and Romesberg, F.E. 2009. The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation. Nucleic Acids Res. 37:4757-4763.
5. Kolarovic, A., Schweizer, E., Greene, E., Gironda, M., Pallan, P.S., Egli, M., and Rozners, E. 2009. Interplay of structure, hydration and thermal stability in formacetal modified oligonucleotides: RNA may tolerate nonionic modifications better than DNA. J. Am. Chem. Soc. 131:14932-14937.
6. Li, F., Pallan, P.S., Maier, M.A., Rajeev, K.G., Mathieu, S.L., Kreutz, C., Fan, Y., Sanghvi, J., Micura, R., Rozners, E., Manoharan, M., and Egli, M. 2007. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: Insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res. 35:6424-6438.
7. Parsegian, V.A., Rand, R.P., and Rau, D.C. 1995. Macromolecules and water: Probing with osmotic stress. Methods Enzymol. 259:43-94.
8. Parsegian, V.A., Rand, R.P, and Rau, D.C. 2000. Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives. Proc. Natl. Acad. Sci. U.S.A. 97:3987-3992.
9. Pilch, D.S. 2000. Calorimetry of nucleic acids. Curr. Protoc. Nucleic Acid Chem. 0:7.4.1-7.4.9.
10. Qu, X. and Chaires, J.B. 1999. Contrasting hydration changes for ethidium and daunomycin binding to DNA. J. Am. Chem. Soc. 121:2649-2650.
11. Qu, X. and Chaires, J.B. 2001. Hydration changes for DNA intercalation reactions. J. Am. Chem. Soc. 123:1-7.
12. Robinson, C.R. and Sligar, S.G. 1995. Hydrostatic and osmotic pressure as tools to study macromolecular recognition. Methods Enzymol. 259:395-427.
13. Rozners, E. and Moulder, J. 2004. Hydration of short DNA, RNA, and 2'-OMe oligonucleotides determined by osmotic stressing. Nucleic Acids Res. 32:248-254.
14. Rozners, E., Smicius, R., and Uchiyama, C. 2005. Expanding functionality of RNA: Synthesis and properties of RNA containing imidazole modified tandem G-U wobble base pairs. Chem. Commun. 46:5778-5780.
15. Spink, C.H. and Chaires, J.B. 1999. Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA. Biochemistry 38:496-508.
16. Timasheff, S.N. 1998. In disperse solution, "osmotic stress" is a restricted case of preferential interactions. Proc. Natl. Acad. Sci. U.S.A. 95:7363-7367.
17. Watts, J.K., Martin-Pintado, N., Gomez-Pinto, I., Schwartzentruber, J., Portella, G., Orozco, M., Gonzalez, C, and Damha, M.J. 2010. Differential stability of 2'F-ANA-RNA and ANA-RNA hybrid duplexes: Roles of structure, pseu-dohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res. 38:2498-2511.