Hostname: page-component-586b7cd67f-2plfb Total loading time: 0 Render date: 2024-11-29T09:27:46.288Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting

Published online by Cambridge University Press:  11 February 2011

Hai Long  and
George C. Schatz
Hai Long
Affiliation:
Department of Chemistry, Northwestern University, Evanston IL 60208–3113
George C. Schatz
Affiliation:
Department of Chemistry, Northwestern University, Evanston IL 60208–3113
Get access

Abstract

We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius Rcounter which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated Rcounter, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates.

Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 735: Symposium C – Bioinspired Nanoscale Hybrid Systems , 2002 , C10.1
Copyright
Copyright © Materials Research Society 2003

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

1. (a) Mirkin, C. A., Letsinger, R. L., Mucic, R. C., and Storhoff, J. J., Nature 382, 607 (1996);Google Scholar
(b) Elghanian, R., Storhoff, J. J., Mucic, R. C., Letsinger, R. L., and Mirkin, C. A., Science 277, 1078 (1997).Google Scholar
2. Rongcao, J., Guosheng, W., Zhi, L., Mirkin, C. A., and Schatz, G. C., J. Am. Chem. Soc, in press (2003).Google Scholar
3. Storhoff, J. J., Elghanian, R., Mucic, R. C., Mirkin, C. A., and Letsinger, R. L., J. Am. Chem. Soc. 120, 1959 (1998).Google Scholar
4. Andrew, T. T., Mirkin, C. A., and Letsinger, R. L., Science 289, 1757 (2000).Google Scholar
5. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Zerz, K. M. Jr, Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. and Pollman, P. A., J. Am. Chem. Soc. 117, 5179 (1995).Google Scholar
6. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E. III, Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Radmer, R.J., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A., AMBER 6, University of California, San Francisco (1999).Google Scholar
7. (a) Storhoff, J. J., Lazarides, A. A., Mucic, R. C., Mirkin, C. A., Letsinger, R. L., and Schatz, G. C., J. Am. Chem. Soc. 122, 4640 (2000);Google Scholar
(b) Demers, L. M., Mirkin, C. A., Mucic, R. C., Reynolds, R. A. III, Letsinger, R. L., Elghanian, R., and Viswanadham, G., Analytical Chemistry 72, 5535 (2000).Google Scholar
8. Young, M. A., Ravishanker, G., and Beveridge, D. L., Biophys. J. 73, 2313 (1997).Google Scholar
9. Kollman, P., Chem. Rev. 93, 2395 (1993).Google Scholar