Buffer B (10X) - FAQs

For optimal results with fast reaction and 100% buffer compatibility, we highly recommend using FastDigest restriction enzymes in double digestion. In certain cases however, it may be possible to perform double digestion using a mix of Thermo Scientific conventional and Fastdigest restriction enzymes. For specific recommendations, please contact our technical service with detailed information about the enzymes and DNA template you plan to use.

We recommend only 2 µl 10X Buffer in digestion of unpurified PCR products in 30 ul since salts and ions from the PCR reaction would be carried over to the digestion reaction.

Find additional tips, troubleshooting help, and resources within our Restriction Enzyme Cloning Support Center.

Star activty may be contributed by:

• Prolonged incubation
• High enzyme concentration
• High glycerol concentration (usually 5% or higher)
• Small reaction volume

Find additional tips, troubleshooting help, and resources within our Restriction Enzyme Cloning Support Center.

Unexpected cleavage patterns may be caused by the following reasons:

• Star activity of the restriction enzyme: Make sure to follow the reaction recommendations as specified in the protocol. Star activity may be improved by changing several key factors such as decreasing the reaction time, increasing the reaction volume, and decreasing the enzyme amount.

• Partial or incomplete cleavage (incomplete restriction reaction): Efficiency of the enzyme can be improved by adding more enzyme, prolonging the reaction time, or purifying DNA samples to remove inhibitory contaminants.

• Contamination with non-specific endonucleases: Non-specific endonucleases may be introduced to the DNA sample and/or the enzyme from improper handling, pipetting, etc.

•Improper reaction setup: Mix the digestion reaction thoroughly.

Find additional tips, troubleshooting help, and resources within ourRestriction Enzyme Cloning Support Center.

The main reason for DNA cleavage reaction failure is the presence of contaminating inhibitors in the template DNA (for example: phenol, chloroform, detergents, ethanol, excess salts, EDTA, etc.). The best way to troubleshoot is to perform control reactions:

1) negative control (experimental DNA in the reaction buffer without the restriction enzyme) to access degradation of DNA by contaminants in the DNA template and/or reaction buffer
2) positive control reaction I (digestion of highly pure control DNA with the restriction enzyme) to access reaction conditions and enzyme activity
3) positive control reaction II (highly pure control DNA + experimental DNA + Restriction Enzyme) to access possible issues with the experimental DNA.

In addition, please check for sensitivity of the restriction enzymes to template DNA methylation.

Find additional tips, troubleshooting help, and resources within our Restriction Enzyme Cloning Support Center.

The optimal range of DNA concentration is 0.02-0.1 µg/µL in the restriction digestion mixture. We would recommend the volume of the DNA sample not to exceed 30% of the total reaction volume to avoid potential reaction inhibition. To resolve inhibition from impurities of the DNA solution, we recommend increasing the overall volume of the reaction while keeping the volume of the DNA solution the same.

Find additional tips, troubleshooting help, and resources within ourRestriction Enzyme Cloning Support Center.

To remove the enzymes without using phenol/chloroform, we would recommend silica column based purification such as GeneJET Gel Extraction and DNA Cleanup Micro Kit (Cat. Nos. K0831/2) or GeneJET PCR Purification Kit (Cat. Nos. K0701/2).

Find additional tips, troubleshooting help, and resources within our Restriction Enzyme Cloning Support Center.

Enzymes may freeze during shipment on dry ice. This does not affect their quality as all Thermo Scientific enzymes are tested 100% active after at least three freeze-thaw cycles. For 24-48 hour delivery, enzymes may be shipped on blue ice because their quality is not affected by short exposure to 4 degrees C.

Thermo Scientific restriction enzymes are shipped with their optimal digestion buffer(s). The buffers are available separately for purchase as well.

First, please note that we changed our restriction enzymes and buffer formulations in 2010. The REact buffers 1-10 were discontinued in favor of a smaller group of universal buffers: B, G, O, R and Tango (Y). The new buffers are not compatible with older restriction enzymes, and it is not recommended to do a double digest with an old enzyme (with REact buffer) and a new enzyme.

When performing any double digest, there may be buffer incompatibilities and enzyme steric hindrance problems. These can be avoided by performing sequential digests, separated by buffer exchange or chloroform extraction and ethanol precipitation. However, if these issues are understood and a double digest will be performed, you can evaluate enzyme combinations using our buffer compatibility chart: https://www.thermofisher.com/us/en/home/brands/thermo-scientific/molecular-biology/thermo-scientific-restriction-modifying-enzymes/restriction-enzymes-thermo-scientific/conventional-restriction-enzymes-thermo-scientific/reaction-conditions-for-restriction-enzymes.html.