pCR-XL-TOPO

Parental vector for TOPO® TA cloning of long PCR products.

Sequence Author: Thermo Fisher (Invitrogen)

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HomePlasmidsI.M.A.G.E. Consortium PlasmidspCR-XL-TOPO
PciI (3394) DraI (2639) DraIII (2591) FseI (2514) CsiI - SexAI * (2401) SgrAI (2352) SmaI (2328) TspMI - XmaI (2326) AatII (2284) ZraI (2282) BssHII - MauBI (2274) HincII (2248) SfiI (2238) TsoI (1894) lac operator MluI (248) HindIII (276) Acc65I (282) KpnI (286) Eco53kI (290) SacI (292) BamHI (294) SpeI (300) AflII (334) PstI (352) EcoRV (355) NotI (370) PaeR7I - PspXI - XhoI (376) XbaI (388) EcoO109I - PspOMI (394) ApaI (398) PvuI (549) BsiWI - SnaBI (579) BsrGI - TatI (639) BsaI (804) XcmI (1181) BclI * (1206) PflFI - Tth111I (1483) BsrDI (1598) RsrII (1881) pCR®-XL-TOPO® 3519 bp
PciI  (3394)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
DraI  (2639)
1 site		 T T T A A A A A A T T T
DraIII  (2591)
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.
FseI  (2514)
1 site		 G G C C G G C C C C G G C C G G
FseI gradually loses activity when stored at -20°C.
CsiI  (2401)
1 site		 A C C W G G T T G G W C C A
Sticky ends from different CsiI sites may not be compatible.
SexAI  (2401)
1 site		 A C C W G G T T G G W C C A
* Blocked by Dcm methylation.
Sticky ends from different SexAI sites may not be compatible.
SgrAI  (2352)
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.
SmaI  (2328)
1 site		 C C C G G G G G G C C C
SmaI can be used at 37°C for brief incubations.
TspMI  (2326)
1 site		 C C C G G G G G G C C C
XmaI  (2326)
1 site		 C C C G G G G G G C C C
Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
AatII  (2284)
1 site		 G A C G T C C T G C A G
ZraI  (2282)
1 site		 G A C G T C C T G C A G
BssHII  (2274)
1 site		 G C G C G C C G C G C G
BssHII is typically used at 50°C, but is 75% active at 37°C.
MauBI  (2274)
1 site		 C G C G C G C G G C G C G C G C
HincII  (2248)
1 site		 G T Y R A C C A R Y T G
SfiI  (2238)
1 site		 G G C C N N N N N G G C C C C G G N N N N N C C G G
Efficient cleavage requires at least two copies of the SfiI recognition sequence.
Sticky ends from different SfiI sites may not be compatible.
TsoI  (1894)
1 site		 T A R C C A ( N ) 9 N N A T Y G G T ( N ) 9
Sticky ends from different TsoI sites may not be compatible.
After cleavage, TsoI can remain bound to DNA and alter its electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
MluI  (248)
1 site		 A C G C G T T G C G C A
HindIII  (276)
1 site		 A A G C T T T T C G A A
Acc65I  (282)
1 site		 G G T A C C C C A T G G
KpnI  (286)
1 site		 G G T A C C C C A T G G
Eco53kI  (290)
1 site		 G A G C T C C T C G A G
SacI  (292)
1 site		 G A G C T C C T C G A G
BamHI  (294)
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.
SpeI  (300)
1 site		 A C T A G T T G A T C A
AflII  (334)
1 site		 C T T A A G G A A T T C
PstI  (352)
1 site		 C T G C A G G A C G T C
EcoRV  (355)
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  (370)
1 site		 G C G G C C G C C G C C G G C G
PaeR7I  (376)
1 site		 C T C G A G G A G C T C
PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (376)
1 site		 V C T C G A G B B G A G C T C V
XhoI  (376)
1 site		 C T C G A G G A G C T C
XbaI  (388)
1 site		 T C T A G A A G A T C T
EcoO109I  (394)
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  (394)
1 site		 G G G C C C C C C G G G
ApaI  (398)
1 site		 G G G C C C C C C G G G
ApaI can be used between 25°C and 37°C.
PvuI  (549)
1 site		 C G A T C G G C T A G C
BsiWI  (579)
1 site		 C G T A C G G C A T G C
BsiWI is typically used at 55°C, but is 50% active at 37°C.
SnaBI  (579)
1 site		 T A C G T A A T G C A T
BsrGI  (639)
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  (639)
1 site		 W G T A C W W C A T G W
BsaI  (804)
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.
XcmI  (1181)
1 site		 C C A N N N N N N N N N T G G G G T N N N N N N N N N A C C
The 1-base overhangs produced by XcmI may be hard to ligate.
Sticky ends from different XcmI sites may not be compatible.
BclI  (1206)
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.
PflFI  (1483)
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  (1483)
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.
BsrDI  (1598)
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.
RsrII  (1881)
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.
NeoR/KanR
1237 .. 2031  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin®)
NeoR/KanR
1237 .. 2031  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin®)
lacZα
217 .. 576  =  360 bp
120 amino acids  =  13.5 kDa
Product: LacZα fragment of β-galactosidase
lacZα
217 .. 576  =  360 bp
120 amino acids  =  13.5 kDa
Product: LacZα fragment of β-galactosidase
ccdB
586 .. 888  =  303 bp
100 amino acids  =  11.6 kDa
Product: CcdB, a bacterial toxin that poisons DNA gyrase
Plasmids containing the ccdB gene cannot be propagated in standard E. coli strains.
ccdB
586 .. 888  =  303 bp
100 amino acids  =  11.6 kDa
Product: CcdB, a bacterial toxin that poisons DNA gyrase
Plasmids containing the ccdB gene cannot be propagated in standard E. coli strains.
ori
2750 .. 3338  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2750 .. 3338  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
BleoR
2238 .. 2612  =  375 bp
124 amino acids  =  13.8 kDa
Product: antibiotic-binding protein
confers resistance to bleomycin, phleomycin, and Zeocin™
BleoR
2238 .. 2612  =  375 bp
124 amino acids  =  13.8 kDa
Product: antibiotic-binding protein
confers resistance to bleomycin, phleomycin, and Zeocin™
lac promoter
143 .. 173  =  31 bp
3 segments
   Segment 1:  -35  
   143 .. 148  =  6 bp
promoter for the E. coli lac operon
lac promoter
143 .. 173  =  31 bp
3 segments
   Segment 2:  
   149 .. 166  =  18 bp
promoter for the E. coli lac operon
lac promoter
143 .. 173  =  31 bp
3 segments
   Segment 3:  -10  
   167 .. 173  =  7 bp
promoter for the E. coli lac operon
lac promoter
143 .. 173  =  31 bp
3 segments
promoter for the E. coli lac operon
CAP binding site
107 .. 128  =  22 bp
CAP binding activates transcription in the presence of cAMP.
CAP binding site
107 .. 128  =  22 bp
CAP binding activates transcription in the presence of cAMP.
lac operator
181 .. 197  =  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
181 .. 197  =  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).
T7 promoter
407 .. 425  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
407 .. 425  =  19 bp
promoter for bacteriophage T7 RNA polymerase
M13 rev
205 .. 221  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
205 .. 221  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
432 .. 448  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
432 .. 448  =  17 bp
common sequencing primer, one of multiple similar variants
ORF:  217 .. 888  =  672 bp
ORF:  223 amino acids  =  25.5 kDa
ORF:  1237 .. 2031  =  795 bp
ORF:  264 amino acids  =  29.0 kDa
ORF:  383 .. 682  =  300 bp
ORF:  99 amino acids  =  11.1 kDa
ORF:  1409 .. 1795  =  387 bp
ORF:  128 amino acids  =  14.6 kDa
ORF:  2238 .. 2612  =  375 bp
ORF:  124 amino acids  =  13.8 kDa
ORF:  1546 .. 2079  =  534 bp
ORF:  177 amino acids  =  19.9 kDa
ORF:  2210 .. 2518  =  309 bp
ORF:  102 amino acids  =  10.9 kDa
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Individual Sequences & Maps

Lafmid BA
pcDNAII
pCR2.1-TOPO (linearized)
pExpress-1
pAD-GAL4
pcDNA3.1(+)
pCR3.1
pME18S-FL3
pAMP1
pcDNA3.1(-)
pCR3.1 (linearized)
pOTB7
pAMP10
pcDNA3.1 Zeo(+)
pCR4-TOPO
pOTB7-3
pBK-CMV
pCMV SPORT
pCR4-TOPO (linearized)
pOTB7a
pBluescribe (modified)
pCMV SPORT2
pCS105
pPCR-Script Amp SK(+)
pBluescript II SK(+)
pCMV SPORT4
pCS107
pRKW2
pBluescript KS(+)
pCMV SPORT6
pCS108
pSPORT 1
pBluescript SK(+)
pCMV SPORT6.1
pCS2+
pSPORT 2
pBluescript SK(-)
pCMV SPORT6ccdB
pCS22+
pT7T3D-PacI
pBluescript-FL
pCR-Blunt II-TOPO
pCS2G
pUC19
pBluescript II KS(+)
pCR-Blunt II-TOPO (linearized)
pDNR-Dual
pYX-Asc
pBluescriptR
pCR-XL-TOPO
pDNR-LIB
pZErO-2
pcDNA3
pCR-XL-TOPO (linearized)
pDONR201
pZL1
pcDNAI
pCR2.1-TOPO
pDONR223

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