RNA structure and dynamics play critical roles in regulating biological processes. Understanding the conformational landscape is essential for unraveling RNA functionality, stability, and use as both a therapeutic and a therapeutic target. Microfluidic Modulation Spectroscopy (MMS) is a novel solution-state infrared spectroscopy technique that is sensitive to changes in nucleic acid base conformation and hydrogen bonding patterns. The studies detailed here utilize the latest generation of MMS instrumentation from RedShiftBio, the AuroraTX. In these studies, we build the case for the use of MMS in RNA structural analysis. First, we present MMS IR spectra of individual RNA nucleotides, as well as polyA and polyU RNAs, showcasing the Amide I IR spectra of unpaired nucleotides. Second, we highlight the ability of MMS to resolve i-motif and G-quadruplex secondary structures in polyC and polyG RNAs, respectively. Third, we investigate GC, AU, and GU base pairing using self-complementary duplexed RNAs, demonstrating the capacity of MMS to detect and distinguish different types of base pairing. Finally, thermal melt data for GC and AU duplexes reveal the ability of MMS to monitor the melting dynamics and melting temperature of specific basepairing interactions. In addition to measuring native RNA structure, MMS can also detect structural changes caused by ligand binding. To demonstrate this, we present MMS data on interactions between S-adenosylmethionine (SAM) and the SAM-I riboswitch, as well as PreQ1 and the PreQ1 riboswitch. This pair of studies demonstrate the potential utility of MMS as a functional assay in the discovery of small molecule therapeutics that modulate RNA structure. Our findings establish MMS as a powerful tool for investigating RNA structure, base-pairing dynamics, and ligand-induced conformational changes, laying the foundation for integrating the AuroraTX platform into future RNA-targeted and RNA-based therapeutic development. Video poster bit.ly/3YOkq3o