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Plasmid Files

pVAX1

Nonoptimized first generation DNA vaccine vector.

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pVAX1.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Thermo Fisher (Invitrogen)
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PciI (2990) ApaLI (2676) AlwNI (2581) PmlI (2211) RsrII (1870) NaeI (1856) NgoMIV (1854) BsrDI (1587) NmeAIII (1578) NruI (9) MluI (29) HincII (35) NdeI (285) SnaBI (391) Bts α I (639) BsaI (677) NheI (696) BmtI (700) PmeI (705) AflII (709) HindIII (712) Acc65I (718) KpnI (722) BamHI (730) BstXI (749) ApoI - EcoRI (753) PstI (762) EcoRV (765) BstXI (775) NotI (780) AvaI - BsoBI - PaeR7I - PspXI - XhoI (786) BmeT110I (787) XbaI (792) EcoO109I - PspOMI (798) ApaI (802) PmeI (807) BbsI (1018) XcmI (1170) BsaBI * (1213) MscI (1436) FspI (1456) PflFI - Tth111I (1472) pVAX1 2999 bp
PciI  (2990)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
ApaLI  (2676)
1 site
G T G C A C C A C G T G
AlwNI  (2581)
1 site
C A G N N N C T G G T C N N N G A C

Sticky ends from different AlwNI sites may not be compatible.
PmlI  (2211)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
RsrII  (1870)
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.
NaeI  (1856)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NaeI recognition sequence.
NgoMIV  (1854)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NgoMIV recognition sequence.
BsrDI  (1587)
1 site
G C A A T G N N C G T T A C

Sticky ends from different BsrDI sites may not be compatible.
NmeAIII  (1578)
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).
NruI  (9)
1 site
T C G C G A A G C G C T
MluI  (29)
1 site
A C G C G T T G C G C A
HincII  (35)
1 site
G T Y R A C C A R Y T G
NdeI  (285)
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  (391)
1 site
T A C G T A A T G C A T
BtsαI  (639)
1 site
G C A G T G N N C G T C A C

Sticky ends from different BtsαI sites may not be compatible.
BsaI  (677)
1 site
G G T C T C N C C A G A G N ( N ) 4

Sticky ends from different BsaI sites may not be compatible.
BsaI can be used between 37°C and 50°C.
NheI  (696)
1 site
G C T A G C C G A T C G
BmtI  (700)
1 site
G C T A G C C G A T C G
PmeI  (705)
2 sites
G T T T A A A C C A A A T T T G
AflII  (709)
1 site
C T T A A G G A A T T C
HindIII  (712)
1 site
A A G C T T T T C G A A
Acc65I  (718)
1 site
G G T A C C C C A T G G
KpnI  (722)
1 site
G G T A C C C C A T G G
BamHI  (730)
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  (749)
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.
ApoI  (753)
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.
EcoRI  (753)
1 site
G A A T T C C T T A A G
PstI  (762)
1 site
C T G C A G G A C G T C
EcoRV  (765)
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  (775)
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  (780)
1 site
G C G G C C G C C G C C G G C G
AvaI  (786)
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  (786)
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  (786)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (786)
1 site
V C T C G A G B B G A G C T C V
XhoI  (786)
1 site
C T C G A G G A G C T C
BmeT110I  (787)
1 site
C Y C G R G G R G C Y C
XbaI  (792)
1 site
T C T A G A A G A T C T
EcoO109I  (798)
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  (798)
1 site
G G G C C C C C C G G G
ApaI  (802)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
PmeI  (807)
2 sites
G T T T A A A C C A A A T T T G
BbsI  (1018)
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.
XcmI  (1170)
1 site
C C A N N N N N N N N N T G G G G T N N N N N N N N N A C C

The 1-base overhangs produced by XcmI may be hard to ligate.
Sticky ends from different XcmI sites may not be compatible.
BsaBI  (1213)
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.
MscI  (1436)
1 site
T G G C C A A C C G G T
FspI  (1456)
1 site
T G C G C A A C G C G T
PflFI  (1472)
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  (1472)
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.
NeoR/KanR
1226 .. 2020  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin®)
NeoR/KanR
1226 .. 2020  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin®)
ori
2346 .. 2934  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2346 .. 2934  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
CMV enhancer
36 .. 415  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
36 .. 415  =  380 bp
human cytomegalovirus immediate early enhancer
bGH poly(A) signal
829 .. 1053  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
829 .. 1053  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
416 .. 619  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
416 .. 619  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
MCS
696 .. 811  =  116 bp
multiple cloning site
MCS
696 .. 811  =  116 bp
multiple cloning site
T7 promoter
664 .. 682  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
664 .. 682  =  19 bp
promoter for bacteriophage T7 RNA polymerase
ORF:  1226 .. 2020  =  795 bp
ORF:  264 amino acids  =  29.0 kDa
ORF:  1398 .. 1784  =  387 bp
ORF:  128 amino acids  =  14.6 kDa
ORF:  1535 .. 2068  =  534 bp
ORF:  177 amino acids  =  19.9 kDa
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