Poster abstracts

Poster number 126 submitted by Danyang Liu

Thermodynamic characterization of RNA secondary structures motifs containing inosine

Danyang Liu (Saint Louis University), Kip Friend (Saint Louis University), Esha Dani (Saint Louis University), Brent M. Znosko (Saint Louis University)

Abstract:
Several algorithms and software packages are available to predict RNA secondary structure from sequence. However, one limitation of these algorithms is that they cannot accommodate non-standard nucleotides. There are over 150 naturally occurring, non-standard nucleotides identified thus far. One of these non-standard nucleotides, inosine (I), results from the deamination of A by adenosine deaminases that act on RNA (ADARs). I can pair with A, C, or U. Our lab has previously reported the thermodynamics of I-U (Wright et al. 2007) and I-C pairs (Wright et al. 2018). However, in order to predict RNA secondary structure from sequence, thermodynamic data is needed for I when found in other secondary structure motifs such as terminal mismatches, tandem mismatches, bulges, and dangling ends This study utilized Optical Melting experiments, MeltR software, and the nearest neighbor model to characterize the thermodynamic data of 36 inosine motifs. This resulted in the characterization of free energy, entropy, enthalpy and melt temperature for 36 samples. These thermodynamic data will be used to derive nearest neighbor parameters that can be incorporated into secondary structure prediction algorithms allowing scientists to predict the stability and secondary structure of RNA oligonucleotides containing Inosine.

References:
Wright, D. J., Force, C. R., & Znosko, B. M. (2018). Stability of RNA duplexes containing inosine·cytosine pairs. Nucleic Acids Research, 46(22), 12099–12108. https://doi.org/10.1093/nar/gky907
Wright, D. J., Rice, J. L., Yanker, D. M., & Znosko, B. M. (2007). Nearest neighbor parameters for inosine x uridine pairs in RNA duplexes. Biochemistry, 46(15), 4625–4634. https://doi.org/10.1021/bi0616910
Zuber, J., Sun, H., Zhang, X., McFadyen, I., & Mathews, D. H. (2017). A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction. Nucleic Acids Research, 45(10), 6168–6176. https://doi.org/10.1093/nar/gkx170

Keywords: Inosine, Nearest neighbor parameters, RNA secondary structure prediction