Plasmid Files

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HindIII  (28) 1 site

NdeI  (3661) 1 site

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

MscI  (3474) 1 site

* Blocked by Dcm methylation.

BseRI  (3353) 1 site

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.

SalI  (3108) 1 site

NaeI  (2909) 1 site

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

NgoMIV  (2907) 1 site

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

DraIII  (2806) 1 site

Sticky ends from different DraIII sites may not be compatible.

XmnI  (2263) 1 site

BamHI  (79) 1 site

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

BspDI  (87) 1 site

ClaI  (87) 1 site

BstBI  (92) 1 site

EcoRI  (94) 1 site

StuI  (103) 1 site

AvaI  (107) 1 site

Sticky ends from different AvaI sites may not be compatible.

BsoBI  (107) 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.

PaeR7I  (107) 1 site

PaeR7I does not recognize the sequence CTCTCGAG.

XhoI  (107) 1 site

BmeT110I  (108) 1 site

XbaI  (115) 1 site

SnaBI  (140) 1 site

HpaI  (278) 1 site

MfeI  (287) 1 site

EagI  (346) 1 site

NotI  (346) 1 site

BtgI  (349) 1 site

Sticky ends from different BtgI sites may not be compatible.

SacII  (352) 1 site

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

BstXI  (364) 1 site

Sticky ends from different BstXI sites may not be compatible.

NsiI  (364) 1 site

PspOMI  (367) 1 site

ApaI  (371) 1 site

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

Acc65I  (373) 1 site

KpnI  (377) 1 site

BssHII  (410) 1 site

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

PvuII  (595) 1 site

BspQI  (655) 1 site

Sticky ends from different BspQI sites may not be compatible.

SapI  (655) 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.

AflIII  (771) 1 site

Sticky ends from different AflIII sites may not be compatible.

PciI  (771) 1 site

PciI is inhibited by nonionic detergents.

NspI  (775) 1 site

AlwNI  (1187) 1 site

Sticky ends from different AlwNI sites may not be compatible.

AhdI  (1664) 1 site

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

BpmI  (1734) 1 site

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.

NmeAIII  (1812) 1 site

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).

CMV IE94 promoter 3111 .. 4095  =  985 bp enhancer/promoter region of simian cytomegalovirus major immediate early transcription unit IE94

CMV IE94 promoter 3111 .. 4095  =  985 bp enhancer/promoter region of simian cytomegalovirus major immediate early transcription unit IE94

AmpR 1591 .. 2451  =  861 bp 286 amino acids  =  31.6 kDa    Segment 2:      1591 .. 2382  =  792 bp    263 amino acids  =  28.9 kDa Product: β-lactamase confers resistance to ampicillin, carbenicillin, and related antibiotics

AmpR 1591 .. 2451  =  861 bp 286 amino acids  =  31.6 kDa    Segment 1:  signal sequence      2383 .. 2451  =  69 bp    23 amino acids  =  2.6 kDa Product: β-lactamase confers resistance to ampicillin, carbenicillin, and related antibiotics

AmpR 1591 .. 2451  =  861 bp 286 amino acids  =  31.6 kDa 2 segments Product: β-lactamase confers resistance to ampicillin, carbenicillin, and related antibiotics

ori 832 .. 1420  =  589 bp high-copy-number ColE1/pMB1/pBR322/pUC origin of replication

ori 832 .. 1420  =  589 bp high-copy-number ColE1/pMB1/pBR322/pUC origin of replication

f1 ori 2582 .. 3037  =  456 bp f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis

f1 ori 2582 .. 3037  =  456 bp f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis

SV40 poly(A) signal 144 .. 278  =  135 bp SV40 polyadenylation signal

SV40 poly(A) signal 144 .. 278  =  135 bp SV40 polyadenylation signal

AmpR promoter 2452 .. 2556  =  105 bp

AmpR promoter 2452 .. 2556  =  105 bp

lac promoter 478 .. 508  =  31 bp    Segment 3:  -10      478 .. 484  =  7 bp promoter for the E. coli lac operon

lac promoter 478 .. 508  =  31 bp    Segment 2:      485 .. 502  =  18 bp promoter for the E. coli lac operon

lac promoter 478 .. 508  =  31 bp    Segment 1:  -35      503 .. 508  =  6 bp promoter for the E. coli lac operon

lac promoter 478 .. 508  =  31 bp 3 segments promoter for the E. coli lac operon

SP6 promoter 35 .. 53  =  19 bp promoter for bacteriophage SP6 RNA polymerase

SP6 promoter 35 .. 53  =  19 bp promoter for bacteriophage SP6 RNA polymerase

T3 promoter 391 .. 409  =  19 bp promoter for bacteriophage T3 RNA polymerase

T3 promoter 391 .. 409  =  19 bp promoter for bacteriophage T3 RNA polymerase

M13 rev 430 .. 446  =  17 bp common sequencing primer, one of multiple similar variants

M13 rev 430 .. 446  =  17 bp common sequencing primer, one of multiple similar variants

lac operator 454 .. 470  =  17 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 454 .. 470  =  17 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).

stop codons 117 .. 144  =  28 bp stop codons in all three reading frames

stop codons 117 .. 144  =  28 bp stop codons in all three reading frames

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