The molecular dynamics study of the double-stranded RNA-binding motive of ADAR2 bound to dsRNA

J. Pašulka, J. Koča and R. Štefl

National Centre for Biomolecular Research, Faculty of Science, Masaryk

University, Kotlarska 2, Brno, 611 37, Czech Republic

The members of an enzyme family known as ADARs (adenosine deaminases that act on RNA) play an important role in the RNA editing process in higher eukaryotes. ADARs can convert adenosines to inosines within double-stranded structures of their RNA substrates in a site-specific fashion. The mechanism for such site-specific editing remains unclear, albeit several studies have suggested that the specificity could be imposed by the presence of non-canonical elements in the dsRNA structure (e.g. mismatches, bulges, and loops). We study the second double-stranded RNA binding motif of ADAR2 bound to dsRNA with non-canonical elements using molecular dynamics (MD) simulations. Our goal in this work is to explain the role of non-canonical elements in dsRNA and their flexibility for the ADAR2-dsRNA complex.