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Plasmid Files

pDD

Vector encoding the 12 kDa destabilization domain (DD), a mutant of FKBP12.

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pDD Sequence and MappDD.dna
Map and Sequence File   
Sequence Author:  Clontech
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 SacII (3026) BtgI (3023) KpnI (3022) Acc65I (3018) BanII - SacI (3016) Eco53kI (3014) ApoI - EcoRI (3006) PluTI (2849) SfoI (2847) NarI (2846) KasI (2845) BstAPI (2795) NdeI (2794) PfoI (2656) EcoO109I (2599) AatII (2545) ZraI (2543) SspI (2427) XmnI (2222) ScaI (2103) TsoI (2022) NmeAIII (1771) BsrFI (1703) BsaI (1684) AhdI (1623) AarI - BfuAI - BspMI (0) BsgI (28) AvaI - BsoBI - TspMI - XmaI (119) BmeT110I (120) SmaI (121) BbsI (288) PflMI (337) BamHI (341) XbaI (347) PstI (363) SphI (369) HindIII (371) BspQI - SapI (614) AflIII - PciI (730) AlwNI (1146) pDD 3040 bp
SacII  (3026)
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.
BtgI  (3023)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
KpnI  (3022)
1 site
G G T A C C C C A T G G
Acc65I  (3018)
1 site
G G T A C C C C A T G G
BanII  (3016)
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  (3016)
1 site
G A G C T C C T C G A G
Eco53kI  (3014)
1 site
G A G C T C C T C G A G
ApoI  (3006)
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  (3006)
1 site
G A A T T C C T T A A G
PluTI  (2849)
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  (2847)
1 site
G G C G C C C C G C G G
NarI  (2846)
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  (2845)
1 site
G G C G C C C C G C G G
BstAPI  (2795)
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.
NdeI  (2794)
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  (2656)
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  (2599)
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  (2545)
1 site
G A C G T C C T G C A G
ZraI  (2543)
1 site
G A C G T C C T G C A G
SspI  (2427)
1 site
A A T A T T T T A T A A
XmnI  (2222)
1 site
G A A N N N N T T C C T T N N N N A A G
ScaI  (2103)
1 site
A G T A C T T C A T G A
TsoI  (2022)
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).
NmeAIII  (1771)
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).
BsrFI  (1703)
1 site
R C C G G Y Y G G C C R

Efficient cleavage requires at least two copies of the BsrFI
recognition sequence.
After cleavage, BsrFI can remain bound to DNA and alter its
electrophoretic mobility.
BsaI  (1684)
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.
AhdI  (1623)
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.
AarI  (0)
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 AarI
recognition sequence.
Sticky ends from different AarI sites may not be compatible.
After cleavage, AarI can remain bound to DNA and alter its
electrophoretic mobility.
BfuAI  (0)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BfuAI
recognition sequence.
Sticky ends from different BfuAI sites may not be compatible.
BfuAI is typically used at 50°C, but is 50% active at 37°C.
BspMI  (0)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BspMI
recognition sequence.
Sticky ends from different BspMI sites may not be compatible.
BsgI  (28)
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).
AvaI  (119)
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  (119)
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  (119)
1 site
C C C G G G G G G C C C
XmaI  (119)
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.
BmeT110I  (120)
1 site
C Y C G R G G R G C Y C
SmaI  (121)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
BbsI  (288)
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.
PflMI  (337)
1 site
C C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
BamHI  (341)
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.
XbaI  (347)
1 site
T C T A G A A G A T C T
PstI  (363)
1 site
C T G C A G G A C G T C
SphI  (369)
1 site
G C A T G C C G T A C G
HindIII  (371)
1 site
A A G C T T T T C G A A
BspQI  (614)
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  (614)
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  (730)
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  (730)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AlwNI  (1146)
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.
AmpR
1550 .. 2410  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   1550 .. 2341  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1550 .. 2410  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   2342 .. 2410  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1550 .. 2410  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
791 .. 1379  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
791 .. 1379  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
DD
1 .. 324  =  324 bp
108 amino acids  =  11.9 kDa
   Segment 1:  
   1 .. 3  =  3 bp
   1 amino acid  =  149.2 Da
Product: destabilization domain that can be
stabilized by Shield1 in the ProteoTuner™ system
L106P mutant of FKBP12
DD
1 .. 324  =  324 bp
108 amino acids  =  11.9 kDa
   Segment 2:  
   4 .. 324  =  321 bp
   107 amino acids  =  11.8 kDa
Product: destabilization domain that can be
stabilized by Shield1 in the ProteoTuner™ system
L106P mutant of FKBP12
DD
1 .. 324  =  324 bp
108 amino acids  =  11.9 kDa
2 segments
Product: destabilization domain that can be
stabilized by Shield1 in the ProteoTuner™ system
L106P mutant of FKBP12
AmpR promoter
2411 .. 2515  =  105 bp
AmpR promoter
2411 .. 2515  =  105 bp
M13 rev
389 .. 405  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
389 .. 405  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
2989 .. 3005  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
2989 .. 3005  =  17 bp
common sequencing primer, one of multiple similar
variants
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