= RNA degradation
{c}
\b[RNA degradation] is the chemical or enzymatic breakdown of <RNA>, including cleavage of its <phosphodiester bonds> into shorter strands. Fragmentation can remove the continuity needed for an <RNA> molecule's function even while much of its <nucleotide sequence> remains present. <Ribonucleases> catalyze RNA cleavage; chemical cleavage also occurs without an <enzyme>.
A chemical route exploits the <hydroxyl group> at the $2'$ position of <ribose>. Its oxygen can act as a <nucleophile> toward the adjacent backbone phosphorus, producing an internal <transesterification> that breaks the chain. In their 1999 primary study, <Yingfu Li> and <Ronald R. Breaker> used chimeric <DNA>/<RNA> substrates to measure hydroxide-dependent cleavage of RNA <phosphodiester bonds>. Such a substrate isolates a susceptible linkage within a defined molecular context, allowing chemical instability to be measured separately from a complex sample's overall fragmentation pattern.<Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2′-Hydroxyl Group by Yingfu Li and Ronald R. Breaker>[Abstract and p. 5364: substrates and internal phosphoester-transfer mechanism]{ref}
An illustrative kinetic model follows the number $N$ of molecules that remain intact under constant conditions. If each intact molecule has a constant probability per unit time $k$ of undergoing its first destructive cleavage, then
$$
\frac{dN}{dt}=-kN,\qquad N(t)=N_0e^{-kt},\qquad t_{1/2}=\frac{\ln2}{k}.
$$
The last quantity is an <RNA half-life> in this model. With stipulated $k=0.020\,\mathrm{min^{-1}}$, half the starting molecules remain intact after about $34.7\,\mathrm{min}$, and $e^{-1.2}\approx30.1\%$ after an hour. The numerical rate is an example, not a universal value for RNA or a measurement from the cited experiment.
A cleavage need not remove material from the tube: breaking one long <RNA> into two pieces initially preserves its total number of <nucleotides>. Consequently a concentration measurement can stay almost unchanged while <RNA integrity> declines. An <electropherogram> can reveal redistribution toward shorter fragments, while a short target region may remain detectable by <reverse transcription> and <polymerase chain reaction>. The relevant question is which molecular continuity the intended assay requires.
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