Circular Dichroism Analysis of RNA Oligonucleotides

Circular dichroism (CD) studies were performed on Jasco 815. RNA oligonucleotides (n = 6) were purchased from Merck for all biophysical experiments. RNA oligonucleotides were prepared in a final concentration of 10 μM with 10 mM sodium cacodylate buffer (pH −7.4) and 100 mM potassium chloride (KCl). The samples were slowly cooled to room temperature after heating at 90 °C for 5 min. Spectra at 220 to 320 nm wavelength range were recorded in a quartz cuvette of 1 mm path length, keeping a 1 nm step size and time of 1s per point. CD melt curves were obtained over 20 to 95 °C using the same oligonucleotide concentration (10 μM), either with or without BRACO19 as previously described by Kumar et al. (69 (link)). Melting temperatures (Tm) were calculated by fitting the curve into the Boltzmann function with Origin 9.7.5 (Origin Lab Corp).