What is RNA strand cleavage

RNA strand cleavage is a fundamental process that involves breaking the phosphodiester bonds in the sugar-phosphate backbone of an RNA molecule.  RNA strand cleavage consists of the cutting or hydrolysis of the RNA strand.

Strand cleavage directly involves the 2'-hydroxyl (2'-OH) group of the ribose sugar, undergoing intramolecular nucleophilic attack at the neighboring phosphate, breaking the 3'-5' phosphodiester bond. During this chemical reaction, an electron-rich nucleophile donates a pair of electrons to an electron-poor electrophile, forming a new bond. The nonenzymatic intramolecular transesterification of RNA is known as "in-line" cleavage.

Nucleophilic attack occurs spontaneously under nonenzymatic conditions, especially at elevated pH. Deprotonation of the 2'-hydroxyl group generates a highly reactive 2'-oxyanion or nuclease enzymes provide general acid/base catalysis and promote the required conformation changes for this attack. In the ribonuclease III (RNase III) family, Mg2+ is critical in the formation and stabilization of the catalytic site assembly. Two Mg2+ ions are required for the cleavage of each phosphodiester bond.

During RNA processing and maturation larger precursor RNA molecules are broken down into final, functional RNAs such as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Furthermore, gene regulation also involves cleaving and degrading of messenger RNA (mRNA) to control gene expression, for example, in RNA interference (RNAi). Decay and quality control eliminate damaged, unnecessary, or foreign RNA.

RNA cleavage is primarily carried out by specific enzymes or through a spontaneous chemical reaction involving Ribonucleases (RNases), enzymes that catalyze the cleavage of the RNA backbone. RNase H is a well-known example that specifically cleaves the RNA strand when it is paired with a DNA strand (an RNA-DNA hybrid), leaving the DNA intact. RNase III and related enzymes (like Dicer) cleave double-stranded RNA (dsRNA) in pathways like RNAi.

Ribozymes are RNA molecules that possess catalytic activity, act as enzymes to cleave other RNA molecules or even themselves, known as self-cleaving ribozymes). Examples include the hammerhead and hairpin ribozymes.

However, a regulatory function has been clearly shown for only the glmS ribozyme, which cleaves off the 5′-mRNA regions. This cleavage most likely results in mRNA degradation, downregulating the expression of the amidotransferase gene. 

RNA is naturally less stable than DNA because it has a hydroxyl (OH) group at the 2'-position of its ribose sugar. In basic or alkaline solution, the 2’-OH group can be deprotonated, making it a powerful nucleophile that can attack the adjacent phosphodiester bond, causing spontaneous cleavage. This process is called base-catalyzed hydrolysis or auto-hydrolysis.

References

Cedergren R., Lang B.F., Gravel D. A mechanism for the RNA-catalyzed formation of 5’-phosphates. The origin of nucleases. FEBS Lett. 1987; 226:63–66. [PubMed]

Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol. 2008 Jan;67(1):143-54. [PubMed]

Kierzek R. Nonenzymatic hydrolysis of oligoribonucleotides. Nucleic Acids Res. 1992 Oct 11;20(19):5079-84. [PMC]

Nicholson AW. Ribonuclease III mechanisms of double-stranded RNA cleavage. Wiley Interdiscip Rev RNA. 2014 Jan-Feb;5(1):31-48. [PMC]

Ribozyme Wiki

RNA Hydrolysis Wiki

Rosta E, Nowotny M, Yang W, Hummer G. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc. 2011 Jun 15;133(23):8934-41. [PMC]

Serganov A, Patel DJ. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet. 2007 Oct;8(10):776-90. [PMC]

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