Replication initiation in E. coli cell

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In E. coli cell, replication of genome starts at the single origin oriC. OriC is an AT rich sequence, composed of  232 – 245 bp. At the beginning, initiator protein DnaA will recognize and bind to DnaA boxes of oriC which contains 9 bp repeats, to form a large protein – DNA complex. Among the DnaA boxes, 3 boxes R1, R2, R4 have highest affinity with DnaA. This complex contributes to melting of A-T rich DNA unwinding element (DUE) which consists of three 13 bp repeats. Continue Reading →

DNA replication origin

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Replication origin is the sequences where replication started. Usually, DNA structure is the double helix, to be used as the template for replication, the duplex parental strands must be opened, by breaking hydrogen bonds between two strands. Therefore, usually, replication origin is the A-T rich sequences, as A-T base pairs contain fewer hydrogen bond than G-C base pairs. In E. coli, there is only a single origin for genome replication called OriC (232 – 245 bp). The initiator proteins bind this sequence and start replication in Continue Reading →

E. coli replisome structure

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Replisome is a multiple protein complex that works together on the template in order to synthesize new DNA. Basically,  E. coli replisome contains a hexamer helicase, single stranded binding protein SSB, primase DnaG, 2 Polymerase III core, a gamma complex (also known as clamp loader) and β clamp. Helicase is a homohexamer that encircles the lagging strand like a ring. It translocates along the ssDNA and separate the duplex DNA using energy from ATP hydrolysis. The unwinding of double stranded DNA and discontinuous synthesis of lagging strand leaves Continue Reading →

Collisions between the replisome and a transcribing RNA polymerase

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It is widely reported that DNA replication progression is effected by many factors such as DNA damage, lesion or protein, acid nucleic … , that can lead to fork arrest or sometimes fork collapse. Depending on the situation, cell have different pathways to rescue fork progression or post-replication pathways to faithfully maintain genetic information such as DNA repair …. In the cell, it’s highly possible that RNA transcription can occur simultaneously with DNA replication. In this case, the collision between replisome and transcription complex is unavoidable. Continue Reading →

Synthesis of lagging strand, how does the lagging strand polymerase recycle?

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Based on the polarity of double stranded DNA molecule and characteristic of DNA polymerase III Holoenzyme that can only synthesize DNA in 5′-3′ direction, replication is carried in a discontinuous manner. There are two core polymerase on the replisome and each core takes part in leading or lagging synthesis. On the leading template, the new strand is synthesized continuously in the same direction with the fork progression, while on lagging template, the synthesis occurs in the opposite direction with fork movement. Therefore, the synthesis of lagging Continue Reading →

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