Bard1, DNA ligase I, TOP2 alpha, CDK1 (p34), FEN1, E2F4/DP1 complex, RFC1, Ribonuclease H1, WRN, E2F1/DP1 complex, PCNA, TOP2, RFC complex, DNA, CDK2, POLD reg (p12), POLD reg (p68), Ubiquitin, POLD reg (p50), DNA, MCM2, POLD cat (p125), TOP1, RNA, Brca1/Bard1, DNA, DNA polymerase alpha/primase, Brca1, DNA polymerase epsilon, Cyclin A
Transition and termination of DNA replication
DNA replication begins in the early S phase. Upon unwinding of DNA by Minichromosome maintenance protein complex (MCM complex) with the help of Origin recognition complex (ORC complex) and Replication proteins (RPA), the DNA polymerase alpha/primase is recruited to DNA (see map Start of DNA replication ) .
DNA polymerase alpha/primase synthesizes RNA/DNA hybrid on the newly unwound DNA at ~ 30 nucleotides per initiation. Then DNA polymerase delta continues synthesis of this fragment. DNA polymerase delta and DNA polymerase epsilon are activated by proliferating cell nuclear antigen ( PCNA ) with help of the Replication factor C . PCNA is a homotrimer that forms a ring shaped structure. PCNA binds to the DNA polymerase delta and DNA polymerase epsilon and acts as a ?sliding clamp?, preventing the polymerases from falling off the DNA. Replication factor C is a member of the AAA + superfamily proteins; it binds to the 3' end of the primer and uses ATP to open up the PCNA ring and close it around the template DNA .
Because of the anti-parallel nature of DNA, the two parental strands are replicated by different mechanisms during the progression of the replication fork. The parental strand, which is 3' to 5' relative to the direction of unwinding, can be replicated continuously by a DNA polymerase alpha/primase and DNA polymerase delta synthesizing 5' to 3'. This is known as the ?leading strand? .
On the other strand (?lagging strand?), however, replication is trickier because DNA polymerases cannot synthesize DNA in a 3' to 5' direction. To circumvent this problem, this strand is replicated discontinuously; as the helicase unwinds DNA, DNA polymerase alpha/primase and DNA polymerase delta (and/or DNA polymerase epsilon ) synthesize short oligonucleotides called Okazaki fragments .
Thus, the lagging strand is synthesized discontinuously as a series of RNA-DNA hybrid molecules. Maturation of Okazaki fragments involves removal of the RNA primers (and perhaps some DNA) by flap endonuclease1 ( FEN1 ). RNA primers are cleaved by Ribonuclease H1. Maturated Okazaki fragments are connected by DNA ligase I. Activites of FEN1  and DNA ligase I  are stimulated by PCNA.
The topology of a DNA molecule changes as it is unwound during DNA replication by topoisomerases. Topoisomerases are grouped into two types, both of which catalyze the cleavage and regulation of the DNA with the formation of an intermediate that is covalently bound to DNA through a phosphotyrosine bond. Topoisomerase I ( TOP1 ) is monomeric and pass a single-stranded region of DNA through a break in the opposite strand . WRN stimulates the ability of TOP I to relax negatively supercoiled DNA and specifically stimulate the religation step of the relaxation reaction , .
Type II topoisomerases ( TOP2 ) are homodimeric or heterotetrameric and pass a region of double-stranded DNA through a break in a second duplex DNA molecule (inter- or intramolecularly) . It is show, that TOP2 may be regulated by tumor suppressor BRCA1 -dependent ubiquitination ,
Termination occurs when two opposing replication forks meet and the nascent DNA from the two forks is ligated together. Replication machinery elements must be displaced before the completion of replication to allow the polymerases to replicate the last bits of sequence .
DNA ligase I inhibits DNA polymerase delta via PCNA . Then, formation of new MCM2/ DNA polymerase alpha/primase complexes might be prevented by CDK2/ CyclinA phosphorylation of DNA polymerase alpha/primase in late-S-phase . Subsequently Cyclin A activates CDK1 which in turn inhibits by phosphorylation functioning FEN1. Phosphorylation of FEN1 by CDK1/ Cyclin A abrogates its PCNA binding, thus, preventing stimulation of FEN1 by PCNA .
Thus, reduplication DNA is completed in late S phase .