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. Ninham31 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.
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
