Although type 1 RNases H require a minimum of four ribonucleotides for hydrolysis, type 2 RNases H can recognize a single ribonucleotide ( Cerritelli and Crouch 2009). There are two distinct classes of RNase H enzymes in bacterial and eukaryotic systems (type 1: RNase HI and RNase H1 and type 2: RNase HII and RNase H2 ) ( Cerritelli and Crouch 2009). Removal of RNA primers is performed partly by a ribonuclease H (RNase H). Specifically, the RNA primers have to be excised from the fragments. These segments need to be further processed to form a fully functional strand of DNA. On the lagging strand the primer is extended by the addition of dNMPs to form short segments of DNA. Because DNA polymerases cannot incorporate dNTPs without a primer terminated by a 3′ hydroxyl, the leading strand and each Okazaki fragment are primed by RNA to initiate synthesis ( Hubscher et al. Presumably, use of a similar mechanism in eukaryotes allows coordination of synthesis between the leading and lagging strands ( Fig. In bacteria, DNA replication proceeds within a fork, wherein the lagging strand loops into a “trombonelike” structure allowing for the replication enzymes to be continually recycled on the DNA for repeated synthesis and joining ( Alberts et al. The replisome machineries of both organisms are minimally composed of helicases, which unwind the duplex strands, primase, which initiates synthesis and DNA polymerases, which duplicate the parental strands of the DNA. PARALLELS BETWEEN PROKARYOTIC AND EUKARYOTIC REPLICATIONĪlthough replication of eukaryotic DNA on a chromatinized DNA template is a relatively more complex process than replication in bacteria, involving more types of proteins and reactions, the fundamental processes of DNA duplication have striking parallels in all cells. (2) Mechanisms of lagging-strand replication must have developed means of avoiding mutagenesis while handling the necessary strand manipulations.

This requirement has two fundamental consequences: (1) The lagging strand must have evolved priming and fragment joining mechanisms involving many additional steps and reactions than needed for leading-strand extension. The strand is synthesized in short segments, named Okazaki fragments, after their discoverer ( Sakabe and Okazaki 1966 Okazaki et al. This can only be accomplished if the strand is made discontinuously ( Kornberg and Baker 1992). The other, or lagging strand, must be periodically extended away from the opening helix. One copied strand, called leading, can conveniently be extended in a continuous manner in the same direction that the helix must open to allow exposure of templates for polymerization. The antiparallel structure of double-helical DNA and the 3′ end extension specificity of all DNA polymerases confine the mechanisms that can be used by the cell for DNA duplication. Replication of cellular chromosomal DNA is initiated by the multienzyme replisome machinery, which unwinds the DNA helix to create a replication fork. The eukaryotic maturation mechanism involves many enzymes, possibly three pathways, and regulation that can shift from high efficiency to high fidelity. The prokaryotic joining mechanism is simple and efficient.

Although the prokaryotic fragments are ∼1200 nucleotides long, the eukaryotic fragments are much shorter, with lengths determined by nucleosome periodicity. In both prokaryotes and eukaryotes the lagging-strand fragments are initiated by RNA primers, which are removed by a joining mechanism involving strand displacement of the primer into a flap, flap removal, and then ligation. Genetic analyses and reconstitution experiments identified proteins and multiple pathways responsible for maturation of the lagging strand. The lagging strand needs to be processed to form a functional DNA segment. The leading strand is elongated continuously in the direction of fork opening, whereas the lagging strand is made discontinuously in the opposite direction. Cellular DNA replication requires efficient copying of the double-stranded chromosomal DNA.

Okazaki fragments meaning