On the DNA Cleavage by Restriction Enzymes – Molecular Motors with Polarization Properties

Abstract

In the paper, on the general physical basis, the attempt was done to explain the operation of restriction enzymes of different types. The physical model lies in the DNA deformation in the protein zone which is caused by catalytic processes taking place here. It is shown that some phenomena are similar to liquid-crystalline effects. The DNA molecule either forms locally a chiral kink moving together with a protein (the II type enzymes) or realizes the translocation through protein (the I and III type enzymes). The velocity of linear motion of the enzymes was estimated on the basis of proper kinetic equations which include the action of a longitudinal stalling force, the role of this force in DNA cleavage being different for different enzymes. The supercoiling of DNA during its translocation is discussed.

Keywords:

• DNA cleavage
• molecular motor
• restriction enzyme

PACS Numbers:

• 87.16.Nn
• 87.16.Dg
• 64.70.Md

Acknowledgments

This work was supported by the Division of Physical Sciences of RAS (program “New Materials and Structures”).