Okazaki fragment maturation in yeast: I. Distribution of functions between FEN1 and DNA2

In the presence of proliferating cell nuclear antigen, yeast DNA polymerase δ (Pol δ) replicated DNA at a rate of 40-60 nt/s. When downstream double-stranded DNA was encountered, Pol δ paused, but most replication complexes proceeded to carry out strand-displacement synthesis at a rate of 1.5 nt/s. In the presence of the flap endonuclease FEN1 (Rad27), the complex carried out nick translation (1.7 nt/s). The Dna2 nuclease/helicase alone did not efficiently promote nick translation, nor did it affect nick translation with FEN1. Maturation in the presence of DNA ligase was studied with various downstream primers. Downstream DNA primers, RNA primers, and small 5′-flaps were efficiently matured by Pol δ and FEN1, and Dna2 did not stimulate maturation. However, maturation of long 5′-flaps to which replication protein A can bind required both DNA2 and FEN1. The maturation kinetics were optimal with a slight molar excess over DNA of Pol δ, FEN1, and proliferating cell nuclear antigen. A large molar excess of DNA ligase substantially enhanced the rate of maturation and shortened the nick-translation patch (nucleotides excised past the RNA/DNA junction before ligation) to 4-6 nt from 8-12 nt with equimolar ligase. These results suggest that FEN1, but not DNA ligase, is a stable component of the maturation complex.