Can restriction enzymes cleave RNA? (View forum version)


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,





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.