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pcDNA™3.1/Hygro(+)

Mammalian expression vector with the CMV promoter. The MCS is in the forward (+) orientation.

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pcDNA3.1 Hygro(+).dna
Map and Sequence File:    Download    Open   
Sequence Author:  Thermo Fisher (Invitrogen)
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SgrDI (5595) SspI (5478) FspI (4896) AhdI (4674) PciI (3784) BspQI - SapI (3668) BstZ17I (3405) BsmI (3353) PfoI (3208) SacII (2898) BglII (12) MfeI (161) Bpu10I (180) NruI (208) MluI (228) SnaBI (590) NheI (895) BmtI (899) AflII (908) HindIII (911) Acc65I (917) KpnI (921) BamHI (929) EcoRV (964) NotI (979) PaeR7I - PspXI - XhoI (985) XbaI (991) EcoO109I - PspOMI (997) ApaI (1001) BbsI (1217) SexAI * (1821) BseRI (2050) StuI (2053) AvrII (2054) TspMI - XmaI (2075) SmaI (2077) PshAI (2145) BsmBI (2186) BfuAI - BspMI (2431) AsiSI (2482) RsrII (2526) pcDNA™3.1/Hygro(+) 5597 bp
SgrDI  (5595)
1 site
C G T C G A C G G C A G C T G C
SspI  (5478)
1 site
A A T A T T T T A T A A
FspI  (4896)
1 site
T G C G C A A C G C G T
AhdI  (4674)
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  (3784)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BspQI  (3668)
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  (3668)
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  (3405)
1 site
G T A T A C C A T A T G
BsmI  (3353)
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.
PfoI  (3208)
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  (2898)
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.
BglII  (12)
1 site
A G A T C T T C T A G A
MfeI  (161)
1 site
C A A T T G G T T A A C
Bpu10I  (180)
1 site
C C T N A G C G G A N T C G

Efficient cleavage requires at least two copies of the Bpu10I recognition sequence.
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  (208)
1 site
T C G C G A A G C G C T
MluI  (228)
1 site
A C G C G T T G C G C A
SnaBI  (590)
1 site
T A C G T A A T G C A T
NheI  (895)
1 site
G C T A G C C G A T C G
BmtI  (899)
1 site
G C T A G C C G A T C G
AflII  (908)
1 site
C T T A A G G A A T T C
HindIII  (911)
1 site
A A G C T T T T C G A A
Acc65I  (917)
1 site
G G T A C C C C A T G G
KpnI  (921)
1 site
G G T A C C C C A T G G
BamHI  (929)
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  (964)
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  (979)
1 site
G C G G C C G C C G C C G G C G
PaeR7I  (985)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (985)
1 site
V C T C G A G B B G A G C T C V
XhoI  (985)
1 site
C T C G A G G A G C T C
XbaI  (991)
1 site
T C T A G A A G A T C T
EcoO109I  (997)
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  (997)
1 site
G G G C C C C C C G G G
ApaI  (1001)
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  (1217)
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.
SexAI  (1821)
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.
BseRI  (2050)
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  (2053)
1 site
A G G C C T T C C G G A
AvrII  (2054)
1 site
C C T A G G G G A T C C
TspMI  (2075)
1 site
C C C G G G G G G C C C
XmaI  (2075)
1 site
C C C G G G G G G C C C

Efficient cleavage requires at least two copies of the XmaI recognition sequence.
Full cleavage with XmaI may require a long incubation.
SmaI  (2077)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
PshAI  (2145)
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.
BsmBI  (2186)
1 site
C G T C T C N G C A G A G N ( N ) 4

Sticky ends from different BsmBI sites may not be compatible.
BfuAI  (2431)
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  (2431)
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  (2482)
1 site
G C G A T C G C C G C T A G C G
RsrII  (2526)
1 site