Resources
Plasmid Files

pCR®3.1

Parental mammalian expression vector for TA cloning of PCR products.

To see this sequence with restriction sites, features, and translations, please download
 SnapGene or the free  SnapGene Viewer.

pCR3.1.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Thermo Fisher (Invitrogen)
Download Free Trial Get SnapGene Viewer


BssHII - MauBI (1) PsiI (4961) DraIII (4836) XmnI (4283) ScaI (4164) PvuI (4054) AhdI (3684) SexAI * (3436) SfiI (3258) BseRI (3214) StuI (3209) BspDI * - ClaI * (3188) BsaBI * (3171) PluTI (3031) SfoI (3029) NarI (3028) KasI (3027) MscI (2948) PflFI - Tth111I (2911) RsrII (2517) HincII (9) NdeI (259) SnaBI (365) NheI (670) BmtI (674) HindIII (686) Acc65I (692) KpnI (696) BamHI (704) PstI (752) EcoRV (755) NotI (770) AvaI - BsoBI - PaeR7I - PspXI - XhoI (776) BmeT110I (777) XbaI (782) PspOMI (788) ApaI (792) BbsI (1008) AflIII - PciI (1114) PfoI (2256) BstBI (2352) BspQI - SapI (2479) pCR®3.1 5060 bp
BssHII  (1)
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  (1)
1 site
C G C G C G C G G C G C G C G C
PsiI  (4961)
1 site
T T A T A A A A T A T T
DraIII  (4836)
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  (4283)
1 site
G A A N N N N T T C C T T N N N N A A G
ScaI  (4164)
1 site
A G T A C T T C A T G A
PvuI  (4054)
1 site
C G A T C G G C T A G C
AhdI  (3684)
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.
SexAI  (3436)
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  (3258)
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  (3214)
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  (3209)
1 site
A G G C C T T C C G G A
BspDI  (3188)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (3188)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
BsaBI  (3171)
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  (3031)
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  (3029)
1 site
G G C G C C C C G C G G
NarI  (3028)
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  (3027)
1 site
G G C G C C C C G C G G
MscI  (2948)
1 site
T G G C C A A C C G G T
PflFI  (2911)
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  (2911)
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  (2517)
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.
HincII  (9)
1 site
G T Y R A C C A R Y T G
NdeI  (259)
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  (365)
1 site
T A C G T A A T G C A T
NheI  (670)
1 site
G C T A G C C G A T C G
BmtI  (674)
1 site
G C T A G C C G A T C G
HindIII  (686)
1 site
A A G C T T T T C G A A
Acc65I  (692)
1 site
G G T A C C C C A T G G
KpnI  (696)
1 site
G G T A C C C C A T G G
BamHI  (704)
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.
PstI  (752)
1 site
C T G C A G G A C G T C
EcoRV  (755)
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  (770)
1 site
G C G G C C G C C G C C G G C G
AvaI  (776)
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  (776)
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  (776)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (776)
1 site
V C T C G A G B B G A G C T C V
XhoI  (776)
1 site
C T C G A G G A G C T C
BmeT110I  (777)
1 site
C Y C G R G G R G C Y C
XbaI  (782)
1 site
T C T A G A A G A T C T
PspOMI  (788)
1 site
G G G C C C C C C G G G
ApaI  (792)
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  (1008)
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  (1114)
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  (1114)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
PfoI  (2256)
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  (2352)
1 site
T T C G A A A A G C T T
BspQI  (2479)
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  (2479)
1 site
G C T C T T C N C G A <