pcDNAII

Bacterial vector with an extensive polylinker for the cloning and expression of cDNAs.

Sequence Author: Thermo Fisher (Invitrogen)

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HomePlasmidsI.M.A.G.E. Consortium PlasmidspcDNAII
EcoO109I (11) PspOMI (10) NaeI (2704) NgoMIV (2702) BtgZI (2602) BsaAI - DraIII (2601) PsiI (2473) XmnI (2003) BsaHI (1941) ScaI (1884) TatI (1882) NmeAIII (1552) ApaI (14) XbaI (16) SphI (27) AvaI - BsoBI - PaeR7I - PspXI - XhoI (28) NotI (34) BsaBI (51) EcoRV (53) PstI (60) EcoRI (61) SpeI (86) BamHI (92) Eco53kI (100) SacI (102) Acc65I (104) KpnI (108) HindIII (110) BspQI - SapI (395) AflIII - PciI (511) BseYI (815) PspFI (819) AlwNI (927) AhdI (1404) AfeI (1434) BsaI (1465) BpmI (1474) pcDNAII 3013 bp
EcoO109I  (11)
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  (10)
1 site		 G G G C C C C C C G G G
NaeI  (2704)
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  (2702)
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.
BtgZI  (2602)
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.
BsaAI  (2601)
1 site		 Y A C G T R R T G C A Y
DraIII  (2601)
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.
PsiI  (2473)
1 site		 T T A T A A A A T A T T
XmnI  (2003)
1 site		 G A A N N N N T T C C T T N N N N A A G
BsaHI  (1941)
1 site		 G R C G Y C C Y G C R G
BsaHI is typically used at 37°C, but is even more active at 60°C.
ScaI  (1884)
1 site		 A G T A C T T C A T G A
TatI  (1882)
1 site		 W G T A C W W C A T G W
NmeAIII  (1552)
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).
ApaI  (14)
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  (16)
1 site		 T C T A G A A G A T C T
SphI  (27)
1 site		 G C A T G C C G T A C G
AvaI  (28)
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  (28)
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  (28)
1 site		 C T C G A G G A G C T C
PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (28)
1 site		 V C T C G A G B B G A G C T C V
XhoI  (28)
1 site		 C T C G A G G A G C T C
NotI  (34)
1 site		 G C G G C C G C C G C C G G C G
BsaBI  (51)
1 site		 G A T N N N N A T C C T A N N N N T A G
EcoRV  (53)
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  (60)
1 site		 C T G C A G G A C G T C
EcoRI  (61)
1 site		 G A A T T C C T T A A G
SpeI  (86)
1 site		 A C T A G T T G A T C A
BamHI  (92)
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.
Eco53kI  (100)
1 site		 G A G C T C C T C G A G
SacI  (102)
1 site		 G A G C T C C T C G A G
Acc65I  (104)
1 site		 G G T A C C C C A T G G
KpnI  (108)
1 site		 G G T A C C C C A T G G
HindIII  (110)
1 site		 A A G C T T T T C G A A
BspQI  (395)
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  (395)
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.
AflIII  (511)
1 site		 A C R Y G T T G Y R C A
Sticky ends from different AflIII sites may not be compatible.
PciI  (511)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
BseYI  (815)
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.
PspFI  (819)
1 site		 C C C A G C G G G T C G
AlwNI  (927)
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.
AhdI  (1404)
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.
AfeI  (1434)
1 site		 A G C G C T T C G C G A
BsaI  (1465)
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.
BpmI  (1474)
1 site		 C T G G A G ( N ) 14 N N G A C C T C ( N ) 14
Efficient cleavage requires at least two copies of the BpmI recognition sequence.
Sticky ends from different BpmI sites may not be compatible.
After cleavage, BpmI can remain bound to DNA and alter its electrophoretic mobility.
BpmI quickly loses activity at 37°C.
AmpR
1331 .. 2191  =  861 bp
287 codons
2 segments
   Segment 2:  
   1331 .. 2122  =  792 bp
   264 codons
Product: β-lactamase
confers resistance fo ampicillin, carbenicillin, and related antibiotics
AmpR
1331 .. 2191  =  861 bp
287 codons
2 segments
   Segment 1:  signal sequence  
   2123 .. 2191  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance fo ampicillin, carbenicillin, and related antibiotics
AmpR
1331 .. 2191  =  861 bp
287 codons
2 segments
Product: β-lactamase
confers resistance fo ampicillin, carbenicillin, and related antibiotics
lacZα
2582 .. 174  =  606 bp
201 amino acids  =  22.0 kDa
Product: LacZα fragment of β-galactosidase
lacZα
2582 .. 174  =  606 bp
201 amino acids  =  22.0 kDa
Product: LacZα fragment of β-galactosidase
ori
572 .. 1160  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
572 .. 1160  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
AmpR promoter
2192 .. 2296  =  105 bp
AmpR promoter
2192 .. 2296  =  105 bp
lac promoter
218 .. 248  =  31 bp
3 segments
   Segment 3:  -10  
   218 .. 224  =  7 bp
promoter for the E. coli lac operon
lac promoter
218 .. 248  =  31 bp
3 segments
   Segment 2:  
   225 .. 242  =  18 bp
promoter for the E. coli lac operon
lac promoter
218 .. 248  =  31 bp
3 segments
   Segment 1:  -35  
   243 .. 248  =  6 bp
promoter for the E. coli lac operon
lac promoter
218 .. 248  =  31 bp
3 segments
promoter for the E. coli lac operon
lac operator
194 .. 210  =  17 bp
The lac repressor binds to the lac operator to inhibit transcription in E. coli. This inhibition can be relieved by adding lactose or isopropyl-β-D-thiogalactopyranoside (IPTG).
lac operator
194 .. 210  =  17 bp
The lac repressor binds to the lac operator to inhibit transcription in E. coli. This inhibition can be relieved by adding lactose or isopropyl-β-D-thiogalactopyranoside (IPTG).
f1 ori
2377 .. 2832  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
2377 .. 2832  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
MCS
10 .. 122  =  113 bp
multiple cloning site
MCS
10 .. 122  =  113 bp
multiple cloning site
SP6 promoter
134 .. 152  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
134 .. 152  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
T7 promoter
2997 .. 2  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
2997 .. 2  =  19 bp
promoter for bacteriophage T7 RNA polymerase
M13 rev
170 .. 186  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
170 .. 186  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
2974 .. 2990  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
2974 .. 2990  =  17 bp
common sequencing primer, one of multiple similar variants
ORF:  1461 .. 1727  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  1331 .. 1567  =  237 bp
ORF:  78 amino acids  =  8.3 kDa
ORF:  1568 .. 2191  =  624 bp
ORF:  207 amino acids  =  23.2 kDa
ORF:  2582 .. 174  =  606 bp
ORF:  201 amino acids  =  22.0 kDa
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Individual Sequences & Maps

Lafmid BA
pcDNAII
pCR2.1-TOPO (linearized)
pExpress-1
pAD-GAL4
pcDNA3.1(+)
pCR3.1
pME18S-FL3
pAMP1
pcDNA3.1(-)
pCR3.1 (linearized)
pOTB7
pAMP10
pcDNA3.1 Zeo(+)
pCR4-TOPO
pOTB7-3
pBK-CMV
pCMV SPORT
pCR4-TOPO (linearized)
pOTB7a
pBluescribe (modified)
pCMV SPORT2
pCS105
pPCR-Script Amp SK(+)
pBluescript II SK(+)
pCMV SPORT4
pCS107
pRKW2
pBluescript KS(+)
pCMV SPORT6
pCS108
pSPORT 1
pBluescript SK(+)
pCMV SPORT6.1
pCS2+
pSPORT 2
pBluescript SK(-)
pCMV SPORT6ccdB
pCS22+
pT7T3D-PacI
pBluescript-FL
pCR-Blunt II-TOPO
pCS2G
pUC19
pBluescript II KS(+)
pCR-Blunt II-TOPO (linearized)
pDNR-Dual
pYX-Asc
pBluescriptR
pCR-XL-TOPO
pDNR-LIB
pZErO-2
pcDNA3
pCR-XL-TOPO (linearized)
pDONR201
pZL1
pcDNAI
pCR2.1-TOPO
pDONR223

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