Laser-induced temperature jump infrared measurements of RNA folding.

Probing a sample using infrared spectroscopy following a laser-induced temperature jump is a powerful method to monitor fast relaxation kinetics. Here, we describe how this approach is used to study the kinetics of RNA folding. We begin with a concise summary of the infrared spectral properties of RNA in the 1500-1800cm(-1) region. The infrared transitions in this region are directly related to the double bond stretching vibrations and ring modes of the nucleotide bases. When RNA undergoes a conformational change, the local environments of the nucleotides are altered. Consequently, the changes in the corresponding infrared spectrum are associated with the structural changes. Experimentally, temperature is used to systematically vary the RNA structure. When a short laser pulse is used to produce a rapid temperature increase in the sample, the structural changes that ensue can be followed in real time. In this contribution, we discuss experimental methods including sample preparation, instrumentation, and data analysis. We conclude with several experimental examples that highlight usefulness of the technique.