On the Distinction of the Mechanisms of DNA Cleavage
by Restriction EnzymesThe I-, II-,
and III-Type Molecular Motors¹

S. A. Pikin

Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninski pr. 59, Moscow, 119333 Russia
e-mail: pikin@ns.crys.ras.ru

Received February 19, 2008

Abstract—A comparative physical description is given for the functioning of various restriction enzymes and
for their processes of DNA cleavage. The previously proposed model system of kinetic equations is applied to
the I- and III-type enzymes, which use ATP molecules as an energy source, while the II-type enzymes work
thanks to catalytic reactions with participation of an electric field. All the enzymes achieved bending and twist-
ing DNA, providing for either the linear motion of the II-type enzyme along the DNA chain or the DNA trans-
location by the I- and III-type enzymes due to moving chiral kinks. A comparative estimation of the considered
linear and angular velocities is performed. The role of stalling forces for enzyme–DNA complexes, which
induce the observed cutting of the DNA either inside the enzyme (II) or in some “weak” places outside enzymes
I and III, which results in the supercoiling of the DNA, is shown. The role of ionic screening for the described
processes is discussed.

PACS numbers: 87.16.Nn, 87.16.Dg, 64.70.Md

DOI: 10.1134/S1063774508050222

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