Modulating RNA secondary and tertiary structures by mismatch binding ligands.

Modulating RNA secondary and tertiary structures by mismatch binding ligands.

Publication date: May 09, 2019

Much recent attention has been focused on small organic molecules binding to non-canonical structures of nucleic acids, especially, RNA. The Human Genome Project and the ENCODE (encyclopedia of DNA elements) project revealed that more than 75% of the human genome is transcribed into RNA, while only ∼3% of the human genome encodes a protein. These non-protein-coding RNAs are thought to play significant roles in many cellular processes and are promising targets for drug discovery. Emerging roles of the non-coding RNAs in a variety of diseases provides enormous opportunities for pharmaceutical research on developing drugs targeting undruggable and rare diseases. During the last two decades, our laboratory has focused attention on small molecules binding to non-canonical DNA and RNA structures, especially to mismatched base pairs. Mismatch binding ligands (MBLs) we have developed are synthetic molecules designed in silico based on the hypothesis of hydrogen-bonding and semi-intercalation to DNA and RNA. Most of MBLs consists of two heterocycles having hydrogen bonding surfaces fully or partially complementary to that of nucleotide bases. In our design, each heterocycle binds to one of the mismatched bases by hydrogen bonding to form pseudo-base pairs, which would be stacked with the adjacent base pairs. The hypothesis allows us in principle to design small molecules binding to any mismatched base pairs, but it turned out not to be the case in reality. However, we have so far succeeded in developing several MBLs binding to DNA and RNA motifs of biological significance. In this review, we shall describe the hypothesis of molecular design of MBLs and its outcome regarding RNA targeting.

Murata, A., Nakamori, M., and Nakatani, K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. 06484. 2019 Methods.

Concepts Keywords
Base Pairs Drug discovery
Drug Discovery DNA
ENCODE Non-coding RNA
Genome Molecular binding
Heterocycle Base pair
Hydrogen Bonding Biotechnology
Intercalation Molecular biology
Ligands Molecular genetics
Nucleic Acids RNA
Nucleotide Branches of biology
Organic Molecules Nucleic acids
Pharmaceutical RNAs diseases
Protein Undruggable rare diseases


Type Source Name
disease DOID Huntington disease
disease MESH Myotonic dystrophy
disease MESH Huntington disease
disease MESH rare diseases


Original Article

Leave a Comment

Your email address will not be published. Required fields are marked *