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Plasmid Files

pCR®3.1

Parental mammalian expression vector for TA cloning of PCR products.

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pCR3.1 Sequence and MappCR3.1.dna
Map and Sequence File   
Sequence Author:  Invitrogen (Life Technologies)
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 BssHII - MauBI (1) AanI - 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) BbeI (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) BstXI (723) EcoRI (727) EcoRI (743) PstI (752) EcoRV (755) BstXI (765) 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
AanI  (4961)
1 site
T T A T A A A A T A T T
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.
BbeI  (3031)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the BbeI
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.
BstXI  (723)
2 sites
C C A N N N N N N T G G G G T N N N N N N A C C

Sticky ends from different BstXI sites may not be compatible.
EcoRI  (727)
2 sites
G A A T T C C T T A A G
EcoRI  (743)
2 sites
G A A T T C C T T A A G
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.
BstXI  (765)
2 sites
C C A N N N N N N T G G G G T N N N N N N A C C

Sticky ends from different BstXI sites may not be compatible.
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 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.
AmpR
3611 .. 4471  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   3611 .. 4402  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
3611 .. 4471  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   4403 .. 4471  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
3611 .. 4471  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
1175 .. 1763  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
1175 .. 1763  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
f1 ori
4603 .. 5058  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
4603 .. 5058  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
CMV enhancer
10 .. 389  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
10 .. 389  =  380 bp
human cytomegalovirus immediate early enhancer
SV40 promoter
3194 .. 3551  =  358 bp
SV40 enhancer and early promoter
SV40 promoter
3194 .. 3551  =  358 bp
SV40 enhancer and early promoter
bGH poly(A) signal
819 .. 1043  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
819 .. 1043  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
390 .. 593  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
CMV promoter
390 .. 593  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
AmpR promoter
4472 .. 4576  =  105 bp
AmpR promoter
4472 .. 4576  =  105 bp
HSV TK poly(A) signal
2092 .. 2139  =  48 bp
herpesvirus thymidine kinase polyadenylation signal
HSV TK poly(A) signal
2092 .. 2139  =  48 bp
herpesvirus thymidine kinase polyadenylation signal
T7 promoter
638 .. 656  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
638 .. 656  =  19 bp
promoter for bacteriophage T7 RNA polymerase
SV40 ori
3208 .. 3343  =  136 bp
SV40 origin of replication
SV40 ori
3208 .. 3343  =  136 bp
SV40 origin of replication
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