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Junction ribonuclease (JRNase) recognizes the transition from RNA to DNA of an RNA–DNA⁄DNA hybrid, such as an Okazaki fragment, and cleaves it, leaving a mono-ribonucleotide at the 5¢ terminus of the RNA– DNA junction. Although this JRNase activity was originally reported in calf RNase H2, some other RNases H have recently been suggested to pos-sess it. | ễFEBS Journal Junction ribonuclease activity specified in RNases HII 2 Naoto Ohtani Masaru Tomita and Mitsuhiro Itaya Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan Keywords JRNase Okazaki fragment paralogous gene RNA-DNA junction RNase HII 2 Correspondence N. Ohtani Institute for Advanced Biosciences Keio University Tsuruoka Yamagata 997-0017 Japan Fax 81 235 29 0529 Tel 81 235 29 0526 E-mail ohtani@ttck.keio.ac.jp Received 1 August 2008 revised 5 September 2008 accepted 8 September 2008 doi 10.1111 j.1742-4658.2008.06673.x Junction ribonuclease JRNase recognizes the transition from RNA to DNA of an RNA-DNA DNA hybrid such as an Okazaki fragment and cleaves it leaving a mono-ribonucleotide at the 5 terminus of the RNA-DNA junction. Although this JRNase activity was originally reported in calf RNase H2 some other RNases H have recently been suggested to possess it. This paper shows that these enzymes can also cleave an RNA-DNA RNA heteroduplex in a manner similar to the RNA-DNA DNA substrate. The cleavage site of the RNA-DNA RNA substrate corresponds to the RNA RNA duplex region indicating that the cleavage activity cannot be categorized as RNase H activity which specifically cleaves an RNA strand of an RNA DNA hybrid. Examination of several RNases H with respect to JRNase activity suggested that the activity is only found in RNase HII orthologs. Therefore RNases HIII which are RNase HII paralogs are distinguished from RNases HII by the absence of JRNase activity. Whether a substrate can be targeted by JRNase activity would depend only on whether or not an RNA-DNA junction consisting of one ribonucleotide and one deoxyribonucleotide is included in the duplex. In addition although the activity has been reported not to occur on completely singlestranded RNA-DNA it can recognize a single-stranded RNA-DNA junction if a double-stranded region is located adjacent to the junction. Ribonuclease H RNase H EC 3.1.26.4 is an enzyme that .
