Elementary plant Biochemistry and Biotechnology (2+1)

Semidiscontinuous replication

• Watson and Crick’s semi conservative model of DNA replication predicted the existence of a replication fork, a dynamic Y-shaped structure with a barrel composed of parental duplex DNA and arms composed of daughter duplex DNA, each daughter duplex consisting of one parental and one daughter strand (Fig). At the center of the fork, the parental duplex would be unwound and nucleotides would be added to the growing daughter strands. However, this model has a paradox, which can be summarized as follows:
1. Cellular DNA replication is semi conservative
2. Both daughter strands are extended simultaneously
3. The strands of the parental duplex are antiparellel
4. DNA polymerases extend DNA only in the 5’ → 3’ direction.


• How can simultaneous 5’→ 3’ elongation of both daughter strands occur at a replication fork when the parental templates have opposite polarity? This can be achieved by semidiscontinuous replication, where one strand is extended continuously and the other is synthesized discontinuously as a collection of short fragments. The mechanism of semidiscontinuous DNA replication can be formally expressed as leading strand – lagging strand model (Figure).


• The leading strand is the nascent strand, which is synthesized continuously in the direction of fork movement because its 3’ end is exposed to the DNA polymerase. The leading strand template is thus the forward template. The lagging strand is the nascent strand, which is synthesized discontinuously in the opposite direction to the fork movement because its 5’ end, the end that Leading strand – lagging strand model cannot be extended, is exposed to the DNA polymerase.


• The lagging strand is thus the retrograde template. The mechanism can be summarized as follows: as the replication fork moves forward and the leading strand is extended, a portion of retrograde template is exposed. DNA polymerase can then synthesize a small fragment of DNA, an Okazaki fragment, by moving backwards over the template in relation to the fork progression. The lagging strand is so called because the leading strand must be synthesized first to uncover the corresponding portion of lagging strand template.


• The enzyme dissociates from the template when it reaches the previously synthesized Okazaki fragment, by which time a further portion of retrograde template has been exposed. The enzyme can then reinitiate and synthesize a new Okazaki fragment. By repeating this back-stitching process over and over, the lagging strand would appear to grow in the 3’→5’ direction.