Abstract

RNA modifications are known to influence the local structure and thermodynamics of RNA. These nucleotide modifications are present in various RNAs including functionally important regions of ribosomal RNA. A pseudouridine (Ψ) and 7-methyl guanine (m7G) modified nucleotides are present at positions 516 and 524 of 16S rRNA. This research focuses on understanding the structural and thermodynamic effects of these two modification as observed in the Helix 18 region of 16S rRNA. In Helix 18 specifically, I study the thermodynamics and kinetics of folding and unfolding of the Helix 18 pseudoknot and how these modified nucleotides influence its folding dynamics. I plan to detect conformational changes using Foster Resonance Energy Transfer (FRET) experiments. Helix 18 model RNA was constructed using two synthetic RNA oligos. Each oligo was fluorescently labeled with Cy3 and Cy5 dyes. My electromobility gel shift assay showed the equilibrium dissociation constant between the two oligos was 5nM. The FRET signal increased with an increase in Mg2+ concentration.

Modified Abstract

Nucleotide modifications are present in various RNAs including functionally important regions of ribosomal RNA. A pseudouridine (Ψ) and 7-methyl guanine (m7G) modified nucleotides are present in 16S rRNA. This research focuses on understanding the structural and thermodynamic effects of these two modifications and the pseudoknot as observed in the Helix 18 region of 16S rRNA and how these modified nucleotides influence folding dynamics. Conformational changes were detected using Foster Resonance Energy Transfer (FRET) experiments. The Helix 18 model RNA was constructed using two synthetic, fluorescently labeled RNA oligos. The electromobility gel shift assay showed the equilibrium dissociation constant between the two oligos was 5nM and the FRET signal increased with an increase in Mg2+ concentration.

Research Category

Physics/Chemisty/Liquid Crystal

Primary Author's Major

Chemistry

Mentor #1 Information

Dr. Sanjaya Abeysirigunawardena

Presentation Format

Poster

Start Date

21-3-2017 1:00 PM

Research Area

Biochemistry

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Mar 21st, 1:00 PM

Investigation of the Dynamics of the Helix 18 Pseudoknot in 16S rRNA

RNA modifications are known to influence the local structure and thermodynamics of RNA. These nucleotide modifications are present in various RNAs including functionally important regions of ribosomal RNA. A pseudouridine (Ψ) and 7-methyl guanine (m7G) modified nucleotides are present at positions 516 and 524 of 16S rRNA. This research focuses on understanding the structural and thermodynamic effects of these two modification as observed in the Helix 18 region of 16S rRNA. In Helix 18 specifically, I study the thermodynamics and kinetics of folding and unfolding of the Helix 18 pseudoknot and how these modified nucleotides influence its folding dynamics. I plan to detect conformational changes using Foster Resonance Energy Transfer (FRET) experiments. Helix 18 model RNA was constructed using two synthetic RNA oligos. Each oligo was fluorescently labeled with Cy3 and Cy5 dyes. My electromobility gel shift assay showed the equilibrium dissociation constant between the two oligos was 5nM. The FRET signal increased with an increase in Mg2+ concentration.