UROP Research Abstract Assignment

Student Name: Bennett Hendricks Student Peer Advisor: Julien Heidt

RNA Kinetics and Dynamics: The Folding of a Bacterial Riboswitch during Transcription

Recent studies have unraveled complex networks of non-coding RNAs across all domains of life.
It is understood that noncoding RNAs play a vital role in gene regulation. However,
nucleotide-resolution analysis is required to one day inform biomedical RNA therapies and the
development of inhibitory molecules. This investigation focuses on riboswitches, a special class
of noncoding RNAs that begin folding cotranscriptionally upon synthesis in the bacterial
cytoplasm. Alternative ligand-mediated folding pathways create a mechanism by which genes
may be “switched” either on or off. In the case of the bacterial fluoride riboswitch, sufficient
fluoride concentration induces the formation of a pseudoknot, preventing the full formation of a
terminator hairpin loop, thereby allowing RNA polymerase to continue transcription. We are
using single-molecule FRET technology to gather information about conformational changes in
the riboswitch at various fluoride and magnesium ion concentrations. In this regard, I have been
using a program in Matlab to perform data analysis on previously conducted experiments. Some
experiments immobilized the RNA by binding it to a complementary locked nucleic acid (LNA)
sequence secured to the slide through biotin-streptavidin interactions. Other trials were
conducted in the presence of an RNA polymerase complex bound to the slide in the same
manner. In this regard, I have been performing the slide cleaning and preparation procedure. We
are truncating our riboswitch at various lengths across trials to determine relationships between
primary sequence and structure.

Research Mentor (Print):

Mentor Signature: __________________________________________ Date: ___________

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embedded references, footnotes, etc?)
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this student about the objectives and/or bigger picture of this research project?

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