Biomaterial Database

Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations. 1999

G R Pack, and L Wong, and G Lamm

Department of Chemistry, University of Louisville, KY 40292, USA.

The predictions of counterion condensation theory for divalent ions were tested by comparison with the results of Monte Carlo calculations on an all-atom model of DNA. Monovalent-divalent competition at the polyelectrolyte surface was investigated by varying the partial molar volume of divalent ions. To assess the viability of using Poisson-Boltzmann (PB) calculations for determining divalent ion concentrations at DNA surfaces, Monte Carlo (MC) calculations were compared with PB calculations using different models of the dielectric continuum. It was determined that, while standard PB calculations of divalent ion surface densities are about 25-30% below those predicted by MC techniques, and somewhat larger than errors previously determined for monovalent ions, errors due to the use of the mean-field approximation of PB theory are smaller than those arising from common assumptions regarding the dielectric continuum.

UI	MeSH Term	Description	Entries
D009010	Monte Carlo Method	In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)	Method, Monte Carlo
D002413	Cations, Divalent	Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis.	Divalent Cations
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D016012	Poisson Distribution	A distribution function used to describe the occurrence of rare events or to describe the sampling distribution of isolated counts in a continuum of time or space.	Distribution, Poisson
D055672	Static Electricity	The accumulation of an electric charge on a object	Electrostatic,Electrostatics,Static Charge,Charge, Static,Charges, Static,Electricity, Static,Static Charges