RNA repair

RNA repair restores damaged RNA chemistry or chain continuity. For a strand break, repair can require preparing compatible termini and then using an RNA ligase to form a new phosphodiester bond. The chemical state of an end is therefore part of the substrate: an RNA cyclic phosphate end and a free $3^{\prime }$ hydroxyl group need not enter the same joining pathway.^[ref]

In 2011, purified Escherichia coli RtcB joined a broken transfer RNA-like stem-loop with cyclic-phosphate and $5^{\prime }$ hydroxyl termini. Radioactive labelling and denaturing polyacrylamide gel electrophoresis distinguished starting fragments from joined product.^[ref] This established biochemical joining activity and motivated a cellular repair hypothesis. The assay alone did not establish every physiological substrate or prove recovery of all biological functions.

For a chain-inventory example, cut an eight-nucleotide RNA into fragments containing three and five nucleotides. Correctly reconnecting their original ends restores eight units in one chain. If one nucleotide has instead been lost, joining the remaining pieces produces seven units; ligation alone does not recreate missing sequence information. Product length, junction chemistry, nucleotide sequence and biological activity consequently provide different tests of what has been restored.