2012 Impact factor 1.824
EPJ E - Soft Matter and Biological Physics
Soft Matter and Biological Physics


Eur. Phys. J. E 4, 411-417

Co-ion dependence of DNA nuclease activity suggests hydrophobic cavitation as a potential source of activation energy

H.-K. Kim1, E. Tuite2, B. Nordén1 and B.W. Ninham3

1  Department of Physical Chemistry, Chalmers University of Technology, SE 412 96, Gothenburg, Sweden
2  Department of Chemistry, Bedson Building, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
3  Department of Applied Mathematics, Research School of Physical Sciences and Engineering, Australian National University, ACT 0200 Australia

norden@phc.chalmers.se

(Received 19 June 2000 and Received in final form 17 October 2000)

Abstract
The source of the activation energy that allows cutting of DNA by restriction enzymes is unclear. A systematic study of the cutting efficiency of the type-II restriction endonuclease EcoRI, with varying background electrolyte ion pair and buffer reported here, shows only a modest dependence of efficiency on cation type. Surprisingly, efficiency does depend strongly on the presumed indifferent anion of the background salt. What emerges is that competition between the background salt anion and the buffer anion for the enzyme and DNA surfaces is crucial. The results are unexpected and counterintuitive from the point of view of conventional electrolyte theory. However, taken together with recent developments in surface chemistry, the results do fall into place and could also suggest a novel mechanism for enzyme activity as an alternative to metal-activated hydrolysis: microscopic cavitation in a hydrophobic pocket might be the source of activation energy.

PACS
87.14.Ee - Proteins.
87.14.Gg - DNA, RNA.
87.15.Nn - Properties of solutions, aggregation and cristallization of macromolecules.


© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2001