Effects of metal ions and catalytic loop sequences on the complex formation of a deoxyribozyme and its RNA substrate

Abstract

A deoxyribozyme is a catalytic DNA that catalyzes a site-specific RNA cleavage activity and requires various divalent cations. Earlier we have reported that by downsizing the catalytic loop of a deoxyribozyme from 15-mer to 11-mer it resulted in a short and novel Ca 2+-dependent deoxyribozyme. In this paper, we investigate the complex formation of deoxyribozymes with their RNA substrates by using surface plasmon resonance (SPR) in order to determine quantitatively the effect of Ca 2+ or Mg 2+ on the recognition step between a deoxyribozyme and its RNA substrate. The results indicate that both the association and dissociation rate constants ( k a and k d) for the deoxyribozyme–RNA complex depends on metal ions as well as the loop size of the deoxyribozyme. Metal ions with high RNA cleavage activity induced an increase in k a and a decrease in k d. On the basis of the results, we propose that Ca 2+ ions may play a role in the rearrangement of the 11-mer catalytic loop of the short Ca 2+-dependent deoxyribozyme.