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Plasmid Files

pPZP100

Agrobacterium binary vector for plant transformation, with a chloramphenicol-resistance gene.

 
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pPZP100.dna
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PmeI (6485) BlpI (6441) HindIII (6438) PstI - SbfI (6430) SalI (6420) XbaI (6414) BamHI (6408) SmaI (6405) KpnI - TspMI - XmaI (6403) Acc65I (6399) BanII - SacI (6397) Eco53kI (6395) EcoRI (6387) BclI * (6056) PvuII (5652) BspEI (5552) BpmI (5432) SspI (5240) HpaI (5033) NsiI (4913) BssS α I (4360) BstZ17I (3960) PluTI (3765) SfoI (3763) NarI (3762) KasI (3761) AgeI (3470) BsaI (3379) EcoNI (3289) BbsI (56) BsaBI * (1299) BsiWI (2860) NheI (2976) BmtI (2980) BspDI * - ClaI * (3056) FspI (3193) BseRI (3253) pPZP100 6637 bp
PmeI  (6485)
1 site
G T T T A A A C C A A A T T T G
BlpI  (6441)
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.
HindIII  (6438)
1 site
A A G C T T T T C G A A
PstI  (6430)
1 site
C T G C A G G A C G T C
SbfI  (6430)
1 site
C C T G C A G G G G A C G T C C
SalI  (6420)
1 site
G T C G A C C A G C T G
XbaI  (6414)
1 site
T C T A G A A G A T C T
BamHI  (6408)
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.
SmaI  (6405)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
KpnI  (6403)
1 site
G G T A C C C C A T G G
TspMI  (6403)
1 site
C C C G G G G G G C C C
XmaI  (6403)
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.
Acc65I  (6399)
1 site
G G T A C C C C A T G G
BanII  (6397)
1 site
G R G C Y C C Y C G R G

Sticky ends from different BanII sites may not be compatible.
SacI  (6397)
1 site
G A G C T C C T C G A G
Eco53kI  (6395)
1 site
G A G C T C C T C G A G
EcoRI  (6387)
1 site
G A A T T C C T T A A G
BclI  (6056)
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.
PvuII  (5652)
1 site
C A G C T G G T C G A C
BspEI  (5552)
1 site
T C C G G A A G G C C T
BpmI  (5432)
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.
SspI  (5240)
1 site
A A T A T T T T A T A A
HpaI  (5033)
1 site
G T T A A C C A A T T G
NsiI  (4913)
1 site
A T G C A T T A C G T A
BssSαI  (4360)
1 site
C A C G A G G T G C T C
BstZ17I  (3960)
1 site
G T A T A C C A T A T G
PluTI  (3765)
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.
SfoI  (3763)
1 site
G G C G C C C C G C G G
NarI  (3762)
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.
KasI  (3761)
1 site
G G C G C C C C G C G G
AgeI  (3470)
1 site
A C C G G T T G G C C A
BsaI  (3379)
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.
EcoNI  (3289)
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.
BbsI  (56)
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.
BsaBI  (1299)
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.
BsiWI  (2860)
1 site
C G T A C G G C A T G C

BsiWI is typically used at 55°C, but is 50% active at 37°C.
NheI  (2976)
1 site
G C T A G C C G A T C G
BmtI  (2980)
1 site
G C T A G C C G A T C G
BspDI  (3056)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (3056)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
FspI  (3193)
1 site
T G C G C A A C G C G T
BseRI  (3253)
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.
pVS1 RepA
2245 .. 3318  =  1074 bp
357 amino acids  =  39.9 kDa
Product: replication protein from Pseudomonas plasmid pVS1
pVS1 RepA
2245 .. 3318  =  1074 bp
357 amino acids  =  39.9 kDa
Product: replication protein from Pseudomonas plasmid pVS1
CmR
5107 .. 5766  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
5107 .. 5766  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
pVS1 StaA
1187 .. 1816  =  630 bp
209 amino acids  =  22.1 kDa
Product: stability protein from Pseudomonas plasmid pVS1
pVS1 StaA
1187 .. 1816  =  630 bp
209 amino acids  =  22.1 kDa
Product: stability protein from Pseudomonas plasmid pVS1
ori
4248 .. 4836  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
4248 .. 4836  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
pVS1 oriV
3384 .. 3578  =  195 bp
origin of replication for the Pseudomonas plasmid pVS1 (Heeb et al., 2000)
pVS1 oriV
3384 .. 3578  =  195 bp
origin of replication for the Pseudomonas plasmid pVS1 (Heeb et al., 2000)
bom
3922 .. 4062  =  141 bp
basis of mobility region from pBR322
bom
3922 .. 4062  =  141 bp
basis of mobility region from pBR322
MCS
6387 .. 6443  =  57 bp
pUC18 multiple cloning site
MCS
6387 .. 6443  =  57 bp
pUC18 multiple cloning site
LB T-DNA repeat
6294 .. 6318  =  25 bp
left border repeat from nopaline C58 T-DNA
LB T-DNA repeat
6294 .. 6318  =  25 bp
left border repeat from nopaline C58 T-DNA
RB T-DNA repeat
6500 .. 6524  =  25 bp
right border repeat from nopaline C58 T-DNA
RB T-DNA repeat
6500 .. 6524  =  25 bp
right border repeat from nopaline C58 T-DNA
ORF:  202 .. 888  =  687 bp
ORF:  228 amino acids  =  25.1 kDa
ORF:  2143 .. 3318  =  1176 bp
ORF:  391 amino acids  =  43.9 kDa
ORF:  6031 .. 6372  =  342 bp
ORF:  113 amino acids  =  12.1 kDa
ORF:  1187 .. 1816  =  630 bp
ORF:  209 amino acids  =  22.1 kDa
ORF:  5919 .. 6161  =  243 bp
ORF:  80 amino acids  =  9.1 kDa
ORF:  653 .. 925  =  273 bp
ORF:  90 amino acids  =  9.9 kDa
ORF:  925 .. 1239  =  315 bp
ORF:  104 amino acids  =  12.0 kDa
ORF:  2113 .. 2685  =  573 bp
ORF:  190 amino acids  =  20.6 kDa
ORF:  5107 .. 5907  =  801 bp
ORF:  266 amino acids  =  31.0 kDa
ORF:  234 .. 584  =  351 bp
ORF:  116 amino acids  =  12.6 kDa
ORF:  2091 .. 2348  =  258 bp
ORF:  85 amino acids  =  9.6 kDa
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