KEY WORDS: RNA, thermodynamics of nucleic acids, secondary structure mapping of RNA, natural and viral RNAs
Research topic: the research concerns the determination of the thermodynamic rules of natural RNA folding in cellular-like conditions and the implementation of the obtained thermodynamic parameters into the RNAstructure program. This program is used to predict RNA folding based on thermodynamic rules. The next step is to compare the structures of the influenza RNA experimentally determined in cellular-like conditions with the structure of the same RNA generated with the RNAstructure program.
Principal Investigator: prof. dr hab. Ryszard Kierzek
I. Project description
The correlations of RNA structure and function are very well known. In order to change the biological functions of RNA, including pathogenic human RNA, it is necessary to know the structure of native RNAs. RNA secondary structure determination is relatively straightforward for RNA in vitro and relies on chemical, enzymatic and microarray mappings as well as RNA structure determination using thermodynamic rules. RNA secondary structure folding is based on the nearest-neighbor model and uses thermodynamic parameters for duplexes and nonhelical RNA structural motifs determined in a buffer containing 1M sodium chloride. Determining the RNA structure in the cellular environment (in vivo, in cellulo) is a difficult and long-lasting process and is currently based mainly on chemical mapping in cells and analysis of mapping results using next generation sequencing (NGS) methods. The overall aim of the project is to study the rules of RNA folding in cells to be able to bioinformatically correctly predict native RNA structures. In the presented project, we propose:
(1) determination of the thermodynamic parameters of RNA folding in in vivo-like conditions to predict RNA folding under native conditions. To achieve this goal, we will determine the thermodynamic stability of model RNAs in a cellular-like buffer.
(2) implementation of the cell thermodynamics parameters into RNAstructure. This will allow to determine RNA folding in the cellular environment and compare the thermodynamic stability and RNA structure in vitro and in cellular conditions,
(3) compare the folding of the same RNAs determined by the cellular RNAstructure and the structure determined by RNA mapping using the NGS method. In this group of studies, we will especially focus on segment 8 of the influenza virus vRNA (vRNA8).
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