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Plasmid Files

pOptiVEC™-TOPO® (linearized)

Linearized vector with 3'-T overhangs and bound topoisomerase, for TOPO® TA cloning of PCR products into a bicistronic vector with a DHFR selectable marker.

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pOptiVEC-TOPO (linearized) Sequence and MappOptiVEC-TOPO (linearized).dna
Map and Sequence File   
Sequence Author:  Invitrogen (Life Technologies)
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 SspI (3571) TsoI (3166) PvuI (3137) FspI (2989) NmeAIII (2915) AhdI (2767) PspFI (2185) BseYI (2181) DrdI (1985) BspQI - SapI (1761) PvuII (1701) BstAPI (1491) SgrDI (3688) SpeI (3725) NdeI (3960) BtgZI (4060) SnaBI (4066) BsmBI (4315) BspEI (4377) XbaI (4384) End (4402) Start (1) EagI - NotI (26) HpaI (38) PspOMI (159) ApaI (163) AvrII (197) HindIII (270) PmlI (362) AarI - BfuAI - BspMI (385) DraIII (409) Acc65I (487) KpnI (491) BmgBI (589) MscI (624) BglII (630) Bpu10I (723) SexAI * (810) BstXI (920) AflII (932) ApoI (1065) EcoNI (1143) PfoI * (1150) PmeI (1225) pOptiVEC™-TOPO® 4401 bp
SspI  (3571)
1 site
A A T A T T T T A T A A
TsoI  (3166)
1 site
T A R C C A ( N ) 9 N N A T Y G G T ( N ) 9

Sticky ends from different TsoI sites may not be compatible.
After cleavage, TsoI can remain bound to DNA and alter its
electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
PvuI  (3137)
1 site
C G A T C G G C T A G C
FspI  (2989)
1 site
T G C G C A A C G C G T
NmeAIII  (2915)
1 site
G C C G A G ( N ) 18-19 N N C G G C T C ( N ) 18-19

Efficient cleavage requires at least two copies of the NmeAIII
recognition sequence.
Sticky ends from different NmeAIII sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
AhdI  (2767)
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.
PspFI  (2185)
1 site
C C C A G C G G G T C G
BseYI  (2181)
1 site
C C C A G C G G G T C G

After cleavage, BseYI can remain bound to DNA and alter its
electrophoretic mobility.
DrdI  (1985)
1 site
G A C N N N N N N G T C C T G N N N N N N C A G

Sticky ends from different DrdI sites may not be compatible.
BspQI  (1761)
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  (1761)
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.
PvuII  (1701)
1 site
C A G C T G G T C G A C
BstAPI  (1491)
1 site
G C A N N N N N T G C C G T N N N N N A C G

Sticky ends from different BstAPI sites may not be compatible.
SgrDI  (3688)
1 site
C G T C G A C G G C A G C T G C
SpeI  (3725)
1 site
A C T A G T T G A T C A
NdeI  (3960)
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.
BtgZI  (4060)
1 site
G C G A T G ( N ) 10 C G C T A C ( N ) 10 ( N ) 4

Sticky ends from different BtgZI sites may not be compatible.
After cleavage, BtgZI can remain bound to DNA and alter its
electrophoretic mobility.
BtgZI is typically used at 60°C, but is 75% active at 37°C.
SnaBI  (4066)
1 site
T A C G T A A T G C A T
BsmBI  (4315)
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.
BspEI  (4377)
1 site
T C C G G A A G G C C T
XbaI  (4384)
1 site
T C T A G A A G A T C T
End  (4402)
0 sites
Start  (1)
0 sites
EagI  (26)
1 site
C G G C C G G C C G G C
NotI  (26)
1 site
G C G G C C G C C G C C G G C G
HpaI  (38)
1 site
G T T A A C C A A T T G
PspOMI  (159)
1 site
G G G C C C C C C G G G
ApaI  (163)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
AvrII  (197)
1 site
C C T A G G G G A T C C
HindIII  (270)
1 site
A A G C T T T T C G A A
PmlI  (362)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
AarI  (385)
1 site
C A C C T G C ( N ) 4 G T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the AarI
recognition sequence.
Sticky ends from different AarI sites may not be compatible.
After cleavage, AarI can remain bound to DNA and alter its
electrophoretic mobility.
BfuAI  (385)
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  (385)
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.
DraIII  (409)
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.
Acc65I  (487)
1 site
G G T A C C C C A T G G
KpnI  (491)
1 site
G G T A C C C C A T G G
BmgBI  (589)
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.
MscI  (624)
1 site
T G G C C A A C C G G T
BglII  (630)
1 site
A G A T C T T C T A G A
Bpu10I  (723)
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.
SexAI  (810)
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.
BstXI  (920)
1 site
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.
AflII  (932)
1 site
C T T A A G G A A T T C

The sticky ends produced by AflII are hard to ligate.
ApoI  (1065)
1 site
R A A T T Y Y T T A A R

ApoI is typically used at 50°C, but is 50% active at 37°C.
EcoNI  (1143)
1 site
C C T N N N N N A G G G G A N N N N N T C C

The 1-base overhangs produced by EcoNI may be hard to ligate.
Sticky ends from different EcoNI sites may not be compatible.
PfoI  (1150)
1 site
T C C N G G A A G G N C C T
* Blocked by Dcm methylation.
Sticky ends from different PfoI sites may not be compatible.
PmeI  (1225)
1 site
G T T T A A A C C A A A T T T G
AmpR
2694 .. 3554  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   2694 .. 3485  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
2694 .. 3554  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   3486 .. 3554  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
2694 .. 3554  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
1938 .. 2523  =  586 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
1938 .. 2523  =  586 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
IRES
46 .. 621  =  576 bp
internal ribosome entry site (IRES) of the
encephalomyocarditis virus (ECMV)
IRES
46 .. 621  =  576 bp
internal ribosome entry site (IRES) of the
encephalomyocarditis virus (ECMV)
DHFR
642 .. 1205  =  564 bp
187 amino acids  =  21.6 kDa
Product: mouse dihydrofolate reductase
DHFR
642 .. 1205  =  564 bp
187 amino acids  =  21.6 kDa
Product: mouse dihydrofolate reductase
CMV enhancer
3711 .. 4090  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
3711 .. 4090  =  380 bp
human cytomegalovirus immediate early enhancer
CMV promoter
4091 .. 4294  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
CMV promoter
4091 .. 4294  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
AmpR promoter
3555 .. 3659  =  105 bp
AmpR promoter
3555 .. 3659  =  105 bp
HSV TK poly(A) signal
1287 .. 1335  =  49 bp
herpesvirus thymidine kinase polyadenylation signal
HSV TK poly(A) signal
1287 .. 1335  =  49 bp
herpesvirus thymidine kinase polyadenylation signal
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