pFA6a-TRP1

Plasmid for yeast gene deletion using the S. cerevisiae TRP1 selectable marker.
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PvuII (15) NdeI (3332) PfoI (3194) EcoO109I (3137) AatII (3083) ZraI (3081) SspI (2965) ScaI (2641) TsoI (2560) PvuI (2531) FspI (2383) NmeAIII (2309) BpmI (2231) BanI (2109) BsiWI (25) PstI (35) SalI (37) F1 (42 .. 61) BamHI (43) AvaI - BsoBI - TspMI - XmaI (48) SmaI (50) PacI (58) AscI - BssHII (63) BglII (70) BsrGI (75) BspEI * (88) PmlI (183) BstZ17I (190) BstAPI (302) XbaI (307) MfeI (363) Bsu36I (465) BstXI (521) BsgI (636) PaqCI (656) PmeI (982) Eco53kI (989) SacI (991) EcoRI (993) R1 (979 .. 998) BspDI - ClaI (1000) SpeI (1017) SfiI (1030) BtgI (1034) SacII (1037) HpaI (1089) BspQI - SapI (1152) AflIII - PciI (1268) AlwNI (1684) pFA6a-TRP1 3415 bp
PvuII  (15)
1 site
C A G C T G G T C G A C
NdeI  (3332)
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.
PfoI  (3194)
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.
EcoO109I  (3137)
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.
AatII  (3083)
1 site
G A C G T C C T G C A G
ZraI  (3081)
1 site
G A C G T C C T G C A G
SspI  (2965)
1 site
A A T A T T T T A T A A
ScaI  (2641)
1 site
A G T A C T T C A T G A
TsoI  (2560)
1 site
T A R C C A ( N ) 9 N N A T Y G G T ( N ) 9

Sticky ends from different TsoI sites may not be compatible.
After cleavage, TsoI can remain bound to DNA and alter its electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
PvuI  (2531)
1 site
C G A T C G G C T A G C
FspI  (2383)
1 site
T G C G C A A C G C G T
NmeAIII  (2309)
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).
BpmI  (2231)
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.
BanI  (2109)
1 site
G G Y R C C C C R Y G G

Sticky ends from different BanI sites may not be compatible.
BsiWI  (25)
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.
PstI  (35)
1 site
C T G C A G G A C G T C
SalI  (37)
1 site
G T C G A C C A G C T G
BamHI  (43)
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.
AvaI  (48)
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  (48)
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.
TspMI  (48)
1 site
C C C G G G G G G C C C
XmaI  (48)
1 site
C C C G G G G G G C C C

Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
SmaI  (50)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
PacI  (58)
1 site
T T A A T T A A A A T T A A T T
AscI  (63)
1 site
G G C G C G C C C C G C G C G G
BssHII  (63)
1 site
G C G C G C C G C G C G

BssHII is typically used at 50°C, but is 75% active at 37°C.
BglII  (70)
1 site
A G A T C T T C T A G A
BsrGI  (75)
1 site
T G T A C A A C A T G T

BsrGI is typically used at 37°C, but is even more active at 60°C.
BspEI  (88)
1 site
T C C G G A A G G C C T
* Blocked by Dam methylation.
PmlI  (183)
1 site
C A C G T G G T G C A C
BstZ17I  (190)
1 site
G T A T A C C A T A T G
BstAPI  (302)
1 site
G C A N N N N N T G C C G T N N N N N A C G

Sticky ends from different BstAPI sites may not be compatible.
XbaI  (307)
1 site
T C T A G A A G A T C T
MfeI  (363)
1 site
C A A T T G G T T A A C
Bsu36I  (465)
1 site
C C T N A G G G G A N T C C

Sticky ends from different Bsu36I sites may not be compatible.
BstXI  (521)
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.
BsgI  (636)
1 site
G T G C A G ( N ) 14 N N C A C G T C ( N ) 14

Efficient cleavage requires at least two copies of the BsgI recognition sequence.
Sticky ends from different BsgI sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
PaqCI  (656)
1 site
C A C C T G C ( N ) 4 G T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the PaqCI recognition sequence.
Sticky ends from different PaqCI sites may not be compatible.
Cleavage can be improved with PaqCI Activator.
PmeI  (982)
1 site
G T T T A A A C C A A A T T T G
Eco53kI  (989)
1 site
G A G C T C C T C G A G
SacI  (991)
1 site
G A G C T C C T C G A G
EcoRI  (993)
1 site
G A A T T C C T T A A G
BspDI  (1000)
1 site
A T C G A T T A G C T A
ClaI  (1000)
1 site
A T C G A T T A G C T A
SpeI  (1017)
1 site
A C T A G T T G A T C A
SfiI  (1030)
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.
BtgI  (1034)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
SacII  (1037)
1 site
C C G C G G G G C G C C

Efficient cleavage requires at least two copies of the SacII recognition sequence.
HpaI  (1089)
1 site
G T T A A C C A A T T G
BspQI  (1152)
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  (1152)
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  (1268)
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  (1268)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AlwNI  (1684)
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.
F1
20-mer  /  50% GC
1 binding site
42 .. 61  =  20 annealed bases
Tm  =  54°C
Forward primer for gene deletion. This primer includes a BamHI recognition sequence. A gene-specific sequence should be added at the 5' end of the primer.
R1
20-mer  /  40% GC
1 binding site
979 .. 998  =  20 annealed bases
Tm  =  53°C
Reverse primer for gene deletion or C-terminal tagging. This primer includes an EcoRI recognition sequence. A gene-specific sequence should be added at the 5' end of the primer.
AmpR
2088 .. 2948  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   2088 .. 2879  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2088 .. 2948  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   2880 .. 2948  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2088 .. 2948  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
TRP1
224 .. 898  =  675 bp
224 amino acids  =  24.1 kDa
Product: phosphoribosylanthranilate isomerase, required for tryptophan biosynthesis
yeast auxotrophic marker
TRP1
224 .. 898  =  675 bp
224 amino acids  =  24.1 kDa
Product: phosphoribosylanthranilate isomerase, required for tryptophan biosynthesis
yeast auxotrophic marker
ori
1329 .. 1917  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
1329 .. 1917  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
TRP1 promoter
76 .. 223  =  148 bp
TRP1 promoter
76 .. 223  =  148 bp
AmpR promoter
2949 .. 3053  =  105 bp
AmpR promoter
2949 .. 3053  =  105 bp
T7 promoter
1053 .. 1071  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
1053 .. 1071  =  19 bp
promoter for bacteriophage T7 RNA polymerase
SP6 promoter
3399 .. 2  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
3399 .. 2  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
ORF:  2218 .. 2484  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  224 .. 898  =  675 bp
ORF:  224 amino acids  =  24.1 kDa
ORF:  474 .. 755  =  282 bp
ORF:  93 amino acids  =  10.8 kDa
ORF:  2088 .. 2948  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
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