Poster abstracts

Poster number 7 submitted by Shivam Chaubey

Site-specific labeling of U-rich Internal Loops (URILs) in ncRNA with NMR probe for dynamics and structural Information.

Shivam Chaubey (The Ohio State University), Xue Tang (The Ohio State University)

Abstract:
Structural Information and dynamics of RNA are crucial for understanding the various biological mechanisms and innovation of RNA-based therapeutic tools. Many functional RNAs, known as non-coding RNAs (ncRNA), do not code protein and have critical biological pathways and metabolism functions. Conventional structure determining means does not provide us with reliable data due to the flexible arrangements of RNA. Our approach can complement the traditional biophysical methods like X-ray crystallography. We hypothesize that triplex hybridization of the U-rich Internal Loops (URILs) with bifacial peptide nucleic acids (bPNA) containing NMR probes can provide significant local structural features of the RNA. Different bPNAs were designed and synthesized with varying combinations of a base. The probing can be done by attaching paramagnetic probes on the bPNAs, finally hybridizing with the URIL region of the ncRNAs.

References:
• Strickland, Madeleine, Jonathan Catazaro, Rohith Rajasekaran, Marie-Paule Strub, Colin O’Hern, Guillermo A. Bermejo, Michael F. Summers, Jan Marchant, and Nico Tjandra. 2019. “Long-Range RNA Structural Information via a Paramagnetically Tagged Reporter Protein.” Journal of the American Chemical Society 141 (4): 1430–34.
• Miao, Shiqin, Debmalya Bhunia, Shekaraiah Devari, Yufeng Liang, Oliver Munyaradzi, Sarah Rundell, and Dennis Bong. 2021. “Bifacial PNAs Destabilize MALAT1 by 3’ A-Tail Displacement from the U-Rich Internal Loop.” ACS Chemical Biology 16 (8): 1600–1609.

Keywords: U-Rich Internal Loops, bifacial Peptide Nucleic Acids, non-coding RNA