Gene Ther Mol Biol Vol 2, 83-94. August 7, 1998.
Ribozyme-catalyzed trimming reactions and the direct role of Mg2+ ions in the cleavage of RNA Masaki Warashina1,2,4, Tomoko Kuwabara1,2,4, Yuka Nakamatsu1,2,4, Masayuki Sano1,2,4, Atsushi Shibata1,2,4, Hideki Shizuku1,2,4, Hideyuki Takeda1,2,4, Ryuji Utsunomiya1,2,4, Jing-Min Zhou1,2,4, Tadafumi Uchimaru3, Jun Ohkawa1,2,4 and Kazunari Taira1,2,4,* 1National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba Science City 305-8562, Japan; 2National Institute of Bioscience and Human Technology, 1-1 Higashi, Tsukuba Science City 305-8566, Japan; 3National Institute of Materials and Chemical Research, 1-1 Higashi, Tsukuba Science City 305-8565, Japan; and 4Institute of Applied Biochemistry, University of Tsukuba, Tennoudai 1-1-1, Tsukuba Science City 305-8572, Japan. ______________________________________________________________________________________ ________________ * Correspondence: Professor Kazunari Taira, Institute of Applied Biochemistry , University of Tsukuba, Tennoudai 1-1-1, Tsukuba Science City 305-8572, Japan, Tel/Fax: +81-298-53-4623; E-mail: taira@nibh.go.jp Received 3 June 1998; accepted 15 June 1998 Key words: ribozyme, cleavage, trimming, RNA world, Mg2+ ion, metallo-enzyme
Summary In the hypothetical RNA world divalent Mg2+ ions were exploited for cleavage (or ligation) of ribonucleic acids. Although some Mg2+ ions are involved in forming the tertiary structures of
RNAs, the key Mg2+ ions are directly involved in catalysis not only in the case of hammerhead ribozymes but also in the case of Tetrahymena and, possibly, other types of ribozyme. RNA components bind the indispensable Mg 2+ ions to the phosphodiester bonds that are being broken
(or formed). Our analysis indicates that the chemical cleavage step of reactions catalyzed by the hammerhead ribozyme does not appear to have been perfected and, thus, it seems possible to create RNA-cleaving agents that are significantly more active than the standard hammerhead ribozyme. Moreover, RNA-cleaving mechanisms might converge as one unique and universal mechanism, exploited not only by various kinds of ribozyme but also by artificially created metal-ion-dependent DNAzymes and other RNA-cleaving agents that are yet to be identified.