Updating Restriction Enzyme Information

Enzyme Data can be updated from files consistent with 'format6' used by the REBASE database of Restriction Enzymes.

At the time of writting, such files are available from REBASE on the World Wide Web at

http://rebase.neb.com/rebase/rebase.files.html

and are updated monthly

Pages loaded from this site into your web browser window should be copied and pasted into a word processor and saved on your disk in Text Only format. Saving the file in any other format than 'Text Only' will incorporate word processor specific formatting into the text which DNADynamo will not be able to process, resulting in a 'Wrong Format' error. To replace the Restriction Enzyme Data in DNADynamo with the data in a format6 type file, press the 'Update Enzyme Information From REBASE' button at the bottom of the Enzyme Box's buttons panel. Select the format6 text file in the FileChooser. If the file contains data in the correct format, a window containing a summary of the changes to your enzyme data will be displayed. If you would like to accept the new data, press the Accept button. To decline the update, press the Decline button.

Data Format

The following text elements are required for DNADynamo to read enzyme data from a text file.

Element 1 - a definition of the supplier codes used in the subsequent enzyme entires consisten with the following example...
REBASE codes for commercial sources of enzymes

                A        Amersham Pharmacia Biotech (5/03)
                C        Minotech Biotechnology (4/03)
                E        Stratagene (1/03)
                F        Fermentas AB (3/04)
                G        Qbiogene (4/03)
                H        American Allied Biochemical, Inc. (10/98)
                I        SibEnzyme Ltd. (2/04)
                J        Nippon Gene Co., Ltd. (6/00)
                K        Takara Shuzo Co. Ltd. (1/03)
                M        Roche Applied Science (1/03)
                N        New England Biolabs (5/04)
                O        Toyobo Biochemicals (11/98)
                P        Megabase Research Products (5/99)
                Q        CHIMERx (1/03)
                R        Promega Corporation (6/03)
                S        Sigma Chemical Corporation (1/03)
                U        Bangalore Genei (4/04)
                V        MRC-Holland (1/03)
                X        EURx Ltd. (11/03)


Element 2 - The following text definition that confirms the data structure - note however that changing this structure results in a 'Wrong Format' error

<1><name>
<2><prototype>
<3><recognition sequence>
<4><methylation site>
<5><commercial source>
<6><reference>


Element 3 - an entry in the following format for each restriction enzyme. The following example is for BamH1 taken from a REBASE format6 data file.

<1>BamHI
<2>
<3>G^GATCC
<4>5(4)
<5>ACEFGHIJKMNOQRSUVX
<6>397,1040,1397


REBASE defines the following example for RECOGNITION SEQUENCE NOMENCLATURE:

REBASE Recognition sequences representations use the standard abbreviations
(Eur. J. Biochem. 150: 1-5, 1985) to represent ambiguity: 
                        R = G or A
                        Y = C or T
                        M = A or C
                        K = G or T
                        S = G or C
                        W = A or T
                        B = not A (C or G or T)
                        D = not C (A or G or T)
                        H = not G (A or C or T)
                        V = not T (A or C or G)
                        N = A or C or G or T
These are written from 5' to 3', only one strand being given. If the point of cleavage has been
determined, the precise site is marked with ^. For enzymes such as HgaI, MboII etc.,
which cleave away from their recognition sequence the cleavage sites are indicated in parentheses. For example HgaI GACGC (5/10) indicates cleavage as follows: 5' GACGCNNNNN^ 3' 3' CTGCGNNNNNNNNNN^ 5' Typically, the recognition sequences are oriented so that the cleavage sites lie on their 3' side. ENZYMES WITH UNUSUAL CLEAVAGE PROPERTIES: Enzymes that cut on both sides of their recognition sequences, such as BcgI, Bsp24I, CjeI and CjePI,
have 4 cleavage sites each instead of 2. Bsp24I 5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3' 3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5' This will be described in some REBASE reports as: Bsp24I (8/13)GACNNNNNNTGG(12/7)
Entries that do not conform to this format are excluded by DNADynamo. Note that recognition sites that contain a "^" to indicate the cleavage site must be palindromes. Enzymes that cut on both sides of their recognition sequences result in two cut site entries on tables of restriction enzyme sites and therefore will never appear on graphic maps showing unique cut sites.