Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers: Salt effects and the connection to cooperative DNA melting

Hai Long, George C Schatz

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

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-l.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.

Original languageEnglish
Title of host publicationMaterials Research Society Symposium - Proceedings
EditorsU Simon, G Schmid, S Hong, S.J. Stranick, S.M. Arrivo
Pages143-151
Number of pages9
Volume735
Publication statusPublished - 2003
EventBioinspired Nanoscale Hybrid Systems - Boston, MA, United States
Duration: Dec 2 2002Dec 4 2002

Other

OtherBioinspired Nanoscale Hybrid Systems
CountryUnited States
CityBoston, MA
Period12/2/0212/4/02

Fingerprint

Dimers
Molecular dynamics
Melting
DNA
Salts
Ions
Dimerization
Melting point
Amber
Coulomb interactions
Negative ions
Positive ions
Boundary conditions
Computer simulation

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials

Cite this

Long, H., & Schatz, G. C. (2003). Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers: Salt effects and the connection to cooperative DNA melting. In U. Simon, G. Schmid, S. Hong, S. J. Stranick, & S. M. Arrivo (Eds.), Materials Research Society Symposium - Proceedings (Vol. 735, pp. 143-151)

Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers : Salt effects and the connection to cooperative DNA melting. / Long, Hai; Schatz, George C.

Materials Research Society Symposium - Proceedings. ed. / U Simon; G Schmid; S Hong; S.J. Stranick; S.M. Arrivo. Vol. 735 2003. p. 143-151.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Long, H & Schatz, GC 2003, Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers: Salt effects and the connection to cooperative DNA melting. in U Simon, G Schmid, S Hong, SJ Stranick & SM Arrivo (eds), Materials Research Society Symposium - Proceedings. vol. 735, pp. 143-151, Bioinspired Nanoscale Hybrid Systems, Boston, MA, United States, 12/2/02.
Long H, Schatz GC. Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers: Salt effects and the connection to cooperative DNA melting. In Simon U, Schmid G, Hong S, Stranick SJ, Arrivo SM, editors, Materials Research Society Symposium - Proceedings. Vol. 735. 2003. p. 143-151
Long, Hai ; Schatz, George C. / Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers : Salt effects and the connection to cooperative DNA melting. Materials Research Society Symposium - Proceedings. editor / U Simon ; G Schmid ; S Hong ; S.J. Stranick ; S.M. Arrivo. Vol. 735 2003. pp. 143-151
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