The long-range objectives of this research are the development and application of accurate experimental and rigorous theoretical methods of investigating the molecular detail and thermodynamic consequences of the interactions of cations with nucleic acids. These studies are of fundamental importance in polyelectrolyte chemistry, and have direct applications to the analysis of the interactions of nucleic acids with charged ligands of biological interest, including proteins and therapeutic agents. The stability and specificity of nucleic acid conformations and of complexes with charged ligands in aqueous solution are often determined by the electrolytes present and by competitive ion exchange processes involving cations on DNA. Thermodynamic measurements characterizing processes (conformational changes, ligand-binding) involving polymeric or oligomeric nucleic acids will be analyzed and interpreted by using Grand Canonical Monte Carlo (GCMC) simulations and calculations based on the Poisson-Boltzmann (PB) cell model. In these analyses, the fundamental thermodynamic variables are preferential interaction coefficients which reflect all nonideality due to interactions of electrolyte(s) with the specified state of the oligo- or polyelectrolyte component. Our GCMC and PB methods will be developed further in order to analyze equilibrium dialysis data on four component systems (water, nucleic acid, salt, oligocationic ligand). Current thermodynamic descriptions of salt effects on the extent of association of charged ligands with DNA will be examined at a fundamental level using these preferential interaction coefficients. The interactions of small cations with oligomeric and polymeric DNA will be studied quantitatively by NMR measurements on suitable quadrupolar nuclei in cations of biophysical interest. The dependences of the longitudinal and transverse relaxation rates of the probe nuclei (such as 23Na, 14N and 135Ba) on degree of polymerization, solution composition, temperature and (where appropriate) field strength, will be determined and analyzed to quantify the extent of association of individual cations with DNA, and the relative affinities of pairs of competing cations. These results will be compared with theoretical predictions for corresponding model systems calculated by canonical Monte Carlo (CBC) simulations or the PB cell model. Information about the dynamic character of the association of small ions with oligo- and polymeric nucleic acids will be obtained from determinations of quadrupolar NMR correlation times.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM034351-07
Application #
3285192
Study Section
Biophysical Chemistry Study Section (BBCB)
Project Start
1984-12-01
Project End
1994-11-30
Budget Start
1990-12-01
Budget End
1991-11-30
Support Year
7
Fiscal Year
1991
Total Cost
Indirect Cost
Name
University of Wisconsin Madison
Department
Type
Schools of Arts and Sciences
DUNS #
161202122
City
Madison
State
WI
Country
United States
Zip Code
53715
Holbrook, J A; Capp, M W; Saecker, R M et al. (1999) Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry 38:8409-22
Zhang, W; Ni, H; Capp, M W et al. (1999) The importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (L8+) binding to single-stranded DNA oligomers. Biophys J 76:1008-17
Record Jr, M T; Courtenay, E S; Cayley, S et al. (1998) Biophysical compensation mechanisms buffering E. coli protein-nucleic acid interactions against changing environments. Trends Biochem Sci 23:190-4
Record Jr, M T; Zhang, W; Anderson, C F (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv Protein Chem 51:281-353
Padmanabhan, S; Zhang, W; Capp, M W et al. (1997) Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: thermodynamic analysis of effects of coulombic interactions and alpha-helix induction. Biochemistry 36:5193-206
Zhang, W; Bond, J P; Anderson, C F et al. (1996) Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proc Natl Acad Sci U S A 93:2511-6
Olmsted, M C; Bond, J P; Anderson, C F et al. (1995) Grand canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L8+) to the center of DNA oligomers. Biophys J 68:634-47
Record Jr, M T; Anderson, C F (1995) Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model. Biophys J 68:786-94
Anderson, C F; Record Jr, M T (1995) Salt-nucleic acid interactions. Annu Rev Phys Chem 46:657-700
Bond, J P; Anderson, C F; Record Jr, M T (1994) Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients. Biophys J 67:825-36

Showing the most recent 10 out of 16 publications