info on restriction enzyme

Dana Macelis-Roberts Lab macelis at neb.com
Thu Oct 28 14:08:46 EST 1993


<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
     <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>     
                                                                              
              Dr. Richard J. Roberts Restriction Enzyme Database              
                 Copyright (c) New England BioLabs, Inc. 1993                 
                             All rights reserved.                             
                                                                              
     <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>     
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
                                                                              






                                R E B A S E


       The Restriction Enzyme Database, is a collection of information about
restriction enzymes, methylases, the microorganisms from which they have been
isolated, recognition sequences, cleavage sites, methylation specificity, the
commercial availability of the enzymes, and references - both published and
unpublished observations (dating back to 1952).

       REBASE is updated daily.  Each month, a set of REBASE data files are
released publically and distributed to the scientific community at no charge
via a regular monthly emailing list, and made available at our own anonymous
ftp site (vent.neb.com).  These data files are flat ASCII text files, many of
which we designed specifically for use with a variety of software packages,
such as GCG and IntelliGenetics.  As REBASE expands, an ever-growing number
of new data files are being provided.  Requests for additional formats are
welcome, as we are prepared to support each major sequence analysis package.
REBASE is now accessible via WAIS directly from us as well.


REVIEWS:        See Nucleic Acids Research 21: 3125-3137, 1993.



                        Dr. Richard J. Roberts
                        New England BioLabs
                        32 Tozer Road
                        Beverly, Massachusetts 01915 U.S.A.

                        phone:        (508) 927-5054
                        fax:          (508) 921-1527
                        email:        roberts at neb.com


******************************************************************************

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


COMMERCIAL AVAILABILITY

        Each commercial source of restriction enzymes and/or methylases
        listed in REBASE is assigned a single character abbreviation
        code.  For example:
                          K       Takara (12/92)
                          L       Northumbria Biologicals Ltd. (11/92)
                          M       Boehringer Mannheim (12/92)
                          N       New England Biolabs (11/92)

        The date in parentheses indicates the most recent update of
        that organization's listings in REBASE.



******************************************************************************

REBASE via WAIS:

                  REBASE is accessible via WAIS from vent.neb.com
                           (192.138.220.2 port 210). 
                  We currently have five WAIS sources set up.

     REBASE_help:
           general description of REBASE and what services and data files
           we offer.

     REBASE_enzymes:
           facts about each enzyme in REBASE.

     REBASE_references:
           all the published references stored in REBASE complete with
           abstracts where available.

     REBASE_suppliers:
           commmercial sources of enzymes, includes contact information
           (address, telephone #'s, fax #'s) for each company and a list
           of the enzymes that they sell.

     REBASE_news:
           a report of what's new in REBASE this month, such as any enzyme
           name changes, announcements of new REBASE formats and services,
           new commercial suppliers, etc.

******************************************************************************

REBASE via ANONYMOUS FTP:

	ftp vent.neb.com  (username: anonymous, password: your email address)
	cd pub/rebase     (to enter the correct directory)
	dir               (to list the names of available files)
	get README |more  (to view the file called README, spaces matter!)
	get README        (to copy the file called README to your machine)
	quit              (returns you back to your local system)

******************************************************************************

REBASE via EMAIL:

       To be placed on our monthly emailing list, send your full name, postal
       address, telephone number, fax number (if available), and email address
       to macelis at neb.com

******************************************************************************

    CURRENT EMAILING LIST            FILES to get (### = current version
      & FTP SITE FORMATS                ex. 306 indicates June 1993)


    #1. COMMERCIAL SOURCES             commdata.###
    #2. GCG                            gcg.###
    #3. GCG - with refs                gcgenz.###, gcgref.###
    #4. Nucleic Acids Research         nar.###
    #5. Prototypes                     proto.###
    #6. Type II                        type2.###, type2ref.###
    #7. Type II (with isos)            gtype2.###, type2ref.###
    #8. Type II (with tabs)            itype2.###, type2ref.###
    #9. All Enzymes (w/ ref list)      allenz.###
   #10. All Enzymes (each w/ ref)      withref.###
   #11. All Enzymes (parsed refs)      parsrefs.###
   #12. All Enzymes (by microorg)      orgref.###
   #13. IGSuite                        bionet.###
   #14. ALPHAZYMES                     azymes.###
   #15. CUTZYMES                       cutzymes.###
   #16. STADEN                         staden.###
   #17. DNA Strider                    strider.###
   #18. DNA Strider (commercial)       striderc.###
   #19. Bairoch Format                 bairoch.doc, bairoch.###
   #20. DNASIS                         dnasis.###
   #21. PUBLISHED REFS                 pubrefs.###, pubrefsa.###
   #22. PROCITE REFS                   procite.###, procitea.###
   #23. GENEPRO                        genepro.###
   #24. GENEPRO (commercial)           geneproc.###
   #25. REBASE NEWS (release notes)    NEWS.###



DESCRIPTIONS OF AVAILABLE FORMATS:

******************************************************************************
#1.              COMPLETE COMMERCIAL SOURCE INFORMATION  

GET FILE(S):   commdata.###
DESCRIPTION:   a list of commmercial sources of both restriction enzymes and
               methylases.

               Includes contact information: address, telephone #'s, fax #'s
               and REBASE abbreviations for each company and the names of the
               enzymes that they sell.


******************************************************************************
#2.                            GCG FORMAT   

GET FILE(S):    gcg.###
DESCRIPTION:    format used as input for the Sequence Analysis Software
                Package by Genetics Computer Group.

                (commercial abbreviations as assigned in REBASE)
EXAMPLE:


enzyme name   cut site   rec seq w cut sites marked   overhang  commer abbrs

..
;AatI      3 AGG'CCT        0 !  StuI,Eco147I              >OU
AatII      5 G_ACGT'C      -4 !                            >EGMNOPRSUVX
AccI       2 GT'mk_AC       2 !                            >ABEGIKMNOPRSUVX
;AccII     2 CG'CG          0 !  ThaI,BstUI,MvnI,Bsp50I    >AEGKVX
;AccIII    1 T'CCGG_A       4 !  BspMII,Kpn2I,MroI         >AEGKR
AgeI       1 A'CCGG_T       4 !                            >
AluI       2 AG'CT          0 !                            >ABEFGIKMNOPRSUVX


******************************************************************************
#3.                         GCG - with refs 

GET FILE(S):    gcgenz.###, gcgref.###
DESCRIPTION:    two files: the first can be used as input for the Sequence
                Analysis Software Package by Genetics Computer Group;the 2nd
                contains a reference list for all enzymes named in the first
                file (where the final column in an enzyme entry contains the
                number for the related references). Commercial abbreviations
                as assigned in REBASE.  Same as format #2, except reference
                information is given.

EXAMPLE of enzyme file:


enzyme name   cut site   rec seq w cut sites marked   overhang  commer  refs

..
;AatI  3 AGG'CCT    0 ! StuI,Eco147I                  >OU                  2
AatII  5 G_ACGT'C  -4 !                               >EGJLMNOPRSUVX       2
AccI   2 GT'mk_AC   2 !                               >ABDEGIJKLMNOPQRSUVX 3
;AccII 2 CG'CG      0 ! FnuDII,ThaI,BstUI,MvnI,Bsp50I >ADEGJKQVX         1,3

EXAMPLE of reference file:

References:
1.     Kita, K., Hiraoka, N., Kimizuka, F., Obayashi, A. (1984) Agric. Biol.
       Chem. 48: 531-532
2.     Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M. (1982) Nucl.
       Acids Res. 10: 5747-5752
3.     Zabeau, M., Roberts, R.J. unpublished observations.


******************************************************************************
#4.                           NAR format 

GET FILE(S):   nar.###
DESCRIPTION:   a list of Type II, I and III enzymes in a format close to
               that used in the Nucleic Acids Research Supplement.  Included
               in this list are all prototypes, their neoschizomers, and
               commercially available isoschizomers.

EXAMPLE:

prototype         rec seq w cut site   methylation site, type  commer  refs
   isoschizomer   rec seq w cut site   methylation site, type  commer  refs

AatII             GACGT^C                                      EJLMNO   6
AciI              CCGC(-3/-1)                                  N        3
AhaIII            TTT^AAA                                               8
   DraI           TTT^AAA                                      KLMNO    4
ApaI              GGGCC^C              4(5)                    KLMNOX   5,7
   Bsp120I        G^GGCCC                                      F        1,2


References:

1.     Janulaitis, A.A., Gilvonauskaite, R., Petrusyte, M. unpublished
       observations.
2.     Janulaitis, A.A., Maneliene, Z., Butkus, V. unpublished observations.
3.     Polisson, C., Morgan, R.D. (1990) Nucl. Acids Res. 18: 5911
4.     Purvis, I.J., Moseley, B.E.B. (1983) Nucl. Acids Res. 11: 5467-5474
5.     Seurinck, J., Van de Voorde, A., Van Montagu, M. (1983) Nucl. Acids
       Res. 11: 4409-4415
6.     Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M. (1982) Nucl.
       Acids Res. 10: 5747-5752
7.     Trautner, T.A. unpublished observations.
8.     Whitehead, P.R., Brown, N.L. (1982) FEBS Lett. 143: 296-300


******************************************************************************
#5.                           PROTOTYPES   

GET FILE(S):   proto.###
DESCRIPTION:   a list of all prototypes and their recognition sequences
               (cut sites indicated).
EXAMPLE:

enzyme name                    recognition sequence with cleavage site

AatII                          GACGT^C
AccI                           GT^MKAC
AcyI                           GR^CGYC
AflII                          C^TTAAG
AflIII                         A^CRYGT


******************************************************************************
#6.                          Type II format  

GET FILE(S):    type2.###, type2ref.###
DESCRIPTION:    two files: a list of type II enzymes, and a list of their
                associated references.

EXAMPLE of Type II enzyme list:

<1>enzyme name
<2>isoschizomers
<3>recognition sequence with cleavage site
<4>methylation site and type
<5>commercial source
<6>references

<1>ApaI
<2>
<3>GGGCC^C
<4>4(5)
<5>BDEIJKLMNOPRSUVXY
<6>2,3

<1>Zsp2I
<2>AvaIII
<3>ATGCA^T
<4>
<5>DY
<6>1

EXAMPLE of reference list:

1.     Degtyarev, S.K. unpublished observations.
2.     Seurinck, J., Van de Voorde, A., Van Montagu, M. (1983) Nucl. Acids
       Res. 11: 4409-4415.
3.     Trautner, T.A. unpublished observations.


******************************************************************************
#7.                     Type II with Isoschizomers   

GET FILE(S):    gtype2.###, type2ref.###
DESCRIPTION:    a list of type II enzymes and a list of their associated
                references.  Same as format #1, except that instead of
                just the prototype in field 2, all isoschizomers are listed.
                Separate reference file, as in format #6.
EXAMPLE:

<1>enzyme name
<2>isoschizomers
<3>recognition sequence with cleavage site
<4>methylation site and type
<5>commercial source
<6>references

<1>AluI
<2>BsaLI,MltI,OtuI,OtuNI,OxaI
<3>AG^CT
<4>3(5)
<5>ABDEFGHIJKLMNOPQRSUVX
<6>320,507,700,701

<1>AlwI
<2>BinI,BthII
<3>GGATC(4/5)
<4>
<5>NU
<6>404


******************************************************************************
#8.                      Type II format with tabs  

GET FILE(S):  itype2.###, type2ref.###
DESCRIPTION:  a list of type II enzymes and a list of their associated
              references.  Same as format #1, except that the fields are
              separated by tabs, so that each enzyme entry is on a single
              line.  Separate reference file, as in format #6.

EXAMPLE of Type II enzyme list:

<enzyme name> tab <prototype> tab <recognition sequence with cleavage site>
  tab <methylation site and type> tab <commercial source> tab <references>

AluI               AG^CT      3(5)  ABDEFGHIJKLMNOPQRSUVX    320,507,700,701
AlwI      BinI     GGATC(4/5)       NU                       404
Alw21I    HgiAI    GWGCW^C          DF                       226
Alw26I    BsmAI    GTCTC(1/5)       DFR                      161
Alw44I    ApaLI    G^TGCAC          DFORU                    226
AlwNI              CAGNNN^CTG       NU                       407


******************************************************************************
#9.                     ALL ENZYMES (REFERENCE LIST)  

GET FILE(S):   allenz.###
DESCRIPTION:   A list of all restriction enzymes - Types I, II, and III.
               References are numbered and listed separately at the bottom
               of the report.
EXAMPLE:

<1>enzyme name
<2>prototype
<3>microorganism
<4>source of microorganism
<5>recognition sequence with cleavage site
<6>methylation site and type
<7>commercial source
<8>references

<1>AluI
<2>
<3>Arthrobacter luteus
<4>ATCC 21606
<5>AG^CT
<6>3(5)
<7>ABEFHIJKLMNOPQRSUVX
<8>1,3,4,5

<1>AlwI
<2>BinI
<3>Acinetobacter lwoffi
<4>NEB 402
<5>GGATC(4/5)
<6>
<7>NSU
<8>2

References:

1.    Kramarov, V.M., Smolyaninov, V.V. (1981) Biokhimiya 46: 1526-1529
2.    Morgan, R., Bonventre, J. unpublished observations.
3.    Roberts, R.J., Myers, P.A., Morrison, A., Murray, K. (1976) J. Mol.
      Biol. 102: 157-165
4.    Yoon, H., Suh, H., Han, M.H., Yoo, O.J. (1985) Korean Biochem. J. 18:
      82-87
5.    Yoon, H., Suh, H., Kim, K., Han, M.H., Yoo, O.J. (1985) Korean Biochem.
      J. 18: 88-93


******************************************************************************
#10.                ALL ENZYMES (INDIVIDUALLY REFERENCED)  

GET FILE(S):    withref.###
DESCRIPTION:    a list of all restriction enzymes - Types I, II, and III.
                Similar to format #9 except that instead of including the
                references at the bottom of the report, each enzyme is
                followed by its reference information.
EXAMPLE:

<1>enzyme name
<2>prototype
<3>microorganism
<4>source of microorganism
<5>recognition sequence with cleavage site
<6>methylation site and type
<7>commercial source
<8>references

<1>AluI
<2>
<3>Arthrobacter luteus
<4>ATCC 21606
<5>AG^CT
<6>3(5)
<7>ABEFHIJKLMNOPQRSUVX
<8>Kramarov, V.M., Smolyaninov, V.V. DNA methylase from Arthrobacter luteus
   screens DNA from the action of site-specific endonuclease AluI.  Biokhimiya
   46: 1526-1529 (1981)
 Roberts, R.J., Myers, P.A., Morrison, A., Murray, K. A specific endonuclease
   from Arthrobacter luteus.  J. Mol. Biol. 102: 157-165 (1976)
 Yoon, H., Suh, H., Han, M.H., Yoo, O.J. Purification and characterization of
   AluI methylase.  Korean Biochem. J. 18: 82-87 (1985)
 Yoon, H., Suh, H., Kim, K., Han, M.H., Yoo, O.J. The specificity & catalytic
   properties of AluI methylase.  Korean Biochem. J. 18: 88-93 (1985)

<1>ApaI
<2>
<3>Acetobacter pasteurianus sub.  pasteurianus
<4>NCIB 7215
<5>GGGCC^C
<6>4(5)
<7>BEIJKLMNOPRSUVX
<8>Seurinck, J., Van de Voorde, A., Van Montagu, M. A new restriction
   endonuclease from Acetobacter pasteurianus.  Nucl. Acids Res. 11: 4409-4415
   (1983)
 Trautner, T.A. unpublished observations.


******************************************************************************
#11.                 ALL ENZYMES (PARSED REFERENCES)   

GET FILE(S):   parsrefs.###
DESCRIPTION:   A list of all restriction enzymes - Types I, II, and III.
               In this report, references are listed in a parsed format.
EXAMPLE:

<1>enzyme name
<2>prototype
<3>microorganism
<4>source of microorganism
<5>recognition sequence with cleavage site
<6>methylation site and type
<7>commercial source
<8>references

<1>CviJI
<2>
<3>Chlorella strain NC64A (IL-3A)
<4>J.L. Van Etten
<5>RG^CY
<6>3(5)
<7>
<8>1,603

<1>DdeI
<2>
<3>Desulfovibrio desulfuricans Norway strain
<4>H. Peck
<5>C^TNAG
<6>1(5)
<7>BEGIJLMNOPRUVX
<8>177,232,397

References:

1. <AUTHORS>Agarwal, K.     <U>     unpublished observations.
2. <AUTHORS>Aiken, C., Milarski-Brown, K., Gumport, R.I.     <J>    <YEAR>1986
   <JOURNAL>Fed. Proc.     <VOLUME>45     <PAGES>1914
3. <AUTHORS>Akulinin, G.E., Getko, G.A., Repin, V.E., Degtyarev, S.K.     <J>
   <YEAR>1988     <JOURNAL>Izv Sib Otd Akad. Nauk SSSR Ser Biol Nauk
   <VOLUME>14     <PAGES>105-108


******************************************************************************
#12.                    ALL ENZYMES (SORTED BY ORGANISM)   

GET FILE(S):   orgref.###
DESCRIPTION:   This is a complete list of enzymes currently stored in the
               database. Each enzyme is followed by its reference information.
               The enzymes are sorted by their microorganism names.
EXAMPLE:

<1>enzyme name
<2>prototype
<3>microorganism
<4>source of microorganism
<5>recognition sequence with cleavage site
<6>methylation site and type
<7>commercial source
<8>references

<1>ApaI
<2>
<3>Acetobacter pasteurianus sub. pasteurianus
<4>NCIB 7215
<5>GGGCC^C
<6>4(5)
<7>BDEGIJKLMNOPRUVX
<8>Seurinck, J., Van de Voorde, A., Van Montagu, M. A new restriction
     endonuclease from Acetobacter pasteurianus.  Nucl. Acids Res. 11:
     4409-4415 (1983)
   Trautner, T.A. unpublished observations.


******************************************************************************
#13.                       IG Suite format   

GET FILE(S):   bionet.###
DESCRIPTION:   an alphabetical listing of Type II restriction enzymes, their
               prototypes, and recognition sequences (with cut sites
               indicated).
EXAMPLE:

enzyme name (prototype)        recognition sequence with cleavage site

AaaI (XmaIII)                  C^GGCCG
AacI (BamHI)                   GGATCC
AatI (StuI)                    AGG^CCT
AatII                          GACGT^C
AcaII (BamHI)                  GGATCC


******************************************************************************
#14.                      ALPHAZYMES FORMAT   

GET FILE(S): azymes.###
DESCRIPTION: an alphabetical list of all prototypes and their isoschizomers.
             Each is followed by its recognition sequence and commercial
             sources (company abbreviations as assigned in REBASE).  No
             reference information is included.  This file is used by the
             CSHL sequence analysis programs.
EXAMPLE:


prototype         recognition sequence w cut site   enzyme type   commer
    isoschizomer  recognition sequence w cut site                 commer

AatII             GACGT^C                           2             G,M,N,O
AccI              GT^(A/C)(G/T)AC                   2             M,N,S
    DsaVI         GT(A/C)(G/T)AC
AcyI              GPu^CGPyC                         2             M,R,U
    AhaII         GPu^CGPyC                                       N
    AosII         GPu^CGPyC
    AstWI         GPu^CGPyC
    AsuIII        GPu^CGPyC
    BbiII         GPu^CGPyC                                       A,K
    HgiI          GPu^CGPyC


******************************************************************************
#15.                       CUTZYMES FORMAT   

GET FILE(S):   cutzymes.###
DESCRIPTION:   a list of all prototypes, their recognition sequences, cut
               sites, and enzyme type. No reference information is included.
               This is a file used by the CSHL sequence analysis programs.
EXAMPLE:

code   enzyme name        recognition sequence     cut sites    enzyme type

C      StySQI             AACNNNNNNATACG           99     14         1
C      StySQI             AACNNNNNNATATG           99     14         1
C      StySPI             AACNNNNNNGTAC            99     13         1
C      StySQI             AACNNNNNNGTACG           99     14         1
C      StySQI             AACNNNNNNGTATG           99     14         1
C      StySPI             AACNNNNNNGTGC            99     13         1
C      EcoKI              AACNNNNNNGTGC            99     13         1
C      HindIII            AAGCTT                    1      6         2
C      SspI               AATATT                    3      6         2


******************************************************************************
#16.                       STADEN FORMAT   

GET FILE(S):    staden.###
DESCRIPTION:    a list of type 2 enzymes with known recognition sequences
                that are commercially available.  Cut sites are marked with
                an apostrophe.  No reference information is included.
                This file is used by Rodger Staden's software programs.
EXAMPLE:

enzyme name/recognition sequence with cleavage site//

AatI/AGG'CCT//
AatII/GACGT'C//
AccI/GT'MKAC//
AccII/CG'CG//
AccIII/T'CCGGA//
Alw26I/GTCTCN'NNNN/'NNNNNGAGAC//
Alw44I/G'TGCAC//
AlwI/GGATCNNNN'N/'NNNNNGATCC//
BbvI/GCAGCNNNNNNNN'NNNN/'NNNNNNNNNNNNGCTGC//
BcgI/GCANNNNNNTCGNNNNNNNNNNNN'/NN'NNNNNNNNNNCGANNNNNNTGC//
BsmI/GAATGCN'/NG'CATTC//


******************************************************************************
#17.                      DNA STRIDER FORMAT   

GET FILE(S):    strider.###
DESCRIPTION:    a list of all prototypes with known recognition sequences.
                Cut sites are marked with "/".  "#" before the enzyme name
                indicates an asymmetrical cutter.  This file can be used as
                the data file for DNA Strider.
EXAMPLE:

enzyme name, recognition sequence with cleavage site,

AatII, gacgt/c,
#AciI, ccgc, 2, -2,
AcyI, gr/cgyc,
AhaIII, ttt/aaa,
AluI, ag/ct,
AlwNI, cagnnn/ctg,
ApaBI, gcannnnn/tgc,


******************************************************************************
#18.                 DNA STRIDER FORMAT (commercial)  

GET FILE(S):   striderc.###
DESCRIPTION:   a list of all commercially available prototypes with known
               recognition sequences.  Cut sites are marked with "/".  "#"
               before the enzyme name indicates an asymmetrical cutter.
               Same as format #17, except that only commercially available
               enzymes are included.  This file can be used as the data file
               for DNA Strider.
EXAMPLE:

enzyme name, recognition sequence with cleavage site,

AatII, gacgt/c,
#AciI, ccgc, 2, -2,
AcyI, gr/cgyc,
AhaIII, ttt/aaa,
AluI, ag/ct,
AlwNI, cagnnn/ctg,
ApaBI, gcannnnn/tgc,


******************************************************************************
#19.                        Bairoch format  

GET FILE(S):   bairoch.doc, bairoch.###
DESCRIPTION:   an alphabetical listing of all type I, II and III restriction
               enzymes and methylases, in a format that is compatible with
               PROSITE, SWISS-PROT, EMBL, ENZYME, ECD, EPD, HAEMB data banks.
               Also for use with PC/Gene.

Each enzyme record is organized as follows:

ID   enzyme name
ET   enzyme type
OS   microorganism name
PT   prototype
RS   recognition sequence, cut site
MS   methylation site (type)
CR   commercial sources for the restriction enzyme
CM   commercial sources for the methylase
RN   [count]
RA   authors
RL   jour, vol, pages, year, etc.
//

                         DESCRIPTION OF FIELDS

ID: restriction enzyme name
    (methylase name if no corresponding restriction enzyme with this acronym)

ET: Rn   (where n is the type of the restriction enzyme)
    M    (indicates that there is a corresponding methylase)
    Rn*  (indicates the restriction enzyme is of type n, but only recognizes
          the sequence when it is methylated.)

OS: microorganism from which this enzyme is isolated

PT: prototype of the enzyme

RS: recognition sequence, cut site; [complementary strand rec seq, cut site;]

MS: methylated base(type) [,methylated base(type) for complementary strand];
    (where methylation type is:
                                           N4mC = N4-methylcytosine
                                           5mC  = 5-methylcytosine
                                           6mA  = 6-methyladenosine

CR: REBASE single letter codes for the commercial sources of the restr. enzyme

CM: REBASE single letter codes for the commercial sources of the methylase

RN: [n]  (where n shows the count of references given for this enzyme)

RA: authors  (lastname initials[, lastname initials];

RL: publication name volume:pages(year).  (or Unpublished observations.)

//  (end-of-record marker)


EXAMPLE:

ID   AluI
ET   R2 M
OS   Arthrobacter luteus
PT   AluI
RS   AGCT, 2;
MS   3(5mC);
CR   A,B,E,F,H,I,K,L,M,N,O,P,Q,R,S,U,V,X.
CM   A,E,K,N,U.
RN   [1]
RA   Kramarov V.M., Smolyaninov V.V.;
RL   Biokhimiya 46:1526-1529(1981).
RN   [2]
RA   Roberts R.J., Myers P.A., Morrison A., Murray K.;
RL   J. Mol. Biol. 102:157-165(1976).
RN   [3]
RA   Yoon H., Suh H., Han M.H., Yoo O.J.;
RL   Korean Biochem. J. 18:82-87(1985).
RN   [4]
RA   Yoon H., Suh H., Kim K., Han M.H., Yoo O.J.;
RL   Korean Biochem. J. 18:88-93(1985).
//
ID   M.BamHII
ET   M
OS   Bacillus amyloliquefaciens H
PT   BamHII
RS   GGATCC, ?;
MS   5;
RN   [1]
RA   Connaughton J.E., Vanek P.G., Chirikjian J.G.;
RL   J. Cell Biol. 107:535a-535a(1988).
//
ID   CfuI
ET   R2*
OS   Caulobacter fusiformis BC-25
PT   DpnI
RS   GATC, 2;
RN   [1]
RA   Butkus V., Padegimiene A., Laucys V., Janulaitis A.A.;
RL   Unpublished observations.
RN   [2]
RA   Janulaitis A.A., Marcinkeviciene L.Y., Petrusyte M.P.;
RL   Dokl. Akad. Nauk SSSR 262:241-244(1982).
//

More detailed explanations for each field can be found in the accompanying
user manual file, 'bairoch.doc'.


******************************************************************************
#20.                           DNASIS  

GET FILE(S):    dnasis.###
DESCRIPTION:    restriction enzyme data file formatted for use with DNASIS.


EXAMPLE:

# of enzymes to be listed
restriction enzyme name
recognition sequence, cut site marked with a "!"

333
AatI
AGG!CCT
AatII
GACGT!C
Acc65I
G!GTACC
AccI
GT!MKAC
AccII
CG!CG
AccIII
T!CCGGA


******************************************************************************
#21.                     PUBLISHED REFERENCES   

GET FILE(S):    pubrefsa.### (large! 2.7Mb+), pubrefs.### (update file)
DESCRIPTION:    all the published references stored in REBASE complete with
                abstracts.  A monthly update file of the additions and the
                modifications to this file is maintained.

EXAMPLE:

<1> <authors>
<2> <title>
<3> <journal> or <book, publisher, editor, city>
<4> <volume>
<5> <pages>
<6> <year>
<7> <abstract>
<>

<1>Sanders, M.E., Klaenhammer, T.R.
<2>Phage resistance in a phage-insensitive strain of Streptococcus lactis:
temperature-dependent phage development and host-controlled phage replication
<3>Appl. Environ. Microbiol.
<4>47
<5>979-985
<6>1984
<7>Streptococcus lactis ME2 is a dairy starter strain that is insensitive to a
variety of phage, including Phi18.  The efficiency of plating of Phi18 on ME2
and N1 could be increased from <1 X 10-9 to 5.0 X 10-2 and from 7.6 X 10-7
to 2.1 X 10-2, respectively, when the host strains were subcultured at 40C
before plating the phage and the phage assay plates were incubated at 40C.
Host-dependent replication was demonstrated in N1 at 30C and in N1 and ME2
at 40C, suggesting the operation of a temperature-sensitive restriction and
modification system in MER2 and N1.  The increased sensitivity of ME2 and N1
to Phi18 at 40C was also demonstrated by lysis of broth cultures and increase
in plaque size.  ME2 grown at 40C showed an increased ability to adsorb Phi18
indicating a second target for temperature-dependent phage sensitivity in ME2.
Challenge of N1 with a Phi18 preparation that had been previously modified
for growth on N1 indicated that at 40C phage development was characterized by
a shorter latent period and larger burst size than at 30C.  The evidence
presented suggests that the high degree of phage insensitivity expressed by
ME2 consists of a variety of temperature-sensitive mechanisms, including (i)
the prevention of phage adsorption, (ii) host-controlled restriction of
phage, and (iii) suppression of phage development.  At 30C these factors
appear to act cooperatively to prevent the successful emergence of lytic
phage active against S. lactis ME2.
<>


******************************************************************************
#22.                    PROCITE REFERENCES  

GET FILE(S):   procitea.### (large! 2.7Mb+), procite.### (update file)
DESCRIPTION:   all the published references stored in REBASE complete with
               abstracts, formatted for use with Pro-Cite software.  Also a
               monthly update of the additions and modifications to this
               file is maintained.  This file does not survive email, thus
               those who require this data file must retrieve it from our
               ftp site.

EXAMPLE:

For a journal article:
@D<tab>Author1//Author2 <tab>Title<tab>Journal<tab>Year<tab>Volume<tab>
<tab>Pages<tab><tab><tab>Abstract<tab><tab><return>

For a book article:
@A<tab>Author1//Author2 <tab><tab>Title<tab><tab><tab>Editor1//Editor2 <tab>
<tab>Book<tab><tab><tab><tab>City<tab>Publisher<tab>Year<tab><tab>Volume
<tab><tab>Pages<tab><tab><tab><tab><tab><tab><tab><tab><tab>Abstract<tab>
<tab><return>

@D\tHo, D.K.//Wu, J.C.//Santi, D.V.//Floss, H.G.\tStereochemical studies of
the C-methylation of deoxycytidine catalyzed by Hhal methylase and the
N-methylation of deoxyadenosine catalyzed by EcoRI methylase.\tArch. Biochem.
Biophys.\t1991\t284\t264-269\t\t\tThe steric course of methyl group transfer
catalyzed by two DNA methylases, HhaI methylase, a DNA (cytosine-5)
methyltransferase, and EcoRI methylase, which methylates at N6 of adenosine,
has been studied with (methyl-R)- and (methyl-S)-[methyl-2H1,3H]
adenosylmethionine as the methyl donor, using as substrates poly-d(GC) (HhaI)
and the dodecamer oligonucleotide duplex d(CGCGAATTCGCG) (EcoRI),
respectively. The methylated nucleotides were degraded to convert the chiral
methyl groups into acetic acid for configurational analysis. It was found
that both enzymatic reactions proceed with inversion of configuration of the
methyl group.\t\t


******************************************************************************
#23.                       GENEPRO FORMAT  

GET FILE(S):   genepro.###
DESCRIPTION:   REBASE enzyme data file in a format specifically designed to
               be used with GENEPRO.

EXAMPLE:

<enzyme name> $ tab # <recognition sequence with cut sites marked> * newline

AaaI$   #4C^GGCCG*
AacI$   #4GGATCC*
AaeI$   #4GGATCC*
AagI$   #4AT^CGAT*
AatI$   #4AGG^CCT*
AatII$  #4GACGT^C*
AbrI$   #4C^TCGAG*
AcaI$   #4TTCGAA*
AcaII$  #4GGATCC*
AcaIII$ #4TGCGCA*


******************************************************************************
#24.                 GENEPRO FORMAT (commercial)  

GET FILE(S):   geneproc.###
DESCRIPTION:   REBASE enzyme data file in a format specifically designed to
               be used with GENEPRO.  Differs from the regular genepro format
               inthat only commercially available enzymes are listed.

EXAMPLE:

<enzyme name> $ tab # <recognition sequence with cut sites marked> * newline

AaaI$   #4C^GGCCG*
AacI$   #4GGATCC*
AaeI$   #4GGATCC*
AagI$   #4AT^CGAT*
AbrI$   #4C^TCGAG*
AcaI$   #4TTCGAA*
AcaII$  #4GGATCC*
AcaIII$ #4TGCGCA*
AcaIV$  #4GGCC*
Acc38I$ #4CCWGG*


******************************************************************************
#25.                         REBASE NEWS  

GET FILE(S):   NEWS.###
DESCRIPTION:   A newsletter style report of any special changes since the
               previous REBASE version, such as any enzyme name changes,
               announcements of new REBASE formats, new commercial suppliers,
               corrections, etc.  Automatically sent to each subscriber of
               any of our formats.  (Especially useful for ftp-ers, as an
               email notification indicating a new REBASE version is ready.)

-----------------------------------------------------------------------------



More information about the Methods mailing list