<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><
><><>
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Dr. Richard J. Roberts Restriction Enzyme Database
Copyright (c) New England BioLabs, Inc. 1995
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unpublished observations (dating back to 1952).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.
Dr. Richard J. Roberts
New England BioLabs
32 Tozer Road
Beverly, Massachusetts 01915 U.S.A.
phone:
fax:
(508) 927-5054
(508) 921-1527
email:
REVIEWS:
roberts@neb.com
See Nucleic Acids Research 22: 3628-3639, 1994.
*************************************************************************
*****
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
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' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^
3'
5'
This will be described in some REBASE reports as:
Bsp24I (8/13)GACNNNNNNTGG(12/7)
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
address)
cd pub/rebase
dir
get README |more
get README
quit
(username: anonymous, password: your email
(to enter the correct directory)
(to list the names of available files)
(to view the file called README, spaces matter!)
(to copy the file called README to your machine)
(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@neb.com
*************************************************************************
*****
CURRENT EMAILING LIST
& FTP SITE FORMATS
#1.
#2.
#3.
#4.
#5.
#6.
#7.
#8.
#9.
#10.
#11.
#12.
#13.
#14.
#15.
#16.
#17.
#18.
#19.
#20.
#21.
#22.
#23.
#24.
#25.
#26.
COMMERCIAL SOURCES
GCG
GCG - with refs
Nucleic Acids Research
Prototypes
Type II
Type II (with isos)
Type II (with tabs)
All Enzymes (w/ ref list)
All Enzymes (each w/ ref)
All Enzymes (parsed refs)
All Enzymes (by microorg)
IGSuite
ALPHAZYMES
CUTZYMES
STADEN
DNA Strider
DNA Strider (commercial)
PC/Gene (Bairoch) Format
DNASIS
PUBLISHED REFS
PROCITE REFS
GENEPRO
GENEPRO (commercial)
REBASE NEWS (release notes)
Prototypes and Neoschizomers
FILES to get (### = current version
ex. 406 indicates June 1994)
commdata.###
gcg.###
gcgenz.###, gcgref.###
nar.###
proto.###
type2.###, type2ref.###
gtype2.###, type2ref.###
itype2.###, type2ref.###
allenz.###
withref.###
parsrefs.###
orgref.###
bionet.###
azymes.###
cutzymes.###
staden.###
strider.###
striderc.###
bairoch.doc, bairoch.###
dnasis.###
pubrefs.###, pubrefsa.###
procite.###, procitea.###
genepro.###
geneproc.###
NEWS.###
neos.###
DESCRIPTIONS OF AVAILABLE FORMATS:
*************************************************************************
*****
#1.
COMPLETE COMMERCIAL SOURCE INFORMATION
GET FILE(S):
DESCRIPTION:
and
commdata.###
a list of commmercial sources of both restriction enzymes
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):
DESCRIPTION:
gcg.###
format used as input for the Sequence Analysis Software
Package by Genetics Computer Group.
(commercial abbreviations as assigned in REBASE)
EXAMPLE:
enzyme name
abbrs
cut site
..
;AatI
3 AGG'CCT
AatII
5 G_ACGT'C
AccI
2 GT'mk_AC
>ABEGIKMNOPRSUVX
;AccII
2 CG'CG
;AccIII
1 T'CCGG_A
AgeI
1 A'CCGG_T
AluI
2 AG'CT
>ABEFGIKMNOPRSUVX
rec seq w cut sites marked
0 !
-4 !
2 !
0
4
4
0
!
!
!
!
overhang
commer
StuI,Eco147I
>OU
>EGMNOPRSUVX
ThaI,BstUI,MvnI,Bsp50I
BspMII,Kpn2I,MroI
>AEGKVX
>AEGKR
>
*************************************************************************
*****
#3.
GCG - with refs
GET FILE(S):
DESCRIPTION:
Sequence
gcgenz.###, gcgref.###
two files: the first can be used as input for the
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.
reference
information is given.
EXAMPLE of enzyme file:
Same as format #2, except
enzyme name
refs
cut site
rec seq w cut sites marked
overhang
commer
..
;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):
DESCRIPTION:
nar.###
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
refs
isoschizomer
refs
rec seq w cut site
methylation site, type
commer
rec seq w cut site
methylation site, type
commer
AatII
AciI
AhaIII
DraI
ApaI
5,7
Bsp120I
1,2
GACGT^C
CCGC(-3/-1)
TTT^AAA
TTT^AAA
GGGCC^C
References:
G^GGCCC
EJLMNO
N
4(5)
KLMNO
KLMNOX
F
6
3
8
4
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: 54675474
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):
DESCRIPTION:
proto.###
a list of all prototypes and their recognition sequences
(cut sites indicated).
EXAMPLE:
enzyme name
recognition sequence with cleavage site
AatII
AccI
AcyI
AflII
AflIII
GACGT^C
GT^MKAC
GR^CGYC
C^TTAAG
A^CRYGT
*************************************************************************
*****
#6.
Type II format
GET FILE(S):
DESCRIPTION:
type2.###, type2ref.###
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.
2.
Acids
3.
Degtyarev, S.K. unpublished observations.
Seurinck, J., Van de Voorde, A., Van Montagu, M. (1983) Nucl.
Res. 11: 4409-4415.
Trautner, T.A. unpublished observations.
*************************************************************************
*****
#7.
Type II with Isoschizomers
GET FILE(S):
DESCRIPTION:
gtype2.###, type2ref.###
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):
DESCRIPTION:
itype2.###, type2ref.###
a list of type II enzymes and a
references. Same as format #1,
separated by tabs, so that each
line. Separate reference file,
list of their associated
except that the fields are
enzyme entry is on a single
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
320,507,700,701
AlwI
BinI
Alw21I
HgiAI
Alw26I
BsmAI
Alw44I
ApaLI
AlwNI
AG^CT
GGATC(4/5)
GWGCW^C
GTCTC(1/5)
G^TGCAC
CAGNNN^CTG
3(5)
ABDEFGHIJKLMNOPQRSUVX
NU
DF
DFR
DFORU
NU
404
226
161
226
407
*************************************************************************
*****
#9.
ALL ENZYMES (REFERENCE LIST)
GET FILE(S):
DESCRIPTION:
allenz.###
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.
2.
3.
4.
18:
Kramarov, V.M., Smolyaninov, V.V. (1981) Biokhimiya 46: 1526-1529
Morgan, R., Bonventre, J. unpublished observations.
Roberts, R.J., Myers, P.A., Morrison, A., Murray, K. (1976) J. Mol.
Biol. 102: 157-165
Yoon, H., Suh, H., Han, M.H., Yoo, O.J. (1985) Korean Biochem. J.
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):
DESCRIPTION:
withref.###
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):
DESCRIPTION:
parsrefs.###
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):
DESCRIPTION:
orgref.###
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):
DESCRIPTION:
their
bionet.###
an alphabetical listing of Type II restriction enzymes,
prototypes, and recognition sequences (with cut sites
indicated).
EXAMPLE:
enzyme name (prototype)
recognition sequence with cleavage site
AaaI (XmaIII)
AacI (BamHI)
AatI (StuI)
AatII
AcaII (BamHI)
C^GGCCG
GGATCC
AGG^CCT
GACGT^C
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
isoschizomer
recognition sequence w cut site
recognition sequence w cut site
enzyme type
commer
commer
AatII
AccI
DsaVI
AcyI
AhaII
AosII
AstWI
AsuIII
BbiII
HgiI
GACGT^C
GT^(A/C)(G/T)AC
GT(A/C)(G/T)AC
GPu^CGPyC
GPu^CGPyC
GPu^CGPyC
GPu^CGPyC
GPu^CGPyC
GPu^CGPyC
GPu^CGPyC
2
2
G,M,N,O
M,N,S
2
M,R,U
N
A,K
*************************************************************************
*****
#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
type
enzyme name
recognition sequence
cut sites
C
C
C
C
C
C
C
C
C
StySQI
StySQI
StySPI
StySQI
StySQI
StySPI
EcoKI
HindIII
SspI
AACNNNNNNATACG
AACNNNNNNATATG
AACNNNNNNGTAC
AACNNNNNNGTACG
AACNNNNNNGTATG
AACNNNNNNGTGC
AACNNNNNNGTGC
AAGCTT
AATATT
99
99
99
99
99
99
99
1
3
14
14
13
14
14
13
13
6
6
enzyme
1
1
1
1
1
1
1
2
2
*************************************************************************
*****
#16.
STADEN FORMAT
GET FILE(S):
DESCRIPTION:
staden.###
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:
sequences.
a list of all prototypes with known recognition
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):
DESCRIPTION:
striderc.###
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):
DESCRIPTION:
restriction
bairoch.doc, bairoch.###
an alphabetical listing of all type I, II and III
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
ET
OS
PT
RS
MS
CR
CM
RN
RA
RL
//
enzyme name
enzyme type
microorganism name
prototype
recognition sequence, cut site
methylation site (type)
commercial sources for the restriction enzyme
commercial sources for the methylase
[count]
authors
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)
strand];
(where methylation type is:
N4mC =
5mC =
6mA =
for complementary
N4-methylcytosine
5-methylcytosine
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
ET
OS
PT
RS
MS
CR
CM
RN
RA
RL
RN
RA
RL
RN
RA
RL
RN
RA
RL
//
ID
ET
OS
PT
RS
MS
RN
RA
RL
//
ID
ET
OS
PT
RS
RN
RA
RL
RN
RA
RL
//
AluI
R2 M
Arthrobacter luteus
AluI
AGCT, 2;
3(5mC);
A,B,E,F,H,I,K,L,M,N,O,P,Q,R,S,U,V,X.
A,E,K,N,U.
[1]
Kramarov V.M., Smolyaninov V.V.;
Biokhimiya 46:1526-1529(1981).
[2]
Roberts R.J., Myers P.A., Morrison A., Murray K.;
J. Mol. Biol. 102:157-165(1976).
[3]
Yoon H., Suh H., Han M.H., Yoo O.J.;
Korean Biochem. J. 18:82-87(1985).
[4]
Yoon H., Suh H., Kim K., Han M.H., Yoo O.J.;
Korean Biochem. J. 18:88-93(1985).
M.BamHII
M
Bacillus amyloliquefaciens H
BamHII
GGATCC, ?;
5;
[1]
Connaughton J.E., Vanek P.G., Chirikjian J.G.;
J. Cell Biol. 107:535a-535a(1988).
CfuI
R2*
Caulobacter fusiformis BC-25
DpnI
GATC, 2;
[1]
Butkus V., Padegimiene A., Laucys V., Janulaitis A.A.;
Unpublished observations.
[2]
Janulaitis A.A., Marcinkeviciene L.Y., Petrusyte M.P.;
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):
DESCRIPTION:
DNASIS.
dnasis.###
restriction enzyme data file formatted for use with
This file contains EOLN (end of line) characters which
get
lost via email and while ftping in ascii transfer mode.
So
for best results, ftp it using binary mode.
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):
DESCRIPTION:
with
pubrefsa.### (large! 2.7Mb+), pubrefs.### (update file)
all the published references stored in REBASE complete
abstracts.
A monthly update file of the additions and
the
modifications to this file is maintained.
EXAMPLE:
<1> <authors>
<2> <title>
<3>
<4>
<5>
<6>
<7>
<>
<journal> or <book, publisher, editor, city>
<volume>
<pages>
<year>
<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 107
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):
DESCRIPTION:
with
procitea.### (large! 2.7Mb+), procite.### (update file)
all the published references stored in REBASE complete
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):
DESCRIPTION:
to
genepro.###
REBASE enzyme data file in a format specifically designed
be used with GENEPRO.
EXAMPLE:
<enzyme name> $ tab # <recognition sequence with cut sites marked> *
newline
AaaI$
AacI$
AaeI$
AagI$
AatI$
AatII$
AbrI$
AcaI$
AcaII$
AcaIII$
#4C^GGCCG*
#4GGATCC*
#4GGATCC*
#4AT^CGAT*
#4AGG^CCT*
#4GACGT^C*
#4C^TCGAG*
#4TTCGAA*
#4GGATCC*
#4TGCGCA*
*************************************************************************
*****
#24.
GENEPRO FORMAT (commercial)
GET FILE(S):
DESCRIPTION:
to
geneproc.###
REBASE enzyme data file in a format specifically designed
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$
AacI$
AaeI$
AagI$
AbrI$
AcaI$
AcaII$
AcaIII$
AcaIV$
Acc38I$
#4C^GGCCG*
#4GGATCC*
#4GGATCC*
#4AT^CGAT*
#4C^TCGAG*
#4TTCGAA*
#4GGATCC*
#4TGCGCA*
#4GGCC*
#4CCWGG*
*************************************************************************
*****
#25.
REBASE NEWS
GET FILE(S):
DESCRIPTION:
NEWS.###
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.)
*************************************************************************
*****
#26.
Prototypes and Their Neoschizomers
GET FILE(S):
DESCRIPTION:
neos.###
A list of Type I, II, and III prototypes together with an
example of all neoschizomers known for each specificity.
EXAMPLE:
prototype
neoschizomer
ApaI
Bsp120I
ApaBI
ApaLI
ApoI
AvaI
Nli387/7I
recognition sequence with cleavage site
recognition sequence with cleavage site
GGGCC^C
G^GGCCC
GCANNNNN^TGC
G^TGCAC
R^AATTY
C^YCGRG
CYCGR^G
*************************************************************************
*****
ADDITIONAL NOTES:
Enzyme data file updates are available for Gene Construction Kit
users.
There is a mailing list for REBASE data files that are specially
converted by
Bob Gross at Dartmouth University for use with Gene Construction Kit.
Send
email to Robert.H.Gross@dartmouth.edu to sign up. The service is free.
<end of REBASE.DOC>
-----------------------------------------------------------------------------