DNA replication is the process of creating two identical copies from one original DNA molecule. DNA is composed of two strands and each strand of the original DNA molecule serves as template for the production of the complementary strand. Cellular proofreading and error-checking mechanisms ensure near perfect DNA replication. In a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new strands results in replication forks growing bidirectional from the origin. A number of proteins are associated with the replication fork which helps in terms of the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new DNA by adding complementary nucleotides to the template strand.
DNA polymerases are a family of enzymes that carry out all forms of DNA replication. DNA polymerases in general cannot initiate synthesis of new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer, must be created and paired with the template DNA strand.
DNA polymerase synthesizes a new strand of DNA by extending the 3′ end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds. In general, DNA polymerases are highly accurate. In addition, some DNA polymerases also have proofreading ability; they can remove nucleotides from the end of a growing strand in order to correct mismatched bases. Finally, post-replication mismatch repair mechanisms monitor the DNA for errors that had occurred during DNA replication, being capable of distinguishing mismatches in the newly synthesized DNA strand from the original strand sequence.
DNA Replication Process:
Initiation of DNA Replication:
- For a cell to divide, it must first replicate its DNA.This process is initiated at particular points in the DNA, known as “origins”, which are targeted by initiator proteins. Sequences used by initiator proteins tend to be “AT-rich” (rich in adenine and thymine bases), because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair) which are easier to unzip. Once the origin has been located, these initiators recruit other proteins and form the pre-replication complex, which unzips the double-stranded DNA.
Extension of DNA Replication:
- All known DNA replication systems require a free 3′ hydroxyl group before synthesis can be initiated (Important note: DNA is read in 3′ to 5′ direction whereas a new strand is synthesised in the 5′ to 3′ direction—this is often confused)
- An enzyme called Helicase separates the DNA strands. Once the two strands are separated, primase adds RNA primers to the template strands. The leading strand receives one RNA primer while the lagging strand receives several. The leading strand is continuously extended from the primer by a high processivity, replicative DNA polymerase, while the lagging strand is extended discontinuously from each primer, forming Okazaki fragments. RNase removes the primer RNA fragments, and a low processivity DNA polymerase distinct from the replicative polymerase enters to fill the gaps. When this is complete, a single nick on the leading strand and several nicks on the lagging strand can be found. Ligase works to fill these nicks in, thus completing the newly replicated DNA molecule.
- The leading strand is the strand of nascent DNA which is being synthesized in the same direction as the growing replication fork. A polymerase “reads” the leading strand template and adds complementary nucleotides to the nascent leading strand on a continuous basis.
- The polymerase involved in leading strand synthesis is DNA polymerase III (DNA Pol III) in prokaryotes. In human cells the leading and lagging strands are synthesized by Pol ε and Pol δ, respectively, within the nucleus and Pol γ in the mitochondria. Pol ε can substitute for Pol δ in special circumstances.
- The lagging strand is the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated than that of the leading strand.
- The lagging strand is synthesized in short, separated segments. On the lagging strand template, a primase “reads” the template DNA and initiates synthesis of a short complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the fragments of DNA are joined together by DNA ligase.
- In eukaryotes, primase is intrinsic to Pol α. DNA polymerase III (in prokaryotes) or Pol δ/Pol ε (in eukaryotes) is/are responsible for extension of the primed segments. Primer removal in eukaryotes is also performed by Pol δ. In prokaryotes, primer removal is performed by DNA polymerase I, which “reads” the fragments, removes the RNA using its flap endonuclease domain (RNA primers are removed by 5′-3′ exonuclease activity of polymerase I, and replaces the RNA nucleotides with DNA nucleotides.)
DNA Replication Proteins:
Function in DNA replication
|DNA Helicase||Unwinds the DNA double helix at the Replication Fork.|
|DNA Polymerase||Builds a new duplex DNA strand by adding nucleotides in the 5′ to 3′ direction. Also performs proof-reading and error correction|
|Single-Strand Binding Proteins||Bind to ssDNA and prevent the DNA double helix from re-annealing after DNA helicase unwinds it thus maintaining the strand separation.|
|Topoisomerase||Relaxes the DNA from its super-coiled nature.|
|DNA Gyrase||Relieves strain of unwinding by DNA helicase; this is a specific type of topisomerase|
|DNA Ligase||Re-anneals the semi-conservative strands and joins Okazaki Fragments of the lagging strand.|
|Primase||Provides a starting point of RNA (or DNA) for DNA polymerase to begin synthesis of the new DNA strand.|
|Telomerase||Lengthens telomeric DNA by adding repetitive nucleotide sequences to the ends of eukaryotic chromosomes.|
References for DNA Replication: