Restriction Enzyme Properties
List of restriction enzymes
GenBeans current list of Type II restriction enzymes is based on format #31 list from the Restriction Enzyme Database REBASE release 210 (http://rebase.neb.com).
A prototype is defined as the representative of a set of isoschizomers. GenBeans uses the REBASE list of prototypes and enzyme suppliers by order of preference to assign prototypes. It is possible to adjust the use of REBASE prototypes and the order of preference for suppliers in the Restriction Enzymes option panel.
Restriction enzyme properties
Name
The name of the restriction enzyme.
Cutting Site and Recognition Sequence
Cutting sites are represented with IUPAC nucleotide symbols from 5' to 3'. Cleavage sites located inside the recognition sequences are marked with the symbol '^' and only one strand is given. For cleavage sites located outside the recognition sequences, the number of nucleotides between the 5' end (3' end respectively) and the cleavage position and the number of nucleotides between the 3' end (5' end respectively) and the cleavage position on the other strand are indicated in parentheses on the left side of the recognition sequence (right side respectively). For example, the cutting site for HgaI is noted GACGC (5/10), corresponding to the cleavage 5' GACGCNNNNN^ 3' and the cleavage 3' CTGCGNNNNNNNNNN^ 5' on the other strand; in another example the cutting site for BaeI is noted (10/15)ACNNNNGTAYC(12/7) indicating that four cleavages result from the action of this enzyme on a recognition site.
Cutting size
The cutting size of a restriction enzyme is defined has the number of nucleotides involved in the recognition sequence. The size is ponderated as follow: 1 for a single nucleotide, 1/2 for a degeneracy of 2, 1/4 for a degeneracy of 3, and 0 for any N nucleotides.
Isoschizomers
Restrictions enzymes that share the same cutting site.
Commercial suppliers
Suppliers are defined with the following letter code:
B Life Technologies (7/15)
C Minotech Biotechnology (7/15)
E Agilent Technologies (7/15)
I SibEnzyme Ltd. (12/15)
J Nippon Gene Co., Ltd. (11/15)
K Takara Bio Inc. (9/15)
M Roche Applied Science (11/15)
N New England Biolabs (11/15)
O Toyobo Biochemicals (8/14)
Q Molecular Biology Resources - CHIMERx (11/15)
R Promega Corporation (11/15)
S Sigma Chemical Corporation (11/15)
V Vivantis Technologies (8/14)
X EURx Ltd. (7/15)
Y SinaClon BioScience Co. (11/15)