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Plasmid Files

pLenti6.3/V5-TOPO® (linearized)

Linearized lentiviral expression vector with a blasticidin resistance gene with 3'-T overhangs and bound topoisomerase, for TOPO® TA cloning of PCR products.

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pLenti6.3 V5-TOPO (linearized) Sequence and MappLenti6.3 V5-TOPO (linearized).dna
Map and Sequence File   
Sequence Author:  Invitrogen (Life Technologies)
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 PciI (4720) AhdI (3832) ScaI (3351) DraIII (2692) SfiI (2204) BlpI (1561) MscI (1169) PmlI (1097) KasI (5543) NarI (5544) SfoI (5545) PluTI (5547) EcoNI (6072) MfeI (6091) BbvCI - Bpu10I (6326) AleI (6479) KflI (6835) HpaI (6929) BspDI - ClaI (7052) NdeI (7246) SnaBI (7352) BsmBI (7601) BamHI (7657) SpeI (7663) End (7691) Start (1) PstI (16) EcoRV (19) PaeR7I - PspXI - XhoI (40) PspOMI (52) ApaI (56) BstBI (63) MluI (107) PflMI (374) PfoI (406) SexAI * (804) TspMI - XmaI (1058) SmaI (1060) BclI * (1088) pLenti6.3/V5-TOPO® 7690 bp
PciI  (4720)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AhdI  (3832)
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.
ScaI  (3351)
1 site
A G T A C T T C A T G A
DraIII  (2692)
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.
SfiI  (2204)
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.
BlpI  (1561)
1 site
G C T N A G C C G A N T C G

Sticky ends from different BlpI sites may not be compatible.
MscI  (1169)
1 site
T G G C C A A C C G G T
PmlI  (1097)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
KasI  (5543)
1 site
G G C G C C C C G C G G
NarI  (5544)
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.
SfoI  (5545)
1 site
G G C G C C C C G C G G
PluTI  (5547)
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.
EcoNI  (6072)
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.
MfeI  (6091)
1 site
C A A T T G G T T A A C
BbvCI  (6326)
1 site
C C T C A G C G G A G T C G
Bpu10I  (6326)
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.
AleI  (6479)
1 site
C A C N N N N G T G G T G N N N N C A C
KflI  (6835)
1 site
G G G W C C C C C C W G G G

Sticky ends from different KflI sites may not be compatible.
HpaI  (6929)
1 site
G T T A A C C A A T T G
BspDI  (7052)
1 site
A T C G A T T A G C T A
ClaI  (7052)
1 site
A T C G A T T A G C T A
NdeI  (7246)
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  (7352)
1 site
T A C G T A A T G C A T
BsmBI  (7601)
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.
BamHI  (7657)
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.
SpeI  (7663)
1 site
A C T A G T T G A T C A
End  (7691)
0 sites
Start  (1)
0 sites
PstI  (16)
1 site
C T G C A G G A C G T C
EcoRV  (19)
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.
PaeR7I  (40)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (40)
1 site
V C T C G A G B B G A G C T C V
XhoI  (40)
1 site
C T C G A G G A G C T C
PspOMI  (52)
1 site
G G G C C C C C C G G G
ApaI  (56)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
BstBI  (63)
1 site
T T C G A A A A G C T T
MluI  (107)
1 site
A C G C G T T G C G C A
PflMI  (374)
1 site
C C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
PfoI  (406)
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.
SexAI  (804)
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.
TspMI  (1058)
1 site
C C C G G G G G G C C C
XmaI  (1058)
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  (1060)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
BclI  (1088)
1 site
T G A T C A A C T A G T
* Blocked by Dam methylation.
BclI is typically used at 50-55°C, but is 50% active at 37°C.
AmpR
3045 .. 3905  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   3045 .. 3113  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
3045 .. 3905  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   3114 .. 3905  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
3045 .. 3905  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
WPRE
133 .. 721  =  589 bp
woodchuck posttranscriptional regulatory element
WPRE
133 .. 721  =  589 bp
woodchuck posttranscriptional regulatory element
ori
4076 .. 4664  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin
of replication
ori
4076 .. 4664  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin
of replication
f1 ori
2459 .. 2914  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
2459 .. 2914  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
BSD
1166 .. 1564  =  399 bp
132 amino acids  =  13.7 kDa
Product: blasticidin S deaminase
confers resistance to blasticidin
BSD
1166 .. 1564  =  399 bp
132 amino acids  =  13.7 kDa
Product: blasticidin S deaminase
confers resistance to blasticidin
SV40 promoter
736 .. 1052  =  317 bp
SV40 enhancer and early promoter
SV40 promoter
736 .. 1052  =  317 bp
SV40 enhancer and early promoter
CMV enhancer
7073 .. 7376  =  304 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
7073 .. 7376  =  304 bp
human cytomegalovirus immediate early enhancer
3'LTR (ΔU3)
1651 .. 1884  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from
HIV-1
3'LTR (ΔU3)
1651 .. 1884  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from
HIV-1
HIV-1 RRE
6205 .. 6438  =  234 bp
The Rev response element (RRE) of human
immunodeficiency virus type 1 allows for
Rev-dependent mRNA export from the nucleus to
the cytoplasm.
HIV-1 RRE
6205 .. 6438  =  234 bp
The Rev response element (RRE) of human
immunodeficiency virus type 1 allows for
Rev-dependent mRNA export from the nucleus to
the cytoplasm.
RSV promoter
5131 .. 5354  =  224 bp
Rous sarcoma virus promoter
RSV promoter
5131 .. 5354  =  224 bp
Rous sarcoma virus promoter
CMV promoter
7377 .. 7580  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
CMV promoter
7377 .. 7580  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
5' LTR
5360 .. 5540  =  181 bp
truncated 5' long terminal repeat (LTR) from HIV-1
5' LTR
5360 .. 5540  =  181 bp
truncated 5' long terminal repeat (LTR) from HIV-1
HIV-1 ψ
5587 .. 5712  =  126 bp
packaging signal of human immunodeficiency virus
type 1
HIV-1 ψ
5587 .. 5712  =  126 bp
packaging signal of human immunodeficiency virus
type 1
SV40 poly(A) signal
1956 .. 2077  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
1956 .. 2077  =  122 bp
SV40 polyadenylation signal
HIV-1 cPPT
6933 .. 7050  =  118 bp
central polypurine tract from pol gene of human
immunodeficiency virus type 1
HIV-1 cPPT
6933 .. 7050  =  118 bp
central polypurine tract from pol gene of human
immunodeficiency virus type 1
AmpR promoter
2940 .. 3044  =  105 bp
AmpR promoter
2940 .. 3044  =  105 bp
EM7 promoter
1100 .. 1147  =  48 bp
synthetic bacterial promoter
EM7 promoter
1100 .. 1147  =  48 bp
synthetic bacterial promoter
V5 tag
68 .. 109  =  42 bp
14 amino acids  =  1.4 kDa
Product: epitope tag from simian virus 5
V5 tag
68 .. 109  =  42 bp
14 amino acids  =  1.4 kDa
Product: epitope tag from simian virus 5
SV40 ori
903 .. 1038  =  136 bp
SV40 origin of replication
SV40 ori
903 .. 1038  =  136 bp
SV40 origin of replication
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