Probing Nucleic Acids using Steady-State and Ultrafast Fluorescence Spectroscopy

By Julia Widom, University of Oregon

  • Event Type: Seminar
  • Date and Time: 05/08/2023 3:00 pm - 05/08/2023 4:00 pm
  • Location: Willamette 240D

RNA performs a diverse set of biological functions, many of which require it to fold into specific structures. Many techniques have been developed to study RNA folding, a number of which are based on fluorescence detection. I will first present work in which we used fluorescent analogues of the natural RNA bases to selectively probe the structures of different conformational subpopulations of RNA. We investigated the photophysical properties of base analogues in different structural contexts using a combination of fluorescence-detected circular dichroism spectroscopy and fluorescence lifetime measurements. This approach circumvents the problem of ensemble averaging that limits the power of bulk spectroscopic methods such as CD. I will then my lab's work using ultrafast fluorescence upconversion spectroscopy to measure fluorescence lifetimes and time-resolved emission spectra with a time resolution in the 100s of femtoseconds. I will present the principle of fluorescence upconversion spectroscopy and the optical setup used to perform it. I will then present data on model fluorophores demonstrating the instrument's high sensitivity, as well as preliminary results that illustrate the effect of the nucleic acid environment on the fluorescence of cyanine dyes.