Calf RTH-1 nuclease can remove the initiator RNAs of Okazaki fragments by endonuclease activity

In eukaryotes, the endonucleolytic activity of the calf RTH-1 class 5'- to 3'-exo/endonuclease can function without RNase H1 to remove initiator RNA from Okazaki fragments. Cleavage requires that the RNA be displaced to form an unannealed single-stranded 5'-tail or flap structure. On substrates with RNA-initiated primers, DNA oligomers that competed with the RNA for template binding simulated strand displacement synthesis from an upstream Okazaki fragment. This allowed cutting of displaced RNA segments by RTH-1 nuclease. Requirements for the reaction also were examined on substrates in which the tail was unannealed because it was intentionally mispaired. On both types of substrate, the nuclease slides over the RNA region from the 5'-end and cleaves at the beginning of the annealed region, irrespective of whether ribo- or deoxyribonucleotides are at the cleavage site. Presence of a triphosphate or a 7-methyl 3'G5'ppp5' G cap structure at the 5'-end of the RNA does not affect cleavage. The previously reported stimulation of the nuclease by an upstream primer was not always observed, suggesting that not every site in the downstream Okazaki fragment is equally susceptible to cleavage during displacement synthesis in vivo. The biological role of the endonuclease activity of RTH-1 nuclease in Okazaki fragment processing is discussed.