= RNA repair
{c}
<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 $3'$ <hydroxyl group> need not enter the same joining pathway.<GTP-dependent RtcB RNA splicing by Anupam K. Chakravarty and Stewart Shuman>[Abstract and Figure1, end processing and sealing chemistry]{ref}
In 2011, purified <Escherichia coli> <RtcB> joined a broken <transfer RNA>-like <stem-loop> with cyclic-phosphate and $5'$ hydroxyl termini. Radioactive labelling and <denaturing polyacrylamide gel electrophoresis> distinguished starting fragments from joined product.<RtcB is the RNA ligase component of an Escherichia coli RNA repair operon by Naoko Tanaka and Stewart Shuman>[Abstract and Figure1, model substrate and product analysis]{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.
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