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Plasmid Files

pBAD-TOPO® (linearized)

Linearized vector with 3'-T overhangs and bound topoisomerase, for TOPO® TA cloning and arabinose-inducible expression.

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pBAD-TOPO (linearized) Sequence and MappBAD-TOPO (linearized).dna
Map and Sequence File   
Sequence Author:  Invitrogen (Life Technologies)
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 PflMI (3660) BspEI (3455) NruI (3448) EcoRV (3126) AflII (3041) BsaBI (2981) BmeT110I (2895) AvaI - BsoBI (2894) NsiI (2749) SphI (2747) MauBI (2725) BsmBI (2659) PfoI (2657) PflFI - Tth111I (2558) BsaAI (2552) BstZ17I (2533) AccI (2532) NdeI (2481) PciI (2302) AlwNI (1893) BanI (1461) BstEII (3817) BsmI (3837) RBS BtgI - NcoI - StyI (4084) ATG BanII (4092) End (4127) Start (1) BseRI (28) PmeI (91) HincII (872) ScaI (933) PvuI (1045) FspI (1191) AseI (1239) NmeAIII (1267) BglI (1296) AhdI (1414) pBAD-TOPO® 4126 bp
PflMI  (3660)
1 site
C C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
BspEI  (3455)
1 site
T C C G G A A G G C C T
NruI  (3448)
1 site
T C G C G A A G C G C T
EcoRV  (3126)
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.
AflII  (3041)
1 site
C T T A A G G A A T T C

The sticky ends produced by AflII are hard to ligate.
BsaBI  (2981)
1 site
G A T N N N N A T C C T A N N N N T A G
BmeT110I  (2895)
1 site
C Y C G R G G R G C Y C
AvaI  (2894)
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  (2894)
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.
NsiI  (2749)
1 site
A T G C A T T A C G T A
SphI  (2747)
1 site
G C A T G C C G T A C G
MauBI  (2725)
1 site
C G C G C G C G G C G C G C G C
BsmBI  (2659)
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.
PfoI  (2657)
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.
PflFI  (2558)
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  (2558)
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.
BsaAI  (2552)
1 site
Y A C G T R R T G C A Y
BstZ17I  (2533)
1 site
G T A T A C C A T A T G
AccI  (2532)
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.
NdeI  (2481)
1 site
C A T A T G G T A T A C

Prolonged incubation with NdeI may lead to removal of additional
nucleotides.
PciI  (2302)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AlwNI  (1893)
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.
BanI  (1461)
1 site
G G Y R C C C C R Y G G

Sticky ends from different BanI sites may not be compatible.
BstEII  (3817)
1 site
G G T N A C C C C A N T G G

Sticky ends from different BstEII sites may not be compatible.
BstEII is typically used at 60°C, but is 50% active at 37°C.
BsmI  (3837)
1 site
G A A T G C N C T T A C G N

Sticky ends from different BsmI sites may not be compatible.
BtgI  (4084)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
NcoI  (4084)
1 site
C C A T G G G G T A C C
StyI  (4084)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
BanII  (4092)
1 site
G R G C Y C C Y C G R G

Sticky ends from different BanII sites may not be compatible.
End  (4127)
0 sites
Start  (1)
0 sites
BseRI  (28)
1 site
G A G G A G ( N ) 8 N N C T C C T C ( N ) 8

Sticky ends from different BseRI sites may not be compatible.
BseRI quickly loses activity at 37°C.
Prolonged incubation with BseRI may lead to degradation of the
DNA.
PmeI  (91)
1 site
G T T T A A A C C A A A T T T G
HincII  (872)
1 site
G T Y R A C C A R Y T G
ScaI  (933)
1 site
A G T A C T T C A T G A
PvuI  (1045)
1 site
C G A T C G G C T A G C
FspI  (1191)
1 site
T G C G C A A C G C G T
AseI  (1239)
1 site
A T T A A T T A A T T A
NmeAIII  (1267)
1 site
G C C G A G ( N ) 18-19 N N C G G C T C ( N ) 18-19

Efficient cleavage requires at least two copies of the NmeAIII
recognition sequence.
Sticky ends from different NmeAIII sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
BglI  (1296)
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.
AhdI  (1414)
1 site
G A C N N N N N G T C C T G N N N N N C A G

The 1-base overhangs produced by AhdI may be hard to ligate.
Sticky ends from different AhdI sites may not be compatible.
araC
2836 .. 3714  =  879 bp
292 amino acids  =  33.4 kDa
Product: L-arabinose regulatory protein
araC
2836 .. 3714  =  879 bp
292 amino acids  =  33.4 kDa
Product: L-arabinose regulatory protein
AmpR
627 .. 1487  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 1:  signal sequence  
   627 .. 695  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
627 .. 1487  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 2:  
   696 .. 1487  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
627 .. 1487  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
1658 .. 2246  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin
of replication
ori
1658 .. 2246  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin
of replication
araBAD promoter
3860 .. 4025  =  166 bp
promoter of the L-arabinose operon of E. coli; the
araC regulatory gene is transcribed in the opposite
direction
araBAD promoter
3860 .. 4025  =  166 bp
promoter of the L-arabinose operon of E. coli; the
araC regulatory gene is transcribed in the opposite
direction
AmpR promoter
535 .. 626  =  92 bp
AmpR promoter
535 .. 626  =  92 bp
rrnB T1 terminator
310 .. 396  =  87 bp
transcription terminator T1 from the E. coli rrnB
gene
rrnB T1 terminator
310 .. 396  =  87 bp
transcription terminator T1 from the E. coli rrnB
gene
V5 tag
16 .. 57  =  42 bp
14 amino acids  =  1.4 kDa
Product: epitope tag from simian virus 5
V5 tag
16 .. 57  =  42 bp
14 amino acids  =  1.4 kDa
Product: epitope tag from simian virus 5
rrnB T2 terminator
488 .. 515  =  28 bp
transcription terminator T2 from the E. coli rrnB
gene
rrnB T2 terminator
488 .. 515  =  28 bp
transcription terminator T2 from the E. coli rrnB
gene
6xHis
67 .. 84  =  18 bp
6 amino acids  =  840.9 Da
Product: 6xHis affinity tag
6xHis
67 .. 84  =  18 bp
6 amino acids  =  840.9 Da
Product: 6xHis affinity tag
enterokinase site
4104 .. 4118  =  15 bp
5 amino acids  =  606.5 Da
Product: enterokinase recognition and cleavage site
enterokinase site
4104 .. 4118  =  15 bp
5 amino acids  =  606.5 Da
Product: enterokinase recognition and cleavage site
RBS
4069 .. 4072  =  4 bp
ribosome binding site
RBS
4069 .. 4072  =  4 bp
ribosome binding site
ATG
4086 .. 4088  =  3 bp
1 amino acid  =  149.2 Da
Product: start codon
ATG
4086 .. 4088  =  3 bp
1 amino acid  =  149.2 Da
Product: start codon
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