Evaluation of RNA cleavage reaction based on the prediction parameters for nucleic acid structures

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Toward functionalization of nucleic acids and their uses as a biomaterial, we investigated RNA cleavage reactions based on the prediction parameters for nucleic acid structures. We first carried out determinations of the prediction parameters of nucleic acid conformations and evaluation of the interaction energies. According to our previous results about Watson-Crick and mismatched base pairs, we have determined the thermodynamic parameters for dangling ends and hairpin loop structures which are often found in many ribozymes. Furthermore, important aspects of molecular crowding as well as nucleotide interactions with metal ions and water molecules have also been addressed in this research. On the basis on the quantitative data for the nucleic interactions and structures, we also have successfully constructed polymer receptors for nucleotides, a deoxyribozyme with modified functions, and a molecular sensor that can discriminate an RNA sequence and conformation. In addition, we have designed adenosine derivatives with a flexible linker, and found that the functional DNA containing the artificial nucleoside could interact with nucleotide bases and cleaved a target RNA sequence in the presence of MgCl_2. In summary, our researches guide the prediction of nucleic acid structures, their thermodynamic stability, and design of artificial nucleic acids with functions including ribozymes and artificial nucleotides that act as an artificial nuclease.