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Home | Molecular Biology | Restriction & Modifying Enzymes | Restriction Enzymes | Conventional

PdiI (NaeI)

5'...G C C↓G G C...3'
3'...C G G↑C C G...5'
Available as a FastDigest enzyme for rapid DNA digestion

FastDigest enzyme available Tango buffer for 100% activity Optimal incubation at 37°C Cleavage blocked or impaired by CpG methylation Thermal inactivation at 65°C in 20 min Genome qualified Recombinant enzyme LO certified

The PdiI (NaeI) restriction enzyme recognizes GCC^GGC sites and cuts best at 37°C in Tango buffer (Isoschizomers: MroNI, NaeI, NgoMIV)
  
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pBR322 DNA digested with PdiI (NaeI)

pBR322 DNA digested with PdiI (NaeI), 0.7% agarose, 4 cleavage sites

Thermo Scientific conventional restriction endonucleases are a large collection of high quality restriction enzymes, optimized to work in one of the buffers of the Five Buffer System. In addition, the universal Tango buffer is provided for convenience in double digestions. All of the enzymes exhibit 100% activity in the recommended buffer and reaction conditions. To ensure consistent performance, Thermo Scientific restriction enzyme reaction buffers contain premixed BSA, which enhances the stability of many enzymes and binds contaminants that may be present in DNA preparations.

Highlights

  • Superior quality – stringent quality control and industry leading manufacturing process
  • Convenient color-coded Five Buffer System
  • Includes universal Tango buffer for double-digestions
  • BSA premixed in reaction buffers
  • Wide selection of restriction endonuclease specificities

Applications

  • Molecular cloning
  • Restriction site mapping
  • Genotyping
  • Southern Blot
  • Restriction fragment length polymorphism (RFLP)
  • SNP

Note

For methylation sensitivity refer to product specifications.

  
Storage Condition-20 C
HazardousNo
Conditions for 100% Activity
  • 1X Buffer Tango: 33 mM Tris-acetate (pH 7.9 at 37°C), 10 mM Mg-acetate, 66 mM K-acetate, and 0.1 mg/mL BSA
  • Incubate at 37°C
Digestion of Agarose-embedded DNAMinimum 20 units of the enzyme are required for complete digestion of 1 µg of agarose-embedded pBR322 DNA in 16 hours.
Double DigestionPerform double digestion using DoubleDigest.
IsoschizomersSearch for commercial isoschizomers using REsearch.
NoteCertain sites in pBR322 are difficult to cleave with PdiI, the same as with its prototype NaeI. Assayed using pBR322 DNA (#SD0041).
Storage BufferPdiI is supplied in: 10 mM Tris-HCl (pH 7.5 at 25°C), 500 mM KCl, 1 mM DTT, 0.1 mM EDTA, 0.2 mg/mL BSA, 0.15% Triton X-100, and 50% (v/v) glycerol.

Reaction conditions

Recommended buffer for 100% activity Optimal temperature Enzyme activity in Thermo Scientific buffers, % Tango buffer for double digestion
B (blue)
1X		 G (green)
1X		 O (orange)
1X		 R (red)
1X		 Tango
(yellow)
1X / 2X
Tango 37°C 50-100 20-50 0-20 0-20 100 50-100 1X or 2X

Methylation Effects

Methylation type Sequence Cleavage effect
CpGGCCGGC Blocked

Cleavage efficiency close to the termini of PCR fragments

bp from the recognition site to fragment end
1 2 3 4 5
0-20 50-100

Number of recognition sites in DNA molecules

Lambda ΦX174 M13mp18/19 pBR322 puc18/19 pUC57
1 0 1 4 0 0
pTZ19R/U pTZ57R pBluescriptIIKS(±) pBluescriptIISK(±) pACYC177 pACYC184
1 1 1 1 0 5

New sites generated by ligation

Newly generated recognition sites resulting from ligation of blunt DNA ends

Recognition sequence Second restriction enzyme Restriction enzymes cleaving the newly generated recognition sequence
GCC^GGC
  • DpnI/FastDigest DpnI (GA^TC)
  • Ecl136II (EcoICRI)/FastDigest Ecl136II (GAG^CTC)
  • MbiI (BsrBI)/FastDigest BsrBI (MbiI)* (CCG^CTC)
  • MnlI/FastDigest MnlI
  • Eco32I (EcoRV)/FastDigest EcoRV (Eco32I) (GAT^ATC)
  • BccI
  • Eco47III (AfeI)/FastDigest AfeI (Eco47III) (AGC^GCT)
  • EheI (SfoI)/FastDigest EheI (GGC^GCC)
  • FspAI/FastDigest FspAI* (RTGC^GCAC)
  • FspAI/FastDigest FspAI* (RTGC^GCAT)
  • NsbI (FspI)/FastDigest FspI (NsbI) (TGC^GCA)
  • SatI (Fnu4HI)/FastDigest Fnu4HI (SatI)
  • SsiI (AciI)/FastDigest AciI (SsiI)
  • TauI/FastDigest TauI
  • MbiI (BsrBI)/FastDigest BsrBI (MbiI)* (GAG^CGG)
  • MspA1I* (CMG^CGG)
  • SmaI/FastDigest SmaI (CCC^GGG)
  • SrfI (GCCC^GGGC)
  • BcnI (NciI)/FastDigest NciI (BcnI)
  • Bme1390I (ScrFI)/FastDigest ScrFI (Bme1390I)
  • BssKI
  • HpaII/FastDigest HpaII
  • MspI (HpaII)/FastDigest MspI