Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
- - - - -

Can restriction enzymes cleave RNA?


  • Please log in to reply
1 reply to this topic

#1 CDB



  • Members
  • Pip
  • 1 posts

Posted 11 May 2015 - 10:05 PM

Hello! I am new here, so please forgive any "newbie" mistakes in this post. Recently I have been researching quite a bit on the subject of molecular biology because of a project that I am doing. However, I have a few questions that, so far, I have been unable to answer.


Before I begin, allow me to give some background on this question. Some restriction enzymes (specifically HaeIII) have been observed to recognize RNA and DNA heteroduplexes (RNA as one chain and DNA as the other), cleaving and cutting both the RNA and the DNA sides at the recognition sequences. This enzyme has also been known to cleave single-stranded DNA.


Since the recognition sequence of HaeIII is GGCC and would not be affected by the Thymine-to-Uracil transition in the DNA to RNA process, is it possible for this enzyme to recognize and cut duplex RNA or single-stranded RNA? Has this ever been observed? If this is not possible, what would prevent this cleavage? Perhaps it could be some sort of structural difference in DNA and RNA, such as the presence (RNA) and absence (DNA) of a 2'-hydroxyl group adjacent to the scissile phosphodiester linkage? What would this change? Is there any way at all to reverse these effects (if present) so that this cleavage, if previously impossible (or, rather, improbable), would somehow occur with ease?


Thank you very much for your help,




#2 perneseblue


    Unlimited ligation works!

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 585 posts

Posted 14 May 2015 - 06:01 AM

Well,  the best I can find is this paper 



Here, they describe RE that will cleave DNA:RNA hetroduplexes, with a few examples of RE that preferentially cleaves the RNA strand of the duplex. (HinfI and HaeIII). However the efficiency of most RE to cleave DNA:RNA duplexes is 2 orders of a magnitude lower than cleavage of DNA:DNA duplexes. The exception being AvaII that cleaves DNA:DNA and RNA:DNA duplexes more or less at equivalent rates when the central base pair is rA:dT.


PNAzyme based RNA cleavage is also possible.


May your PCR products be long, your protocols short and your boss on holiday

Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.