pCR3.1 (linearized)

Linearized mammalian expression vector for TA cloning of PCR products.

Sequence Author: Thermo Fisher (Invitrogen)

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HomePlasmidsI.M.A.G.E. Consortium PlasmidspCR3.1 (linearized)
BssHII - MauBI (4324) PsiI (4224) DraIII (4099) XmnI (3546) ScaI (3427) PvuI (3317) AhdI (2947) CsiI - SexAI * (2699) SfiI (2521) BseRI (2477) StuI (2472) BspDI * - ClaI * (2451) BsaBI * (2434) PluTI (2294) SfoI (2292) NarI (2291) KasI (2290) MscI (2211) PflFI - Tth111I (2174) RsrII (1780) BspQI - SapI (1742) HincII (4332) NdeI (4582) SnaBI (4688) NheI (4993) BmtI (4997) AflII (5006) HindIII (5009) Acc65I (5015) KpnI (5019) BamHI (5027) End (5060) Start (1) PstI (15) EcoRV (18) NotI (33) AvaI - BsoBI - PaeR7I - PspXI - XhoI (39) XbaI (45) PspOMI (51) ApaI (55) BbsI (271) AflIII - PciI (377) PfoI (1519) BstBI (1615) pCR®3.1 5059 bp
BssHII  (4324)
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  (4324)
1 site		 C G C G C G C G G C G C G C G C
PsiI  (4224)
1 site		 T T A T A A A A T A T T
DraIII  (4099)
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.
XmnI  (3546)
1 site		 G A A N N N N T T C C T T N N N N A A G
ScaI  (3427)
1 site		 A G T A C T T C A T G A
PvuI  (3317)
1 site		 C G A T C G G C T A G C
AhdI  (2947)
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.
CsiI  (2699)
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  (2699)
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.
SfiI  (2521)
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.
BseRI  (2477)
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.
StuI  (2472)
1 site		 A G G C C T T C C G G A
BspDI  (2451)
1 site		 A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (2451)
1 site		 A T C G A T T A G C T A
* Blocked by Dam methylation.
BsaBI  (2434)
1 site		 G A T N N N N A T C C T A N N N N T A G
* Blocked by Dam methylation.
PluTI  (2294)
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  (2292)
1 site		 G G C G C C C C G C G G
NarI  (2291)
1 site		 G G C G C C C C G C G G
Efficient cleavage requires at least two copies of the NarI recognition sequence.
KasI  (2290)
1 site		 G G C G C C C C G C G G
MscI  (2211)
1 site		 T G G C C A A C C G G T
PflFI  (2174)
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  (2174)
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.
RsrII  (1780)
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.
BspQI  (1742)
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  (1742)
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.
HincII  (4332)
1 site		 G T Y R A C C A R Y T G
NdeI  (4582)
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.
SnaBI  (4688)
1 site		 T A C G T A A T G C A T
NheI  (4993)
1 site		 G C T A G C C G A T C G
BmtI  (4997)
1 site		 G C T A G C C G A T C G
AflII  (5006)
1 site		 C T T A A G G A A T T C
HindIII  (5009)
1 site		 A A G C T T T T C G A A
Acc65I  (5015)
1 site		 G G T A C C C C A T G G
KpnI  (5019)
1 site		 G G T A C C C C A T G G
BamHI  (5027)
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.
End  (5060)
0 sites
Start  (1)
0 sites
PstI  (15)
1 site		 C T G C A G G A C G T C
EcoRV  (18)
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  (33)
1 site		 G C G G C C G C C G C C G G C G
AvaI  (39)
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  (39)
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  (39)
1 site		 C T C G A G G A G C T C
PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (39)
1 site		 V C T C G A G B B G A G C T C V
XhoI  (39)
1 site		 C T C G A G G A G C T C
XbaI  (45)
1 site		 T C T A G A A G A T C T
PspOMI  (51)
1 site		 G G G C C C C C C G G G
ApaI  (55)
1 site		 G G G C C C C C C G G G
ApaI can be used between 25°C and 37°C.
BbsI  (271)
1 site		 G A A G A C N N C T T C T G N N ( N ) 4
Sticky ends from different BbsI sites may not be compatible.
BbsI gradually loses activity when stored at -20°C.
AflIII  (377)
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  (377)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
PfoI  (1519)
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.
BstBI  (1615)
1 site		 T T C G A A A A G C T T
AmpR
2874 .. 3734  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   2874 .. 3665  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2874 .. 3734  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   3666 .. 3734  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2874 .. 3734  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
ori
438 .. 1026  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
438 .. 1026  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
f1 ori
3866 .. 4321  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
3866 .. 4321  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
CMV enhancer
4333 .. 4712  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
4333 .. 4712  =  380 bp
human cytomegalovirus immediate early enhancer
SV40 promoter
2457 .. 2814  =  358 bp
SV40 enhancer and early promoter
SV40 promoter
2457 .. 2814  =  358 bp
SV40 enhancer and early promoter
bGH poly(A) signal
82 .. 306  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
82 .. 306  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
4713 .. 4916  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
4713 .. 4916  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
AmpR promoter
3735 .. 3839  =  105 bp
AmpR promoter
3735 .. 3839  =  105 bp
HSV TK poly(A) signal
1355 .. 1402  =  48 bp
herpesvirus thymidine kinase polyadenylation signal
HSV TK poly(A) signal
1355 .. 1402  =  48 bp
herpesvirus thymidine kinase polyadenylation signal
T7 promoter
4961 .. 4979  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
4961 .. 4979  =  19 bp
promoter for bacteriophage T7 RNA polymerase
SV40 ori
2471 .. 2606  =  136 bp
SV40 origin of replication
SV40 ori
2471 .. 2606  =  136 bp
SV40 origin of replication
ORF:  3004 .. 3270  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  1175 .. 1408  =  234 bp
ORF:  77 amino acids  =  8.6 kDa
ORF:  1583 .. 2113  =  531 bp
ORF:  176 amino acids  =  19.6 kDa
ORF:  72 .. 380  =  309 bp
ORF:  102 amino acids  =  11.3 kDa
ORF:  1164 .. 1613  =  450 bp
ORF:  149 amino acids  =  16.3 kDa
ORF:  2874 .. 3734  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  1634 .. 2422  =  789 bp
ORF:  262 amino acids  =  28.7 kDa
ORF:  1870 .. 2250  =  381 bp
ORF:  126 amino acids  =  14.3 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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