Plasmid Files

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EcoRI  (5702) 1 site

BspDI  (5678) 1 site

ClaI  (5678) 1 site

HindIII  (5671) 1 site

BlpI  (5434) 1 site

Sticky ends from different BlpI sites may not be compatible.

SpeI  (5427) 1 site

BamHI  (5407) 1 site

After cleavage, BamHI-HF™ (but not the original BamHI) can remain bound to DNA and alter its electrophoretic mobility.

BmtI  (5390) 1 site

NheI  (5386) 1 site

NdeI  (5381) 1 site

Prolonged incubation with NdeI may lead to removal of additional nucleotides.

NcoI  (5315) 1 site

XbaI  (5276) 1 site

BglII  (5210) 1 site

SgrAI  (5169) 1 site

Efficient cleavage requires at least two copies of the SgrAI recognition sequence.

SphI  (5021) 1 site

EcoNI  (4956) 1 site

The 1-base overhangs produced by EcoNI may be hard to ligate. Sticky ends from different EcoNI sites may not be compatible.

MluI  (4488) 1 site

BclI  (4474) 1 site

* Blocked by Dam methylation. BclI is typically used at 50-55°C, but is 50% active at 37°C.

BstEII  (4306) 1 site

Sticky ends from different BstEII sites may not be compatible. BstEII is typically used at 60°C, but is 50% active at 37°C.

ApaI  (4285) 1 site

ApaI can be used between 25°C and 37°C.

PspOMI  (4281) 1 site

BssHII  (4077) 1 site

BssHII is typically used at 50°C, but is 75% active at 37°C.

HpaI  (3986) 1 site

PshAI  (3647) 1 site

PshAI quickly loses activity at 37°C, but can be used at 25°C for long incubations.

EagI  (3420) 1 site

NruI  (3389) 1 site

BfuAI  (3305) 1 site

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  (3305) 1 site

Efficient cleavage requires at least two copies of the BspMI recognition sequence. Sticky ends from different BspMI sites may not be compatible.

BsmI  (3006) 1 site

Sticky ends from different BsmI sites may not be compatible.

BmeT110I  (2935) 1 site

AvaI  (2934) 1 site

Sticky ends from different AvaI sites may not be compatible.

BsoBI  (2934) 1 site

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.

MscI  (2917) 1 site

* Blocked by Dcm methylation.

FspAI  (2907) 1 site

ZraI  (75) 1 site

AatII  (77) 1 site

SspI  (191) 1 site

ScaI  (515) 1 site

PvuI  (627) 1 site

PstI  (754) 1 site

BsaI  (930) 1 site

Sticky ends from different BsaI sites may not be compatible. BsaI can be used between 37°C and 50°C.

AhdI  (996) 1 site

The 1-base overhangs produced by AhdI may be hard to ligate. Sticky ends from different AhdI sites may not be compatible.

AlwNI  (1475) 1 site

Sticky ends from different AlwNI sites may not be compatible.

PciI  (1884) 1 site

PciI is inhibited by nonionic detergents.

BspQI  (2001) 1 site

Sticky ends from different BspQI sites may not be compatible.

SapI  (2001) 1 site

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.

AccI  (2116) 1 site

Efficient cleavage with AccI requires ≥13 bp on each side of the recognition sequence. Sticky ends from different AccI sites may not be compatible.

BstZ17I  (2117) 1 site

BsaAI  (2136) 1 site

PflFI  (2142) 1 site

The 1-base overhangs produced by PflFI may be hard to ligate. Sticky ends from different PflFI sites may not be compatible.

Tth111I  (2142) 1 site

The 1-base overhangs produced by Tth111I may be hard to ligate. Sticky ends from different Tth111I sites may not be compatible.

Bpu10I  (2779) 1 site

Efficient cleavage requires at least two copies of the Bpu10I recognition sequence. This recognition sequence is asymmetric, so ligating sticky ends generated by Bpu10I will not always regenerate a Bpu10I site. Sticky ends from different Bpu10I sites may not be compatible.

lacI 3761 .. 4843  =  1083 bp 360 amino acids  =  38.6 kDa Product: lac repressor 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).

lacI 3761 .. 4843  =  1083 bp 360 amino acids  =  38.6 kDa Product: lac repressor 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).

AmpR 209 .. 1069  =  861 bp 286 amino acids  =  31.5 kDa    Segment 1:  signal sequence      209 .. 277  =  69 bp    23 amino acids  =  2.6 kDa Product: β-lactamase confers resistance to ampicillin, carbenicillin, and related antibiotics

AmpR 209 .. 1069  =  861 bp 286 amino acids  =  31.5 kDa    Segment 2:      278 .. 1069  =  792 bp    263 amino acids  =  28.9 kDa Product: β-lactamase confers resistance to ampicillin, carbenicillin, and related antibiotics

AmpR 209 .. 1069  =  861 bp 286 amino acids  =  31.5 kDa 2 segments Product: β-lactamase confers resistance to ampicillin, carbenicillin, and related antibiotics

ori 1240 .. 1828  =  589 bp high-copy-number ColE1/pMB1/pBR322/pUC origin of replication

ori 1240 .. 1828  =  589 bp high-copy-number ColE1/pMB1/pBR322/pUC origin of replication

rop 2258 .. 2449  =  192 bp 63 amino acids  =  7.2 kDa Product: Rop protein, which maintains plasmids at low copy number

rop 2258 .. 2449  =  192 bp 63 amino acids  =  7.2 kDa Product: Rop protein, which maintains plasmids at low copy number

AmpR promoter 104 .. 208  =  105 bp

AmpR promoter 104 .. 208  =  105 bp

lacI promoter 4844 .. 4921  =  78 bp

lacI promoter 4844 .. 4921  =  78 bp

MCS 5380 .. 5439  =  60 bp multiple cloning site

MCS 5380 .. 5439  =  60 bp multiple cloning site

T7 terminator 5445 .. 5492  =  48 bp transcription terminator for bacteriophage T7 RNA polymerase

T7 terminator 5445 .. 5492  =  48 bp transcription terminator for bacteriophage T7 RNA polymerase

tet promoter 5667 .. 5695  =  29 bp    Segment 3:  -10      5667 .. 5672  =  6 bp E. coli promoter for tetracycline efflux protein gene

tet promoter 5667 .. 5695  =  29 bp    Segment 2:      5673 .. 5689  =  17 bp E. coli promoter for tetracycline efflux protein gene

tet promoter 5667 .. 5695  =  29 bp    Segment 1:  -35      5690 .. 5695  =  6 bp E. coli promoter for tetracycline efflux protein gene

tet promoter 5667 .. 5695  =  29 bp 3 segments E. coli promoter for tetracycline efflux protein gene

lac operator 5249 .. 5273  =  25 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 5249 .. 5273  =  25 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).

TEV Site 5359 .. 5379  =  21 bp 7 amino acids  =  870.0 Da Product: tobacco etch virus (TEV) protease recognition and cleavage site

TEV Site 5359 .. 5379  =  21 bp 7 amino acids  =  870.0 Da Product: tobacco etch virus (TEV) protease recognition and cleavage site

T7 promoter 5230 .. 5248  =  19 bp promoter for bacteriophage T7 RNA polymerase

T7 promoter 5230 .. 5248  =  19 bp promoter for bacteriophage T7 RNA polymerase

6xHis 5329 .. 5346  =  18 bp 6 amino acids  =  840.9 Da Product: 6xHis affinity tag

6xHis 5329 .. 5346  =  18 bp 6 amino acids  =  840.9 Da Product: 6xHis affinity tag

RBS 5304 .. 5309  =  6 bp ribosome binding site

RBS 5304 .. 5309  =  6 bp ribosome binding site

ATG 5317 .. 5319  =  3 bp 1 amino acid  =  149.2 Da Product: start codon

ATG 5317 .. 5319  =  3 bp 1 amino acid  =  149.2 Da Product: start codon

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