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Cfr9I (XmaI)

5'...C↓C C G G G...3'
3'...G G G C C↑C...5'

Unique 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 Cfr9I (XmaI) restriction enzyme recognizes C^CCGGG sites and cuts best at 37°C in its own unique buffer (Isoschizomers: TspMI, XmaCI, XmaI)
  
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Lambda DNA digested with Cfr9I (XmaI)

Lambda DNA digested with Cfr9I (XmaI), 0.7% agarose, 3 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

To achieve complete digestion of substrate with Cfr9I, the concentration of DNA should be no less than 50 µg/mL in the reaction buffer.

For methylation sensitivity refer to product specifications.

  
Storage Condition-20 C
HazardousNo
Compatible EndsBshTI, BsaWI, Cfr10I, Eco88I, Kpn2I, NgoMIV, SgrAI.
Conditions for 100% Activity
  • 1X Buffer Cfr9I: 10 mM Tris-HCl (pH 7.2 at 37°C), 5 mM MgCl2, 200 mM sodium glutamate, and 0.1 mg/mL BSA
  • Incubate at 37°C
Digestion of Agarose-embedded DNAMinimum 5 units of the enzyme are required for complete digestion of 1 µg of agarose-embedded lambda DNA in 16 hours.
Double DigestionPerform double digestion using DoubleDigest.
IsoschizomersSearch for commercial isoschizomers using REsearch.
Storage BufferCfr9I is supplied in: 10 mM Tris-HCl (pH 7.5 at 25°C), 250 mM KCl, 1 mM DTT, 0.1 mM EDTA, 0.2 mg/mL BSA, 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
Crf9I Buffer [Unique] 37°C 0-20 0-20 0-20 0-20 20-50 0-20 1X

Methylation Effects

Methylation type Sequence Cleavage effect
CpGCCCGGG Impaired

Cleavage efficiency close to the termini of PCR fragments

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

Number of recognition sites in DNA molecules

Lambda ΦX174 M13mp18/19 pBR322 puc18/19 pUC57
3 0 1 0 1 1
pTZ19R/U pTZ57R pBluescriptIIKS(±) pBluescriptIISK(±) pACYC177 pACYC184
1 1 1 1 1 0

New sites generated by ligation

Newly generated recognition sites resulting from ligation of protruding compatible DNA ends

Recognition Sequence Second Enzyme Enzymes recognizing newly generated recognition sequence
C^CCGGG
  • BsaWI* (W^CCGGA)
  • BsaWI* (W^CCGGT)
  • BshTI (AgeI)/FastDigest AgeI (BshTI) (A^CCGGT)
  • Cfr10I (BsrFI)/FastDigest BsrFI (Cfr10I)* (R^CCGGC)
  • Cfr10I (BsrFI)/FastDigest BsrFI (Cfr10I)* (R^CCGGT)
  • Kpn2I (BspEI)/FastDigest Kpn2I (T^CCGGA)
  • MreI (Sse232I)/FastDigest MreI (CG^CCGGCG)
  • NgoMIV (G^CCGGC)
  • SgrAI* (CR^CCGGCG)
  • SgrAI* (CR^CCGGTG)
  • BcnI (NciI)/FastDigest NciI (BcnI)
  • Bme1390I (ScrFI)/FastDigest ScrFI (Bme1390I)
  • BssKI
  • HpaII/FastDigest HpaII
  • MspI (HpaII)/FastDigest MspI
  • Eco88I (AvaI)/FastDigest AvaI (Eco88I)* (C^CCGGG)
  • BcnI (NciI)/FastDigest NciI (BcnI)
  • Bme1390I (ScrFI)/FastDigest ScrFI (Bme1390I)
  • BmeT110I
  • BseDI (BsaJI)/FastDigest BsaJI (BseDI)
  • BssKI
  • Cfr9I (XmaI)
  • Eco88I (AvaI)/FastDigest AvaI (Eco88I)
  • HpaII/FastDigest HpaII
  • MspI (HpaII)/FastDigest MspI
  • SmaI/FastDigest SmaI

Newly generated recognition sites resulting from fill-in of 5'-overhang and self-ligation

Recognition Sequence Newly generated sequence after reaction Enzymes that cleave the newly generated sequence
C^CCGGGCCCGGCCGGG
  • [BcnI (NciI)/FastDigest NciI (BcnI)]
  • [Bme1390I (ScrFI)/FastDigest ScrFI (Bme1390I)]
  • Bsh1285I (BsiEI)/FastDigest BsiEI (Bsh1285I)
  • [BssKI]
  • BsuRI (HaeIII)/FastDigest HaeIII (BsuRI)
  • EaeI
  • CviJI
  • Eco52I (EagI)/FastDigest EagI (Eco52I)
  • [HpaII/FastDigest HpaII]
  • [MspI (HpaII)/FastDigest MspI]