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Tuesday, 23 April 2013

DNA Replication

DNA Replication – A brief overview
DNA replication is the basis for biological inheritance. It is a fundamental process occurring in all living organisms to copy their DNA. This process is ‘semiconservative’ in that each strand of the original double-stranded DNA molecule serves as a template for the reproduction of the complementary strand. Hence, the process of DNA replication yields two identical DNA molecules from a single double-stranded molecule. Cellular proof-reading and error-checking mechanisms ensure nearly perfect fidelity of the DNA copies. DNA replication commences at specific locations in the genome called “origins.” The DNA unwinds at the origin to form a replication fork.

DNA replication can proceed in only one direction, from the top of the DNA strand to the bottom. Because the strands that form the DNA double helix align in an antiparallel fashion with the top of one strand juxtaposed to the bottom of the other strand, only one strand at each replication fork has the proper orientation (bottom-to-top) to direct the assembly of a new strand in the top-to-bottom direction. For this leading strand, DNA replication proceeds continuously in the direction of the advancing replication fork.

DNA replication cannot proceed along the lagging strand, i.e. the strand with the top-to-bottom orientation, until the replication bubble expands enough to expose a sizeable stretch of DNA. DNA replication then moves away from the advancing replication fork. It can proceed only a short distance along the ‘top-to-bottom’ oriented strand before the replication process must stop and wait for more of the parent DNA strand to be unwound.
DNA Replication – The Replisome

The replisome is a complex molecular machine that carries out replication of DNA. It is comprised of a number of subcomponents, each performing a specific function during the process of replication. Helicase is an enzyme which breaks the hydrogen bonds between the two strands of DNA, thus separating the strands ahead of DNA synthesis. As helicase unwinds the double helix, it induces the formation of supercoils in other areas of the DNA.

Gyrase relaxes and undoes the supercoiling which has been caused by the helicase by cutting the DNA strands, allowing it to rotate and release the supercoil, and then rejoining the strands. Gyrase is most commonly located upstreak of the replication fork -- where the supercoils are being formed.

Primase adds complementary RNA primers to a DNA strand to begin Okazaki fragments. In addition, because DNA Polymerae can only continue (but not begin) a strand, Primase begins the leading strand as well.

DNA polymerase III is comprised of two catalytic cores -- one for replication of the leading strand and one for the lagging strand. DNA polemerase III, however, cannot stay on the DNA strand long enough to efficiently replicate a daughter strand. Hence, DNA polymerase III stays on the strands via a dimer beta clamp which contains three subunits that come together to enclose the strand -- ensuring that DNA polymerase III will remain on the strand for a few thousand nucleotides as opposed to a few hundred.

DNA polymerase I removes the RNA primers set by Primase and completes the Okazaki fragments. Because there is such a small gap remaining after the action of DNA polymerase I has continued the strand of the Okazaki fragment, ligase is required to fill in the gap. The two ends of the Okazaki fragments are subsequently connected by covalent bonds.

Single-strand binding proteins bind to the exposed bases in an effort to counteract their instability and prevent the single-strand DNA from hydrogen-bonding to itself to form dangerous hairpin structures.

DNA polymerases contain a ‘proofreading’ mechanism, commonly referred to as ‘exonuclease activity’. This removes nucleotides that have been mistakenly added.

DNA Replication – Signature of Design

DNA Replication stands as a fundamental challenge to those who seek to hold to a Darwinian worldview. As the process by which biological information is copied and passed on to succeeding generations, the mechanism is fundamental to the process of self-replication of cells. Yet self-replication of cells is necessary for the operation of any selective process such as natural selection. Thus, to attempt to explain the immense sophistication of this mechanism with reference to natural selection requires one to presuppose the existence of the very thing they wish to explain. Because of its extremely sophisticated nature, most biochemists previously reckoned that the system arose once, prior to the origin of the last universal common ancestor. In addition, many biochemists have long regarded the close functional similarity of DNA replication observed in all life as evidence for the single origin of DNA replication. Yet in 1999 researchers from the National Institutes of Health demonstrated that the core enzymes involved in the DNA replication machinery of bacteria and archae/eukaryotes (the two major trunks of the evolutionary tree of life) did not in fact share a common evolutionary origin. It thus appears as if two identical DNA replication systems have emerged independently in bacteria and archae -- after these two evolutionary lineages supposedly diverged from the last universal common ancestor.

It is phenomenal to think that this engineering marvel evolved a single time, let alone twice. There exists no obvious reason for DNA replication to take place by a semiconservative, RNA primer-dependent, bidirectional mechanism that depends on leading and lagging strands to produce DNA daughter molecules. Even if DNA replication could have evolved independently on two separate occasions, it is reasonable to expect that fundamentally different mechanisms would emerge for bacteria and the archae/eukaryotes given their idiosyncrasies. But, they did not.