Restriction Enzymes in Microbiology, Biotechnology and Biochemistry

Abstract

Since their discovery in the nineteen-seventies, a collection of simple enzymes termed Type II restriction endonucleases, made by microbes to ward off viral infections, have transformed molecular biology, spawned the multi-billion dollar Biotechnology industry, and yielded fundamental insights into the biochemistry of life, health and disease. In this article we describe how these enzymes were discovered, and we review their properties, organizations and genetics. We summarize current ideas about the mechanism underlying their remarkable ability to recognize and bind to specific base pair sequences in DNA, and we discuss why these ideas might not be correct. We conclude by proposing an alternative explanation for sequence-recognition that resolves certain inconsistencies and provides, in our view, a more satisfactory account of the mechanism.Keywords: DNA, specificity, recognition, discrimination, restriction, modification, endonuclease, methyltransferase, X-ray crystallography, major groove, minor groove, hydrogen bond, steric clash, electrostatic attraction, repulsion "The most far-reaching consequence of the emergence of the recombinant DNA technology has been the great strides made in understanding fundamental life processes and the ability to investigate problems that had previously been unapproachable. Emerging from myriad investigations has been the appreciation that nothing in the man-made world rivals the complexity and diversity of this Nathans, 1973) and later modified by Roberts et al., (Roberts et al., 2003) earth's organisms. No man-made information system invented to date comes anywhere close to containing the amount of information encoded in their genomes or encompassing the complexity of the intricate machinery for their functioning. We have learned enough to reveal how much we do not know and to acknowledge that nature's secrets are not beyond our capabilities of discovery." Paul Berg and Janet Mertz. 'Personal reflections on the origins and emergence of recombinant DNA technology' (Berg & Mertz, 2010) Restriction Enzymes in Microbiology, Biotechnology and Biochemistry 20 Encuentro No. 93, 19-48, 2012 * Restriction enzymes are named according to a convention proposed by Smith and Nathans(H. O. Smith &