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Conventional Restriction Enzymes

BdaI

Product information

Reaction conditions

Recommended buffer for 100% activity	Optimal tempThermo Scientificure	Enzyme activity in Thermo Scieitnfic buffers, %						Tango™ buffer for double digestion
		B (blue) 1X	G (green) 1X	O (orange) 1X	R (red) 1X	Tango™ (yellow) 1X / 2X
G +SAM	30°C	NR (+SAM)	100 (+SAM)	0-20 (+SAM)	20-50 (+SAM)	50-100* (+SAM)	50-100 (+SAM)	1X*

* – star activity appears at a greater than 5-fold overdigestion (5 units x 1 hour).

Lambda DNA
0.7% agarose
28 cleavage sites

Conditions for 100% Activity

[1X Buffer G] + SAM:
[10 mM Tris-HCl (pH 7.5 at 37°C), 10 mM MgCl₂, 50 mM NaCl and 0.1 mg/ml BSA] + 0.05 mM S-adenosylmethionine.
Incubate at 30°C.

Storage Buffer

BdaI is supplied in:
10 mM potassium phosphate (pH 7.4 at 25°C), 100 mM NaCl, 1 mM EDTA, 7 mM 2-mercaptoethanol, 0.2 mg/ml BSA and 50% (v/v) glycerol.

Ligation and Recleavage

After 10-fold overdigestion with BdaI, more than 70% of the DNA fragments can be ligated, but none of these can be recut due to the methylation of the recognition sequence by this enzyme.

Note

• BdaI may remain associated with the cleaved DNA. This may cause DNA band shifting during electrophoresis. To avoid atypical DNA band patterns, use the 6X DNA Loading Dye & SDS Solution for sample preparation or heat the digested DNA in the presence of SDS prior to electrophoresis.
• Assayed using lambda DNA (dam-) (#SD0021).
• BdaI is blocked by overlapping dam methylation. To avoid dam methylation, use a dam-, dcm- strain such as GM2163.
• Incubation at 37°C results in 30% activity.
• Requires S-adenosylmethionine for activity. Complete cleavage of some substrates with BdaI is difficult to achieve.
• BdaI concentration is determined by the maximum cleavage level achieved when no change in the fragmentation pattern is observed with further enzyme increase.
• BdaI produces double-strand cuts on both sides of the interrupted recognition site. In certain sequence contexts, the cleavage position may be shifted by one base pair. However, the cleavage position indicated above will predominate.
• Greater than 40-fold overdigestion with BdaI may result in star activity.

Isoschizomers

Search for commercial isoschizomers using REsearch™.

Double Digestion

Perform double digestion using DoubleDigest™.

Methylation Effects

Dam: may overlap – blocked.
Dcm: never overlaps – no effect.
CpG: never overlaps – no effect.
EcoKI: never overlaps – no effect.
EcoBI: never overlaps – no effect.

Methylation type	Sequence	Cleavage effect
Dam (GATC)	5'...TGm6A TC(N)4TCA...3' 3'...AC Tm6AG(N)4AGT...5'	Blocked

Number of recognition sites in DNA molecules

Lambda	ΦX174	M13mp18/19	pBR322	puc18/19	pUC57
28	4	7	4	2	2
pTZ19R/U	pTZ57R	pBluescriptIIKS(-/+)	pBluescriptIISK(-/+)	pACYC177	pACYC184
2	2	2	2	3	6

Patents, Licenses, Trademarks

Protocols & recommendations

RECOMMENDATIONS FOR USE

ADDITIONAL PROTOCOLS

DNA Digestion

We recommend digesting 0.2-1.5 µg DNA with a 2-fold to 10-fold excess of enzyme in a total volume of 20 µl. A typical restriction enzyme digestion protocol is below.

1. Add the following reaction components in the order indicated:

   Water, nuclease-free	16-16.5 µl
   10X recommended buffer for restriction enzyme	2 µl
   Substrate DNA	1 µl (~1 µg)
   Restriction enzyme	0.5-1 µl (5-10 u)
   Total volume	20 µl

2. Mix gently and spin down briefly.
3. Incubate at the optimal reaction temperature for 1-16 hours.

Note

• The digestion reaction may be scaled either up or down.
• Some enzymes require additional components to obtain the stated activity. In these cases, add the required additive and adjust the volume of water appropriately.

Digestion of PCR Products

The most convenient option for digestion of PCR-amplified DNA is the addition of a restriction enzyme directly to the reaction tube after completion of PCR. The majority of Fermentas restriction enzymes are active in Fermentas PCR buffers.
However, digestion of PCR products in the amplification mixture is often inefficient. Therefore, PCR reaction mixture should not make more than 1/3 volume of digestion reaction mixture to avoid inhibitory effects.

1. Add the following reaction components in the order indicated:

   PCR reaction mixture	10 µl (~0.1-0.5 µg of DNA)
   Water, nuclease-free	16-17 µl
   10X recommended buffer for restriction enzyme	2 µl*
   Restriction enzyme	1-2 µl (10-20 u)
   Total volume	30 µl

   * Only 2 µl of 10X reaction buffer is required for unpurified PCR product in a 30 µl reaction volume.
2. Mix gently and spin down briefly.
3. Incubate at the optimal reaction temperature for 1-16 hours.

Note

• For cloning applications, purification of PCR products prior to digestion is necessary to remove the active thermophilic DNA polymerase present in the PCR mixture. DNA polymerases may alter the ends of the cleaved DNA and reduce the yield of ligation.
• If the restriction enzyme requires special additives (e.g., SAM), reduce the amount of water appropriately.
• If cleavage of the PCR product is inefficient purify the PCR products with the GeneJET™ PCR Purification Kit (#K0702) prior to digestion.
• After digestion, gel-purify the PCR product with the GeneJET™ Gel Extraction Kit (#K0692) or Silica Bead DNA Gel Extraction Kit (#K0513) to remove short DNA fragments which compete with the insert in a ligation reaction.

Double Digestion

DoubleDigest™ Engine
Our DoubleDigest™ engine is a great tool to find information on buffer and reaction conditions for your double digests. Simply select two restriction enzymes required for digestion, submit the query and follow the recommendations. The DoubleDigest™ engine is continuously updated with newly released Fermentas restriction enzymes.

Digestion of Agarose-embedded DNA

1. Embed the substrate DNA in 1% low melting temperature agarose, 1 µg / 30 µl.
2. Prepare ~30 µl agarose plugs with a GelSyringe® or similar agarose dispensing system.
3. Equilibrate the plug in 100 µl of the appropriate 1X restriction enzyme buffer for 15 min.
4. Place the plug in 100 µl of fresh 1X buffer containing the restriction enzyme (see Table "Digestion of Agarose-embedded DNA").
5. Incubate at 30-37°C for mesophilic enzymes or at 50-55°C for thermophilic enzymes for 4-16 hours.