Free energy calculations for DNA near surfaces using an ellipsoidal geometry

J. Ambia-Garrido, Bernard Pettitt

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The change in some thermodynamic quantities such as Gibbs' free energy, entropy and enthalpy of the binding of two DNA strands (forming a double helix), while one is tethered to a surface and are analytically calculated. These particles are submerged in an electrolytic solution; the ionic strength of the media allows the linearized version of the Poisson-Boltzmann equation (from the theory of the double layer interaction) to properly describe the interactions [13]. There is experimental and computational evidence that an ion penetrable ellipsoid is an adequate model for the single strand and the double helix [22-25]. The analytic solution provides simple calculations useful for DNA chip design. The predicted electrostatic effects suggest the feasibility of electronic control and detection of DNA hybridization in the fast growing area of DNA recognition.

Original languageEnglish (US)
Pages (from-to)1117-1131
Number of pages15
JournalCommunications in Computational Physics
Volume3
Issue number5
StatePublished - May 2008
Externally publishedYes

Fingerprint

deoxyribonucleic acid
free energy
geometry
strands
helices
electronic control
Gibbs free energy
ellipsoids
enthalpy
chips
interactions
entropy
electrostatics
thermodynamics
ions

Keywords

  • Analytic Poisson-Boltzmann
  • Genetic analysis
  • Microarrays

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)

Cite this

Free energy calculations for DNA near surfaces using an ellipsoidal geometry. / Ambia-Garrido, J.; Pettitt, Bernard.

In: Communications in Computational Physics, Vol. 3, No. 5, 05.2008, p. 1117-1131.

Research output: Contribution to journalArticle

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