Killing that DNA

  1.  You’ve done the hard work – you’ve got good quality RNA.  You’ve seen ribosomal bands on a gel (or *cough* Fragment Analyzer).  A good RQN/RIN (if that’s what you go by) and everything’s great.
  2. Now to get rid of the DNA
  3. Quick check (perform a PCR directly on appropriate amount of RNA) and often there’s still some DNA
  4. Another DNase 1 step … another check and …… go to step 2
  5. Yep, why are the “easiest” steps sometimes the most time consuming?

So let’s look at the process – onen nearly always requiring DNase 1 enzyme.  Yes, there are various kits that promise solutions that will selectively remove DNA but you’re probably going to find a DNase 1 digest is required at the end anyway.  The solution-based digests usually seem to work more efficiently than the on-column digests (column fibres protecting DNA from digestion).

I became interested in DNase 1 action due to a common tech question in a former life …. the DNase 1 enzyme we sold had no buffer – it was just the enzyme.  And thus a lot of questions came on ‘how do we use it?’ A number of interesting papers have been published over the years on the best buffers, temperatures and ways to kill DNase 1.  Some of them from my files include:

  • BioTechniques 20:1012-1020 (June 1996) – compared inactivation temperatures for DNase 1 and showed 75-85°C was optimal.  However no stop buffer was used in this work.
  • BioTechniques 22:1128-1132 (June 1997) – using a reaction buffer containing Mn rather than Mg in order to get blunt cut, non-overlapping fragments … as well as boost the activity of DNase 1.
  • BioTechniques 29:38-42 (July 2000) – further work on DNase 1 inactivation by use of Dtt and/or buffers of a non-neutral pH
  • BoiTechniques 29:252-256 (August 2000) – preventing metal-induced hydrolysis of RNA by first using a stop buffer to chelate metal co-factor ions prior to the heat-kill step.  Indicated that heat-killing without a stop buffer (even at the 75°C above) was detrimental to the RNA

Many commercial systems (including the Quanta one) use this last method to stop buffer plus heat-allowing the DNase-treated RNA to be used directly in the cDNA synthesis step without any further purification.  The Quanta system has been released in order to provide seamless matching of ion co-factors in the DNase 1 step with the concentrations in the cDNA supermix or XLT cDNA supermix.

So, given the required co-factors for DNase 1 activity (and subsequent inactivation), it can be worth using an appropriate buffer for RNA storage ie using low EDTA buffers chelation of ions required for DNase 1 activity.

If you have any modified protocols or procedures for DNase digestions, we’d look forward to hearing from you.



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