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Plasmid Files

pCDF-1b

Bacterial vector with a CloDF13 (CDF) origin for the regulated expression of N-terminally 6xHis-tagged proteins.

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pCDF-1b Sequence and MappCDF-1b.dna
Map and Sequence File   
Sequence Author:  Novagen (EMD Millipore)
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 T7 promoter EcoNI (3594) PfoI (3558) AclI (3466) BstAPI (3450) MluI (3126) ApaI (2923) PspOMI (2919) HpaI (2624) BsmBI (2511) PluTI (2491) SfoI (2489) NarI * (2488) KasI (2487) XbaI (2206) NcoI (69) PmlI (94) Acc65I (98) KpnI (102) BstBI (107) PshAI (126) BspEI * (130) BamHI (133) MfeI (139) Eco53kI (148) BssS α I (149) SacI (150) BsrGI - TatI (153) AscI (161) PstI - SbfI (171) SalI (173) HindIII (179) EagI - NotI (186) AvaI - BsoBI - PaeR7I - PspXI - XhoI (194) BmeT110I (195) PacI (269) AvrII (273) EcoO109I (318) Bsu36I (357) DrdI - PflFI - Tth111I (466) NgoMIV (659) NaeI (661) BglI (683) PvuI (933) SspI (1328) BspHI (1359) NheI (1406) BmtI (1410) PciI (1506) NspI (1510) SgrAI (1533) pCDF-1b 3621 bp
EcoNI  (3594)
1 site
C C T N N N N N A G G G G A N N N N N T C C

The 1-base overhangs produced by EcoNI may be hard to ligate.
Sticky ends from different EcoNI sites may not be compatible.
PfoI  (3558)
1 site
T C C N G G A A G G N C C T

Sticky ends from different PfoI sites may not be compatible.
AclI  (3466)
1 site
A A C G T T T T G C A A
BstAPI  (3450)
1 site
G C A N N N N N T G C C G T N N N N N A C G

Sticky ends from different BstAPI sites may not be compatible.
MluI  (3126)
1 site
A C G C G T T G C G C A
ApaI  (2923)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
PspOMI  (2919)
1 site
G G G C C C C C C G G G
HpaI  (2624)
1 site
G T T A A C C A A T T G
BsmBI  (2511)
1 site
C G T C T C N G C A G A G N ( N ) 4

Sticky ends from different BsmBI sites may not be compatible.
PluTI  (2491)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the PluTI
recognition sequence.
SfoI  (2489)
1 site
G G C G C C C C G C G G
NarI  (2488)
1 site
G G C G C C C C G C G G
* Blocked by Dcm methylation.
Efficient cleavage requires at least two copies of the NarI
recognition sequence.
KasI  (2487)
1 site
G G C G C C C C G C G G
XbaI  (2206)
1 site
T C T A G A A G A T C T
NcoI  (69)
1 site
C C A T G G G G T A C C
PmlI  (94)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
Acc65I  (98)
1 site
G G T A C C C C A T G G
KpnI  (102)
1 site
G G T A C C C C A T G G
BstBI  (107)
1 site
T T C G A A A A G C T T
PshAI  (126)
1 site
G A C N N N N G T C C T G N N N N C A G

PshAI quickly loses activity at 37°C, but can be used at 25°C for
long incubations.
BspEI  (130)
1 site
T C C G G A A G G C C T
* Blocked by Dam methylation.
BamHI  (133)
1 site
G G A T C C C C T A G G

After cleavage, BamHI-HF™ (but not the original BamHI) can
remain bound to DNA and alter its electrophoretic mobility.
MfeI  (139)
1 site
C A A T T G G T T A A C
Eco53kI  (148)
1 site
G A G C T C C T C G A G
BssSαI  (149)
1 site
C A C G A G G T G C T C
SacI  (150)
1 site
G A G C T C C T C G A G
BsrGI  (153)
1 site
T G T A C A A C A T G T

BsrGI is typically used at 37°C, but is even more active at 60°C.
TatI  (153)
1 site
W G T A C W W C A T G W
AscI  (161)
1 site
G G C G C G C C C C G C G C G G
PstI  (171)
1 site
C T G C A G G A C G T C
SbfI  (171)
1 site
C C T G C A G G G G A C G T C C
SalI  (173)
1 site
G T C G A C C A G C T G
HindIII  (179)
1 site
A A G C T T T T C G A A
EagI  (186)
1 site
C G G C C G G C C G G C
NotI  (186)
1 site
G C G G C C G C C G C C G G C G
AvaI  (194)
1 site
C Y C G R G G R G C Y C

Sticky ends from different AvaI sites may not be compatible.
BsoBI  (194)
1 site
C Y C G R G G R G C Y C

Sticky ends from different BsoBI sites may not be compatible.
BsoBI is typically used at 37°C, but can be used at temperatures
up to 65°C.
PaeR7I  (194)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (194)
1 site
V C T C G A G B B G A G C T C V
XhoI  (194)
1 site
C T C G A G G A G C T C
BmeT110I  (195)
1 site
C Y C G R G G R G C Y C
PacI  (269)
1 site
T T A A T T A A A A T T A A T T
AvrII  (273)
1 site
C C T A G G G G A T C C
EcoO109I  (318)
1 site
R G G N C C Y Y C C N G G R

Sticky ends from different EcoO109I sites may not be compatible.
Bsu36I  (357)
1 site
C C T N A G G G G A N T C C

Sticky ends from different Bsu36I sites may not be compatible.
DrdI  (466)
1 site
G A C N N N N N N G T C C T G N N N N N N C A G

Sticky ends from different DrdI sites may not be compatible.
PflFI  (466)
1 site
G A C N N N G T C C T G N N N C A G

The 1-base overhangs produced by PflFI may be hard to ligate.
Sticky ends from different PflFI sites may not be compatible.
Tth111I  (466)
1 site
G A C N N N G T C C T G N N N C A G

The 1-base overhangs produced by Tth111I may be hard to ligate.
Sticky ends from different Tth111I sites may not be compatible.
NgoMIV  (659)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NgoMIV
recognition sequence.
NaeI  (661)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NaeI
recognition sequence.
BglI  (683)
1 site
G C C N N N N N G G C C G G N N N N N C C G

Sticky ends from different BglI sites may not be compatible.
PvuI  (933)
1 site
C G A T C G G C T A G C
SspI  (1328)
1 site
A A T A T T T T A T A A
BspHI  (1359)
1 site
T C A T G A A G T A C T
NheI  (1406)
1 site
G C T A G C C G A T C G
BmtI  (1410)
1 site
G C T A G C C G A T C G
PciI  (1506)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
NspI  (1510)
1 site
R C A T G Y Y G T A C R
SgrAI  (1533)
1 site
C R C C G G Y G G Y G G C C R C

Efficient cleavage requires at least two copies of the SgrAI
recognition sequence.
lacI
2399 .. 3481  =  1083 bp
360 amino acids  =  38.6 kDa
Product: lac repressor
The lac repressor binds to the lac operator to inhibit
transcription in E. coli. This inhibition can be
relieved by adding lactose or
isopropyl-β-D-thiogalactopyranoside (IPTG).
lacI
2399 .. 3481  =  1083 bp
360 amino acids  =  38.6 kDa
Product: lac repressor
The lac repressor binds to the lac operator to inhibit
transcription in E. coli. This inhibition can be
relieved by adding lactose or
isopropyl-β-D-thiogalactopyranoside (IPTG).
SmR
520 .. 1311  =  792 bp
263 amino acids  =  29.3 kDa
Product: aminoglycoside adenylyltransferase
(Murphy, 1985)
confers resistance to spectinomycin and
streptomycin
SmR
520 .. 1311  =  792 bp
263 amino acids  =  29.3 kDa
Product: aminoglycoside adenylyltransferase
(Murphy, 1985)
confers resistance to spectinomycin and
streptomycin
CloDF13 ori
1451 .. 2189  =  739 bp
Plasmids containing the CloDF13 (CDF) origin of
replication can be propagated in E. coli cells that
contain additional plasmids with compatible origins.
CloDF13 ori
1451 .. 2189  =  739 bp
Plasmids containing the CloDF13 (CDF) origin of
replication can be propagated in E. coli cells that
contain additional plasmids with compatible origins.
MCS
69 .. 278  =  210 bp
multiple cloning site
MCS
69 .. 278  =  210 bp
multiple cloning site
AmpR promoter
1312 .. 1403  =  92 bp
AmpR promoter
1312 .. 1403  =  92 bp
lacI promoter
3482 .. 3559  =  78 bp
lacI promoter
3482 .. 3559  =  78 bp
T7 terminator
302 .. 349  =  48 bp
transcription terminator for bacteriophage T7 RNA
polymerase
T7 terminator
302 .. 349  =  48 bp
transcription terminator for bacteriophage T7 RNA
polymerase
lac operator
3 .. 27  =  25 bp
The lac repressor binds to the lac operator to inhibit
transcription in E. coli. This inhibition can be
relieved by adding lactose or
isopropyl-β-D-thiogalactopyranoside (IPTG).
lac operator
3 .. 27  =  25 bp
The lac repressor binds to the lac operator to inhibit
transcription in E. coli. This inhibition can be
relieved by adding lactose or
isopropyl-β-D-thiogalactopyranoside (IPTG).
T7 promoter
3605 .. 2  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
3605 .. 2  =  19 bp
promoter for bacteriophage T7 RNA polymerase
RBS
58 .. 63  =  6 bp
ribosome binding site
RBS
58 .. 63  =  6 bp
ribosome binding site
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