 RNA melting relaxation time

An RNA melting relaxation time characterizes how quickly a perturbed RNA population approaches its new equilibrium. It belongs to a specified kinetic model, temperature, solution and measured signal. It is not an RNA melting temperature or, in general, the mean waiting time for an individual unfolding event.

For a reversible two-state RNA melting model, let $k_u$ be the first-order unfolding rate constant and $k_f$ the refolding rate constant. The unfolded fraction obeysAt fixed temperature,Both directions contribute to the return to equilibrium. For original stipulated values $k_u=20{\mathrm{s}}^{-1}$ and $k_f=80{\mathrm{s}}^{-1}$, $f_{U,\mathrm{eq}}=0.20$ and $\tau =10\mathrm{ms}$. The mean lifetime of an isolated folded state in this model is $1/k_u=50\mathrm{ms}$, which differs from the observed population exponential decay time.

A temperature jump shifts populations rapidly enough to reveal the subsequent motion. A primary study used 4-ns heating pulses, a 12-μm sample path and time-resolved infrared spectroscopy to follow melting and refolding of a UACG-containing RNA hairpin. Thin-cell cooling enabled direct observation of the return process. Its loop is UACG, not a UUCG tetraloop.^[ref]

An RNA relaxation instrument-response correction may be needed if heating, detector response or cooling occur on comparable timescales. A changing sample temperature changes the equilibrium target during the measurement, invalidating a constant-temperature fit across the whole trace. Multiple kinetic states can also produce several decay components. One fitted exponential should therefore be identified as a model-dependent observed relaxation, rather than automatically assigned to a unique molecular step.