pcDNA5 FRT TO-TOPO (linearized)

Linearized vector with 3'-T overhangs and bound topoisomerase, for TOPO® TA cloning of PCR products, FLP recombination, and tetracycline-inducible expression.

Sequence Author: Thermo Fisher (Invitrogen)

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HomePlasmidsTOPO Cloning VectorspcDNA5 FRT TO-TOPO (linearized)
SspI (4047) XmnI (3842) FspI (3465) BsaI (3304) AhdI (3243) PciI (2350) BspQI - SapI (2234) BstZ17I (1971) BsmI (1919) PsiI (1858) PfoI (1774) SacII (1464) MfeI (4327) Bpu10I (4346) NruI (4374) MluI (4394) CMV enhancer SnaBI (4756) tet operator tet operator AflII (5141) End (5155) Start (1) Acc65I (13) KpnI (17) BamHI (25) EcoRV (60) NotI (75) AvaI - BsoBI - PaeR7I - PspXI - XhoI (81) EcoO109I - PspOMI (93) ApaI (97) BclI * (111) SphI (324) MscI (684) PshAI (711) BfuAI - BspMI (997) AsiSI (1048) RsrII (1092) pcDNA™5/FRT/TO-TOPO® 5154 bp
SspI  (4047)
1 site		 A A T A T T T T A T A A
XmnI  (3842)
1 site		 G A A N N N N T T C C T T N N N N A A G
FspI  (3465)
1 site		 T G C G C A A C G C G T
BsaI  (3304)
1 site		 G G T C T C N C C A G A G N ( N ) 4
Sticky ends from different BsaI sites may not be compatible.
BsaI can be used between 37°C and 50°C.
AhdI  (3243)
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.
PciI  (2350)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
BspQI  (2234)
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  (2234)
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.
BstZ17I  (1971)
1 site		 G T A T A C C A T A T G
BsmI  (1919)
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.
PsiI  (1858)
1 site		 T T A T A A A A T A T T
PfoI  (1774)
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.
SacII  (1464)
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.
MfeI  (4327)
1 site		 C A A T T G G T T A A C
Bpu10I  (4346)
1 site		 C C T N A G C G G A N T C G
Cleavage may be enhanced when more than one copy of the Bpu10I recognition sequence is present.
This recognition sequence is asymmetric, so ligating sticky ends generated by Bpu10I will not always regenerate a Bpu10I site.
Sticky ends from different Bpu10I sites may not be compatible.
NruI  (4374)
1 site		 T C G C G A A G C G C T
MluI  (4394)
1 site		 A C G C G T T G C G C A
SnaBI  (4756)
1 site		 T A C G T A A T G C A T
AflII  (5141)
1 site		 C T T A A G G A A T T C
End  (5155)
0 sites
Start  (1)
0 sites
Acc65I  (13)
1 site		 G G T A C C C C A T G G
KpnI  (17)
1 site		 G G T A C C C C A T G G
BamHI  (25)
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.
EcoRV  (60)
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.
NotI  (75)
1 site		 G C G G C C G C C G C C G G C G
AvaI  (81)
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  (81)
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  (81)
1 site		 C T C G A G G A G C T C
PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (81)
1 site		 V C T C G A G B B G A G C T C V
XhoI  (81)
1 site		 C T C G A G G A G C T C
EcoO109I  (93)
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  (93)
1 site		 G G G C C C C C C G G G
ApaI  (97)
1 site		 G G G C C C C C C G G G
ApaI can be used between 25°C and 37°C.
BclI  (111)
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.
SphI  (324)
1 site		 G C A T G C C G T A C G
MscI  (684)
1 site		 T G G C C A A C C G G T
PshAI  (711)
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.
BfuAI  (997)
1 site		 A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4
Efficient cleavage requires at least two copies of the BfuAI recognition sequence.
Sticky ends from different BfuAI sites may not be compatible.
BfuAI is typically used at 50°C, but is 50% active at 37°C.
BspMI  (997)
1 site		 A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4
Efficient cleavage requires at least two copies of the BspMI recognition sequence.
Sticky ends from different BspMI sites may not be compatible.
AsiSI  (1048)
1 site		 G C G A T C G C C G C T A G C G
RsrII  (1092)
1 site		 C G G W C C G G C C W G G C
Efficient cleavage requires at least two copies of the RsrII recognition sequence.
Sticky ends from different RsrII sites may not be compatible.
For full activity, add fresh DTT.
HygR
687 .. 1709  =  1023 bp
340 amino acids  =  37.9 kDa
Product: aminoglycoside phosphotransferase from E. coli
confers resistance to hygromycin
HygR
687 .. 1709  =  1023 bp
340 amino acids  =  37.9 kDa
Product: aminoglycoside phosphotransferase from E. coli
confers resistance to hygromycin
AmpR
3170 .. 4030  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   3170 .. 3961  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3170 .. 4030  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   3962 .. 4030  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3170 .. 4030  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
ori
2411 .. 2999  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2411 .. 2999  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
CMV enhancer
4401 .. 4780  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
4401 .. 4780  =  380 bp
human cytomegalovirus immediate early enhancer
bGH poly(A) signal
124 .. 348  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
124 .. 348  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
4781 .. 4984  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
4781 .. 4984  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
SV40 poly(A) signal
1839 .. 1960  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
1839 .. 1960  =  122 bp
SV40 polyadenylation signal
AmpR promoter
4031 .. 4135  =  105 bp
AmpR promoter
4031 .. 4135  =  105 bp
FRT
632 .. 679  =  48 bp
FLP-mediated recombination occurs in the 8-bp core sequence TCTAGAAA (Turan and Bode, 2011).
FRT
632 .. 679  =  48 bp
FLP-mediated recombination occurs in the 8-bp core sequence TCTAGAAA (Turan and Bode, 2011).
tet operator
4986 .. 5004  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
4986 .. 5004  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
5007 .. 5025  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
5007 .. 5025  =  19 bp
bacterial operator O2 for the tetR and tetA genes
ORF:  345 .. 611  =  267 bp
ORF:  88 amino acids  =  9.3 kDa
ORF:  759 .. 1709  =  951 bp
ORF:  316 amino acids  =  35.2 kDa
ORF:  3300 .. 3566  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  3170 .. 4030  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  660 .. 1442  =  783 bp
ORF:  260 amino acids  =  29.2 kDa
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Individual Sequences & Maps

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pcDNA5 FRT TO-TOPO (linearized)
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pcDNA3.2 V5 GW D-TOPO
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pET100 D-TOPO
pLPS-B (linearized)
pcDNA6.2 cGeneBLAzer-GW D-TOPO
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pET101 D-TOPO
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pcDNA3.1 NT-GFP-TOPO (linearized)
pCR4Blunt-TOPO (linearized)
pET160 GW D-TOPO
pTOP Blunt V2 (linearized)
pcDNA3.1 V5-His-TOPO (linearized)
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pET161 GW D-TOPO
pTrcHis-TOPO (linearized)
pcDNA3.3-TOPO (linearized)
pCR-Blunt II-TOPO (linearized)
pET200 D-TOPO
pTrcHis2-TOPO (linearized)
pcDNA3.4-TOPO (linearized)
pCRII-TOPO (linearized)
pEXP5-CT TOPO (linearized)
pYES2.1 V5-His-TOPO (linearized)
pcDNA4 HisMax-TOPO (linearized)
pEF5 FRT V5-D-TOPO
pEXP5-NT TOPO (linearized)

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