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Fast restriction digests?

Posted in: DNA / RNA Manipulation and Analysis

Content sponsored by New England Biolabs

restriction-digest-microwave.jpgIn the old days, restriction digests were a great excuse for long lunch breaks. Come back 1-2 hours later and it’s done.

But, just to ruin our fun, Fermentas then NEB started to offer ranges of restriction enzymes that do their job in 5 minutes. Nothing changed with these enzymes – someone just figured out that 60-120 minutes was just a number selected at random, probably by someone who wanted a longer lunch break.

But what about this?

After a hint by a friend, I started putting my digests into the microwave oven now for 10 seconds at maximum power (700 Watts) – and it turns out that this is all that is needed for a full digest!

I’ve no idea why this works, but the idea doesn’t seem to be that new.

The only explanation I found is that the microwaves make the molecules faster, increasing the probability that the enzymes find their sites on the DNA but that sounds a bit hand-waving to me. Heat makes molecules move faster, so the microwaves aren’t doing anything special. Are they?

How do you think this works? Or, have tried this method out? I’m looking forward to your comments.

Photo: Aim and Shoot

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  1. didier on August 8, 2019 at 10:38 am

    know this stuff…whta about just adding the RE and walking to the microwave .;it take probably few seconds …at that time simply add sample buffer and run the gel…being old..I am one of those who used to run limited digestion of DNA (this was require before the PCR breakthrought to avoid cutting at internal site within a cDNA!..a real pain in the A..)….even upon dilution of the RE , the cuts were nearly immediate…so my bet is that microwave has nothingto do with the cuts….????

  2. Grace on July 14, 2018 at 6:43 pm

    To clarify Becca’s answer (several years later haha): microwaves transfer energy to the stuff they are heating largely by “flipping” water molecules. This increases the kinetic energy of all of the molecules present in your food/restriction digestion reaction/etc., which directly correlates to an increase in temperature. But the main effect on restriction digest performance is that the molecules present are moving around faster (because of increased kinetic energy/temperature), resulting in an increase in collisions between DNA molecules and restriction enzymes, and increased rate of cleavage of the corresponding restriction sites.

  3. Becca on March 22, 2016 at 5:37 pm

    But microwaves don’t make molecules move faster like other forms of heating. They work by switching the orientation of the water molecules and of any dipole molecule. Would that additional strain make it easier for the enzyme to cut the DNA? Like how it’s easier to cut apart fabric if it’s taut? Someone should write a paper on this.

    • Roni on November 5, 2016 at 3:44 pm

      I like the idea you propose and how you elucidate it with a simple example.

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