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Plasmid Files

pDONR™223

Gateway® donor vector with attP1 and attP2 sites and a spectinomycin resistance marker.

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pDONR223 Sequence and MappDONR223.dna
Map and Sequence File   
Sequence Author:  I.M.A.G.E. Consortium
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 PciI (4999) DrdI (4897) BssS α I (4826) PspFI (4699) BseYI (4695) PaeR7I - PspXI - XhoI (4265) NaeI (4120) NgoMIV (4118) BglI (4101) PvuI (3850) BlpI (3778) BclI * (3667) BstEII (3629) BspHI (3469) XbaI (3112) BseRI (3099) EcoRV (2996) NspI (5003) BspQI - SapI (111) BbsI (437) HpaI (501) M13 fwd AflII (554) PspOMI (563) EcoO109I (564) ApaI - BanII (567) XmnI (1052) PstI (1167) BsaI (1276) BstXI (1305) BmgBI (1384) BsaBI * (1405) TspMI - XmaI (1416) SmaI - SrfI (1418) BbvCI (1561) BstZ17I (1754) BamHI (1832) ScaI (1872) SspI (1977) NcoI (1984) EcoRI (2285) BspEI (2289) pDONR™223 5005 bp
PciI  (4999)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
DrdI  (4897)
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.
BssSαI  (4826)
1 site
C A C G A G G T G C T C
PspFI  (4699)
1 site
C C C A G C G G G T C G
BseYI  (4695)
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.
PaeR7I  (4265)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (4265)
1 site
V C T C G A G B B G A G C T C V
XhoI  (4265)
1 site
C T C G A G G A G C T C
NaeI  (4120)
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  (4118)
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.
BglI  (4101)
1 site
G C C N N N N N G G C C G G N N N N N C C G

Sticky ends from different BglI sites may not be compatible.
PvuI  (3850)
1 site
C G A T C G G C T A G C
BlpI  (3778)
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.
BclI  (3667)
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.
BstEII  (3629)
1 site
G G T N A C C C C A N T G G

Sticky ends from different BstEII sites may not be compatible.
BstEII is typically used at 60°C, but is 50% active at 37°C.
BspHI  (3469)
1 site
T C A T G A A G T A C T
XbaI  (3112)
1 site
T C T A G A A G A T C T
BseRI  (3099)
1 site
G A G G A G ( N ) 8 N N C T C C T C ( N ) 8

Sticky ends from different BseRI sites may not be compatible.
BseRI quickly loses activity at 37°C.
Prolonged incubation with BseRI may lead to degradation of the
DNA.
EcoRV  (2996)
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.
NspI  (5003)
1 site
R C A T G Y Y G T A C R
BspQI  (111)
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  (111)
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.
BbsI  (437)
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.
HpaI  (501)
1 site
G T T A A C C A A T T G
AflII  (554)
1 site
C T T A A G G A A T T C

The sticky ends produced by AflII are hard to ligate.
PspOMI  (563)
1 site
G G G C C C C C C G G G
EcoO109I  (564)
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  (567)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
BanII  (567)
1 site
G R G C Y C C Y C G R G

Sticky ends from different BanII sites may not be compatible.
XmnI  (1052)
1 site
G A A N N N N T T C C T T N N N N A A G
PstI  (1167)
1 site
C T G C A G G A C G T C
BsaI  (1276)
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.
BstXI  (1305)
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.
BmgBI  (1384)
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.
BsaBI  (1405)
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.
TspMI  (1416)
1 site
C C C G G G G G G C C C
XmaI  (1416)
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  (1418)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
SrfI  (1418)
1 site
G C C C G G G C C G G G C C C G
BbvCI  (1561)
1 site
C C T C A G C G G A G T C G
BstZ17I  (1754)
1 site
G T A T A C C A T A T G
BamHI  (1832)
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.
ScaI  (1872)
1 site
A G T A C T T C A T G A
SspI  (1977)
1 site
A A T A T T T T A T A A
NcoI  (1984)
1 site
C C A T G G G G T A C C
EcoRI  (2285)
1 site
G A A T T C C T T A A G
BspEI  (2289)
1 site
T C C G G A A G G C C T
SmR
3471 .. 4262  =  792 bp
263 amino acids  =  29.3 kDa
Product: aminoglycoside adenylyltransferase
confers resistance to spectinomycin and
streptomycin
SmR
3471 .. 4262  =  792 bp
263 amino acids  =  29.3 kDa
Product: aminoglycoside adenylyltransferase
confers resistance to spectinomycin and
streptomycin
CmR
1844 .. 2503  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
1844 .. 2503  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
ori
4355 .. 4943  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
4355 .. 4943  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ccdB
1197 .. 1502  =  306 bp
101 amino acids  =  11.7 kDa
Product: CcdB, a bacterial toxin that poisons DNA
gyrase
Plasmids containing the ccdB gene cannot be
propagaged in standard E. coli strains.
ccdB
1197 .. 1502  =  306 bp
101 amino acids  =  11.7 kDa
Product: CcdB, a bacterial toxin that poisons DNA
gyrase
Plasmids containing the ccdB gene cannot be
propagaged in standard E. coli strains.
attP1
570 .. 801  =  232 bp
recombination site for the Gateway® BP reaction
(pDONR™221 version)
attP1
570 .. 801  =  232 bp
recombination site for the Gateway® BP reaction
(pDONR™221 version)
attP2
2751 .. 2982  =  232 bp
recombination site for the Gateway® BP reaction
(pDONR™221 version)
attP2
2751 .. 2982  =  232 bp
recombination site for the Gateway® BP reaction
(pDONR™221 version)
cat promoter
2504 .. 2606  =  103 bp
promoter of the E. coli cat gene
cat promoter
2504 .. 2606  =  103 bp
promoter of the E. coli cat gene
rrnB T1 terminator
387 .. 473  =  87 bp
transcription terminator T1 from the E. coli rrnB
gene
rrnB T1 terminator
387 .. 473  =  87 bp
transcription terminator T1 from the E. coli rrnB
gene
rrnB T2 terminator
268 .. 295  =  28 bp
transcription terminator T2 from the E. coli rrnB
gene
rrnB T2 terminator
268 .. 295  =  28 bp
transcription terminator T2 from the E. coli rrnB
gene
M13 fwd
537 .. 553  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
537 .. 553  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
3024 .. 3040  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
3024 .. 3040  =  17 bp
common sequencing primer, one of multiple similar
variants
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