Research topics

A research group of Dr. Naoki Sugimoto (Director of FIBER), Dr. Sagar Satpathi (Postdoctoral Research Fellow), and Dr. Tamaki Endoh (Associate Professor) has obtained the results that enable prediction of the thermal stability of pseudoknot structures. This research result was published in Chemical Communications, a scientific journal published by the Royal Society of Chemistry, UK, and was selected as an Inside Front Cover of the issue.

In human genome, a region of only 1.5% encodes functional proteins. On the other hand, it has been suggested that the region nearly 70% is transcribed to RNA. In recent years, the molecular mechanisms by which RNAs proactively regulate biological phenomena depending on their structures are becoming clearer. Among the RNA structures, pseudoknot can be basic for forming more complex higher-order structures. Pseudoknot itself also plays an important role in the regulation of gene expression. In the case of SARS-CoV-2 mRNA, pseudoknot induces ribosomal frameshift and modulate expression levels of two types of viral proteins.

Frontier Institute for Biomolecular Engineering Research (FIBER) at Konan University has been analyzed thermodynamic parameters of nucleic acid structures that enable prediction of their stability based on compositions of adjacent base pairs, which is also known as nearest neighbor base pairs. Since the pseudoknot is consisting of hairpin, in which loop region is intramolecularly forming additional base pairs, the stability of the pseudoknot is potentially predicted from the nearest-neighbor base pairs. However, the applicability of the model, nearest-neighbor model, for predicting stabilities of pseudoknots has not been verified. In this study, we performed thermodynamic analyses of pseudoknots by simple strategy that focuses on one of the two double helical regions in the pseudoknot rather than the entire structure. We demonstrated that the nearest-neighbor model is valuable in the stem region of H-type pseudoknots, enables prediction of pseudoknot structure based on the base pair compositions. The results of this study will be applied for quantitative demonstration of the correlations between pseudoknot stabilities and functions. The results also expected to enable us to discuss how changes in the stability of pseudoknot, which depend on the molecular environment, correlate with changes in RNA functions.

The link to Chemical Communications is here.
The Inside Front Cover of the issue is here.

The paper was published in “Applicability of the nearest-neighbour model for pseudoknot RNAs”
Sagar Satpathi, Tamaki Endoh and Naoki Sugimoto
Chem. Commun., 58, 5952–5955 (2022)

FIBER will continue to contribute to the promotion of science and technology through research and development in the field of biochemistry, and to social contribution through research results.