title: The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.
abstract: Restriction endonucleases are the basic tools of molecular biology. Many restriction endonucleases show relaxed sequence recognition, called star activity, as an inherent property under various digestion conditions including the optimal ones. To quantify this property we propose the concept of the Fidelity Index (FI), which is defined as the ratio of the maximum enzyme amount showing no star activity to the minimum amount needed for complete digestion at the cognate recognition site for any particular restriction endonuclease. Fidelity indices for a large number of restriction endonucleases are reported here. The effects of reaction vessel, reaction volume, incubation mode, substrate differences, reaction time, reaction temperature and additional glycerol, DMSO, ethanol and Mn(2+) on the FI are also investigated. The FI provides a practical guideline for the use of restriction endonucleases and defines a fundamental property by which restriction endonucleases can be characterized.
authors.affiliation: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Wei
authors.forename: Caitlin
authors.initials: C
authors.lastname: Therrien
authors.forename: Aine
authors.initials: A
authors.lastname: Blanchard
authors.forename: Shengxi
authors.initials: S
authors.lastname: Guan
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Zhu
mesh_terms: D002021:Buffers; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004262:DNA Restriction Enzymes / Q000032:analysis* / Q000145:classification / Q000378:metabolism; D004278:DNA, Superhelical / Q000378:metabolism; D016133:Polymerase Chain Reaction; D013379:Substrate Specificity; D013696:Temperature; D009626:Terminology as Topic
chemical_list: D002021:Buffers; D004278:DNA, Superhelical; D004247:DNA; D004262:DNA Restriction Enzymes