Research
- How the flexibility of RNA/DNA molecule contributes their function?
- Translation, duplication or ligation of nucleic acid is regulated and catalyzed by proteins. Such nucleotide binding protein can identify their own cognate sequence and target molecule correctly, although there are many, many structural neighbors or sequence homologues. Why? One of the most important factor is a flexibility of nucleic acids, I think too. My first interest is how structural dynamics or deformability of RNA/DNA molecule would contribute to their function. Molecular dynamics simulation is one of the best approach to figure out their secrets.
- Folding dynamics of nucleic acids.
- 3D structure of RNA/DNA is also essential for their biochemical functions. Therefore, predicting the 3D structure of RNA/DNA from their nucleic acid sequence information will assists many other works. One of the most straight forward method to predict them is "Folding simulation", but it's very difficult and time-consuming even if the target molecule is only several nucleotide length. I'm now studying about new computational approaches and algorithms to study out such problems.
- Tertiary structure prediction of RNA using Monte-Carlo simulation.
- De novo prediction of tertiary structure of RNA is one of the hot topics among RNA researchers. We are challenging to develop the method which can predict tertiary structure of many kinds of compounds, monomeric RNA, RNA-RNA, protein-RNA, and so on. We consider the fragment assembly based method is one of the effective method for our purpose. We are now trying using this method step by step.
- Key words
- Protein - DNA/RNA interaction, DNA/RNA folding, molecular dynamics simulation, dynamics & function, binding free energy, tertiary structure prediction.