One recognition sequence, seven restriction enzymes, five reaction mechanisms

Nucleic Acids Research
Darren M GowersS E Halford

Abstract

The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI, Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence 5'-GGCGCC-3'. Their reactions on plasmids with one or two copies of this sequence revealed five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its recognition sites, but shows full activity only when bound to two sites, which are then cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute requirement for two sites in close physical proximity, which are cleaved concertedly. The range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as is the number of enzymes needing two recognition sites.

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Citations

Jun 1, 2005·Journal of Molecular Biology·Katie M WoodStephen E Halford
Aug 27, 2005·Nucleic Acids Research·Alice SearsMark D Szczelkun
Jan 13, 2006·Nucleic Acids Research·Bram van den BroekGijs J L Wuite
Feb 16, 2008·Nucleic Acids Research·Lucy E CattoStephen E Halford
Jul 10, 2009·Nucleic Acids Research·Niels LaurensGijs J L Wuite
Aug 10, 2010·Nucleic Acids Research·Ildikó Stier, Antal Kiss
Jun 10, 2011·Nucleic Acids Research·Jacqueline J T MarshallStephen E Halford
Oct 14, 2011·Nucleic Acids Research·Christian Pernstich, Stephen E Halford
Jul 27, 2006·Proceedings of the National Academy of Sciences of the United States of America·Gregory J GemmenDouglas E Smith
Feb 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Subramanian P RamanathanRalf Seidel
Apr 14, 2005·Journal of Molecular Biology·Daniel F HeiterGeoffrey G Wilson
Oct 12, 2005·Biochemical and Biophysical Research Communications·Keiki SugimotoDaiya Takai
Jun 1, 2014·Nucleic Acids Research·Alfred PingoudWolfgang Wende
Sep 18, 2007·Journal of Molecular Biology·Stuart R W BellamyStephen E Halford
Feb 3, 2007·Journal of Molecular Biology·Jacqueline J T MarshallStephen E Halford
Jan 18, 2017·Journal of Bacteriology·Anthony W KingstonElisabeth A Raleigh
Sep 22, 2017·Nucleic Acids Research·Giedrius SasnauskasVirginijus Siksnys
Mar 20, 2010·Biochemical Society Transactions·Mark D SzczelkunRalf Seidel
Jul 19, 2017·Scientific Reports·Lorena RuizDouwe van Sinderen
Apr 28, 2020·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yoram ZaraiTamir Tuller

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