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Plasmid Files

pBC KS(-)

Phagemid vector derived from pBluescript II KS(–), with a chloramphenicol resistance gene. The MCS is reversed relative to pBC SK(–).

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pBC KS(-) Sequence and MappBC KS(-).dna
Map and Sequence File   
Sequence Author:  Agilent Technologies
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 NgoMIV (129) XmnI (3083) BclI * (3057) Bsu36I (2993) AgeI (2943) PflFI - Tth111I (2886) BstBI (2869) ScaI (2755) TatI (2753) NcoI - StyI (2639) MscI (2605) BpmI (2460) BsrDI (2357) SnaBI (2344) BspEI (2334) NaeI (131) DraIII (237) PsiI (362) BglI (472) FspI (479) PvuI (500) BmrI (580) Eco53kI (655) SacI (657) AleI (663) SacII (664) BstXI (665) EagI - NotI (670) XbaI (677) SpeI (683) BamHI (689) TspMI - XmaI (695) SmaI (697) PstI (705) EcoRI (707) EcoRV (715) HindIII (719) BspDI - ClaI (726) SalI (734) AccI (735) HincII (736) AbsI - PaeR7I - PspXI - XhoI (740) EcoO109I - PspOMI (749) ApaI (753) Acc65I (755) KpnI (759) M13 rev lac operator BspQI - SapI (1037) AflIII - PciI (1153) NspI (1157) AlwNI (1569) pBC KS(-) 3400 bp
NgoMIV  (129)
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.
XmnI  (3083)
1 site
G A A N N N N T T C C T T N N N N A A G
BclI  (3057)
1 site
T G A T C A A C T A G T
* Blocked by Dam methylation.
BclI is typically used at 50-55°C, but is 50% active at 37°C.
Bsu36I  (2993)
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.
AgeI  (2943)
1 site
A C C G G T T G G C C A

AgeI quickly loses activity at 37°C, but can be used at 25°C for
long incubations.
PflFI  (2886)
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  (2886)
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.
BstBI  (2869)
1 site
T T C G A A A A G C T T
ScaI  (2755)
1 site
A G T A C T T C A T G A
TatI  (2753)
1 site
W G T A C W W C A T G W
NcoI  (2639)
1 site
C C A T G G G G T A C C
StyI  (2639)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
MscI  (2605)
1 site
T G G C C A A C C G G T
BpmI  (2460)
1 site
C T G G A G ( N ) 14 N N G A C C T C ( N ) 14

Efficient cleavage requires at least two copies of the BpmI
recognition sequence.
Sticky ends from different BpmI sites may not be compatible.
After cleavage, BpmI can remain bound to DNA and alter its
electrophoretic mobility.
BpmI quickly loses activity at 37°C.
BsrDI  (2357)
1 site
G C A A T G N N C G T T A C

Sticky ends from different BsrDI sites may not be compatible.
SnaBI  (2344)
1 site
T A C G T A A T G C A T
BspEI  (2334)
1 site
T C C G G A A G G C C T
NaeI  (131)
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.
DraIII  (237)
1 site
C A C N N N G T G G T G N N N C A C

Sticky ends from different DraIII sites may not be compatible.
PsiI  (362)
1 site
T T A T A A A A T A T T
BglI  (472)
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.
FspI  (479)
1 site
T G C G C A A C G C G T
PvuI  (500)
1 site
C G A T C G G C T A G C
BmrI  (580)
1 site
A C T G G G ( N ) 4 N T G A C C C ( N ) 4

The 1-base overhangs produced by BmrI may be hard to ligate.
Sticky ends from different BmrI sites may not be compatible.
Unlike most restriction enzymes, BmrI can cleave DNA in the
absence of magnesium.
Eco53kI  (655)
1 site
G A G C T C C T C G A G
SacI  (657)
1 site
G A G C T C C T C G A G
AleI  (663)
1 site
C A C N N N N G T G G T G N N N N C A C
SacII  (664)
1 site
C C G C G G G G C G C C

Efficient cleavage requires at least two copies of the SacII
recognition sequence.
BstXI  (665)
1 site
C C A N N N N N N T G G G G T N N N N N N A C C

Sticky ends from different BstXI sites may not be compatible.
EagI  (670)
1 site
C G G C C G G C C G G C
NotI  (670)
1 site
G C G G C C G C C G C C G G C G
XbaI  (677)
1 site
T C T A G A A G A T C T
SpeI  (683)
1 site
A C T A G T T G A T C A
BamHI  (689)
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.
TspMI  (695)
1 site
C C C G G G G G G C C C
XmaI  (695)
1 site
C C C G G G G G G C C C

Efficient cleavage requires at least two copies of the XmaI
recognition sequence.
Full cleavage with XmaI may require a long incubation.
SmaI  (697)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
PstI  (705)
1 site
C T G C A G G A C G T C
EcoRI  (707)
1 site
G A A T T C C T T A A G
EcoRV  (715)
1 site
G A T A T C C T A T A G

EcoRV is reportedly more prone than its isoschizomer Eco32I to
delete a base after cleavage.
HindIII  (719)
1 site
A A G C T T T T C G A A
BspDI  (726)
1 site
A T C G A T T A G C T A
ClaI  (726)
1 site
A T C G A T T A G C T A
SalI  (734)
1 site
G T C G A C C A G C T G
AccI  (735)
1 site
G T M K A C C A K M T G

Efficient cleavage with AccI requires ≥13 bp on each side of the
recognition sequence.
Sticky ends from different AccI sites may not be compatible.
HincII  (736)
1 site
G T Y R A C C A R Y T G
AbsI  (740)
1 site
C C T C G A G G G G A G C T C C
PaeR7I  (740)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (740)
1 site
V C T C G A G B B G A G C T C V
XhoI  (740)
1 site
C T C G A G G A G C T C
EcoO109I  (749)
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.
PspOMI  (749)
1 site
G G G C C C C C C G G G
ApaI  (753)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
Acc65I  (755)
1 site
G G T A C C C C A T G G
KpnI  (759)
1 site
G G T A C C C C A T G G
BspQI  (1037)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different BspQI sites may not be compatible.
SapI  (1037)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different SapI sites may not be compatible.
SapI gradually settles in solution, so a tube of SapI should be
mixed before removing an aliquot.
AflIII  (1153)
1 site
A C R Y G T T G Y R C A

Sticky ends from different AflIII sites may not be compatible.
PciI  (1153)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
NspI  (1157)
1 site
R C A T G Y Y G T A C R
AlwNI  (1569)
1 site
C A G N N N C T G G T C N N N G A C

Sticky ends from different AlwNI sites may not be compatible.
CmR
2125 .. 2784  =  660 bp
219 amino acids  =  25.6 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
2125 .. 2784  =  660 bp
219 amino acids  =  25.6 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
ori
1214 .. 1802  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
1214 .. 1802  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
f1 ori
4 .. 459  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
4 .. 459  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
MCS
653 .. 760  =  108 bp
pBluescript multiple cloning site
MCS
653 .. 760  =  108 bp
pBluescript multiple cloning site
cat promoter
2022 .. 2124  =  103 bp
promoter of the E. coli cat gene
cat promoter
2022 .. 2124  =  103 bp
promoter of the E. coli cat gene
lac promoter
860 .. 890  =  31 bp
   Segment 3:  -10  
   860 .. 866  =  7 bp
promoter for the E. coli lac operon
lac promoter
860 .. 890  =  31 bp
   Segment 2:  
   867 .. 884  =  18 bp
promoter for the E. coli lac operon
lac promoter
860 .. 890  =  31 bp
   Segment 1:  -35  
   885 .. 890  =  6 bp
promoter for the E. coli lac operon
lac promoter
860 .. 890  =  31 bp
3 segments
promoter for the E. coli lac operon
T7 promoter
626 .. 644  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
626 .. 644  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T3 promoter
773 .. 791  =  19 bp
promoter for bacteriophage T3 RNA polymerase
T3 promoter
773 .. 791  =  19 bp
promoter for bacteriophage T3 RNA polymerase
M13 fwd
600 .. 616  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
600 .. 616  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
812 .. 828  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
812 .. 828  =  17 bp
common sequencing primer, one of multiple similar
variants
lac operator
836 .. 852  =  17 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
836 .. 852  =  17 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).
lacZα
451 .. 816  =  366 bp
121 amino acids  =  13.5 kDa
Product: LacZα fragment of β-galactosidase
lacZα
451 .. 816  =  366 bp
121 amino acids  =  13.5 kDa
Product: LacZα fragment of β-galactosidase
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