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Plasmid Files

pcDNA™3.1/Zeo(-)

Mammalian expression vector with the CMV promoter. The MCS is in the reverse (-) orientation.

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pcDNA3.1 Zeo(-) Sequence and MappcDNA3.1 Zeo(-).dna
Map and Sequence File   
Sequence Author:  Invitrogen (Life Technologies)
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 SgrDI (5012) SspI (4895) ScaI (4571) PvuI (4461) FspI (4313) AhdI (4091) PciI (3198) BspQI - SapI (3082) BstZ17I (2819) BsmI (2767) BglII (12) MfeI (161) Bpu10I (180) NruI (208) MluI (228) NdeI (484) SnaBI (590) NheI (895) BmtI (899) PspOMI (909) EcoO109I (910) ApaI (913) XbaI (915) PaeR7I - PspXI - XhoI (921) NotI (927) EcoRV (946) PstI (953) EcoRI (954) BamHI (977) Acc65I (989) KpnI (993) HindIII (995) AflII (998) BbsI (1216) StuI (2053) AvrII (2054) MscI (2186) BssHII - MauBI (2219) SgrAI (2297) BmgBI (2317) FseI (2459) pcDNA™3.1/Zeo(-) 5014 bp
SgrDI  (5012)
1 site
C G T C G A C G G C A G C T G C
SspI  (4895)
1 site
A A T A T T T T A T A A
ScaI  (4571)
1 site
A G T A C T T C A T G A
PvuI  (4461)
1 site
C G A T C G G C T A G C
FspI  (4313)
1 site
T G C G C A A C G C G T
AhdI  (4091)
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  (3198)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BspQI  (3082)
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  (3082)
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  (2819)
1 site
G T A T A C C A T A T G
BsmI  (2767)
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.
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
NdeI  (484)
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  (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
PspOMI  (909)
1 site
G G G C C C C C C G G G
EcoO109I  (910)
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.
ApaI  (913)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
XbaI  (915)
1 site
T C T A G A A G A T C T
PaeR7I  (921)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (921)
1 site
V C T C G A G B B G A G C T C V
XhoI  (921)
1 site
C T C G A G G A G C T C
NotI  (927)
1 site
G C G G C C G C C G C C G G C G
EcoRV  (946)
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.
PstI  (953)
1 site
C T G C A G G A C G T C
EcoRI  (954)
1 site
G A A T T C C T T A A G
BamHI  (977)
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.
Acc65I  (989)
1 site
G G T A C C C C A T G G
KpnI  (993)
1 site
G G T A C C C C A T G G
HindIII  (995)
1 site
A A G C T T T T C G A A
AflII  (998)
1 site
C T T A A G G A A T T C

The sticky ends produced by AflII are hard to ligate.
BbsI  (1216)
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.
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
MscI  (2186)
1 site
T G G C C A A C C G G T
BssHII  (2219)
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  (2219)
1 site
C G C G C G C G G C G C G C G C
SgrAI  (2297)
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.
BmgBI  (2317)
1 site
C A C G T C G T G C A G

This recognition sequence is asymmetric, so ligating blunt ends
generated by BmgBI will not always regenerate a BmgBI site.
FseI  (2459)
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.
AmpR
4018 .. 4878  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   4018 .. 4809  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
4018 .. 4878  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   4810 .. 4878  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
4018 .. 4878  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
3259 .. 3847  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
3259 .. 3847  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
f1 ori
1297 .. 1725  =  429 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
1297 .. 1725  =  429 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
CMV enhancer
235 .. 614  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
235 .. 614  =  380 bp
human cytomegalovirus immediate early enhancer
BleoR
2183 .. 2557  =  375 bp
124 amino acids  =  13.8 kDa
Product: antibiotic-binding protein
confers resistance to bleomycin, phleomycin, and
Zeocin™
BleoR
2183 .. 2557  =  375 bp
124 amino acids  =  13.8 kDa
Product: antibiotic-binding protein
confers resistance to bleomycin, phleomycin, and
Zeocin™
SV40 promoter
1739 .. 2069  =  331 bp
SV40 enhancer and early promoter
SV40 promoter
1739 .. 2069  =  331 bp
SV40 enhancer and early promoter
bGH poly(A) signal
1027 .. 1251  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
1027 .. 1251  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
615 .. 818  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
CMV promoter
615 .. 818  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
SV40 poly(A) signal
2687 .. 2808  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
2687 .. 2808  =  122 bp
SV40 polyadenylation signal
MCS
895 .. 1003  =  109 bp
multiple cloning site
MCS
895 .. 1003  =  109 bp
multiple cloning site
AmpR promoter
4879 .. 4983  =  105 bp
AmpR promoter
4879 .. 4983  =  105 bp
EM7 promoter
2117 .. 2164  =  48 bp
synthetic bacterial promoter
EM7 promoter
2117 .. 2164  =  48 bp
synthetic bacterial promoter
T7 promoter
863 .. 881  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
863 .. 881  =  19 bp
promoter for bacteriophage T7 RNA polymerase
SV40 ori
1920 .. 2055  =  136 bp
SV40 origin of replication
SV40 ori
1920 .. 2055  =  136 bp
SV40 origin of replication
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