Figure 3.

Time dependence of AA dissociation from DNA and RNA gaps directly observed with T-jump IR spectroscopy. (a) Transient heterodyned dispersed vibrational echo difference spectra (t-HDVE) at T-jump delays ranging from 5 ns to 180 μs for TTg:AA, TTg, UUg:AA, and UUg following a T-jump from 19°C to 33°C. Spectra are plotted as the change relative to the maximum signal value of the initial temperature spectrum ($\Delta S\left(t\right)=[S\left(t\right)-S\left(T_i\right)]/\max \left[S\left(T_i\right)\right]$). (b) Normalized $\Delta S\left(t\right)$ time traces at 1545 cm⁻¹ (blue, guanine ring mode), 1605 cm⁻¹ (purple, adenine ring mode), and 1672 cm⁻¹ (red, guanine and thymine carbonyl modes) for TTg:AA and UUg:AA (filled circles) as well as TTg and UUg (open circles). The probe frequencies are marked as vertical dashed lines in the t-HDVE spectra. Traces at different frequencies are shifted vertically with respect to one another, and dashed lines indicate respective baselines. AA dissociation is observed as a single kinetic component from 1–10 μs, and additional base-pairing dynamics from the template itself occur on an overlapping timescale. To see this figure in color, go online.