Structural Characterization Of RNA And Detection Of RNA-Ligand Binding Using Microfluidic Modulation Spectroscopy

Riboswitches are short, well-folded mRNA sequences that regulate protein production by undergoing structural changes upon binding to specific small molecules. These structural changes activate the riboswitch, influencing gene expression. In this study, we employed Microfluidic Modulation Spectroscopy (MMS) to examine the structural changes in the SAM-I riboswitch induced by ligand binding. MMS, a sensitive technique, monitors the base pairing and stacking of nucleic acids by probing the Amide-I IR-range. Our findings revealed subtle yet noticeable structural changes in the SAM-I riboswitch upon ligand binding, as evidenced by spectral differences. A dose-dependent titration further corroborated these findings, highlighting two regions of gradual change upon SAM titration.
This study underscores the potential of MMS as a valuable tool for detecting RNA structural changes in the presence of small molecule ligands and for determining apparent Kd of RNA-ligand binding.
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