An Overview of DNA Replication

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Introduction

The process of DNA (Deoxyribonucleic acid) replication plays a very imperative role in providing genetic continuity from one generation to the succeeding one. Knowledge of the structure of the DNA began in 1869, with the discovery of nucleic acids. An accurate model of the DNA molecule was presented in 1952 by Rosalind Franklin, Francis Crick and James Watson. To reproduce, a cell must copy and transmit its genetic information (DNA), to all of its progeny. To do so, the cell must divide following three replication models: dispersive replication, conservative replication, and semi-conservative replication.

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The process involves a series of mechanisms such as unwinding, binding of RNA primase, elongation, and removal of primers, termination and DNA repair. This essay explores the process of DNA replication as a whole including: the definition of DNA replication, mechanism of DNA replication, evidences for semi-conservative DNA replication, and models of replication of prokaryotic DNA. DNA replication in molecular biology is defined as the biological process of producing two identical replicas of DNA from one original DNA molecule (Alberts et al.

, 2002).

Definition of DNA Replication

The process of DNA replication occurs during cell division, during the sub stage of interphase. The process is initiated before the end of the cell cycle in prokaryotes whereas in the eukaryotes, the cells can only initiate DNA replication at the beginning of the S phase. In humans and other eukaryotes, the process occurs in the cell nucleus, whereas it occurs in the cytoplasm in prokaryotes. The existing DNA is used as a template for the synthesis of new DNA strands.

During replication, one strand of DNA can replicate continuously and the other discontinuously or in piece. The continuously replicating strand of DNA is called the leading strand (the strand of nascent DNA being synthesized in the same direction as the direction as the growing replication fork), while the other strand is called the lagging strand (the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork.). When one strand of DNA replicates continuously and the other discontinuously, the process is called discontinuous replication. (Alberts et al., 2002).

The replication of DNA takes place under the control of DNA polymerase, an enzyme which in other words catalyzes the reaction. DNA polymerase, are a family of enzymes that carry out all forms of DNA replication. In general, they cannot initiate the synthesis of a new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a primer (a short fragment of RNA), must be created and paired with the template DNA strand. DNA polymerase adds a new strand of DNA by extending the 3’ end of an existing nucleotide chain via the creation of phosphodiester bonds. In eukaryotes, four types of polymerase enzymes that is: viz, alpha, delta, gamma and epsilon are used. In prokaryotes (E. coli), there are three major DNA polymerases: DNA polymerase I, II and III, which are involved in primary DNA replication and repair, exclusive repair, and major DNA polymerase respectively (Berg, Tymoczko, Stryer and Clarke, 2002).

During this crucial process, the synthesis of one strand takes place in 5-3 and that of the other strand in the opposite direction (3-5). The replication process may occur either in one direction or in both directions from the point of origin. Replication that proceeds in one direction only is called unidirectional replication, otherwise bidirectional replication. Based on the direction of replication, the type of replication can therefore be either unidirectional or bidirectional, whereas continuous or discontinuous based on the continuity. The point of initiation of DNA replication is called the origin. In prokaryotic cells, the rate of replication is 500 bases per second, whereas in eukaryotic cells, the rate of replication is 50 bases per second. Eukaryotic organisms have 100 to 3000 times more DNA than prokaryotes.

Models of DNA replication

There are three models which accurately explain the process of DNA replication: dispersive replication, conservative replication and semiconservative replication.

Dispersive DNA Replication

In this model of DNA replication, the two strands of parental DNA break at several points resulting into several pieces of DNA. Each piece replicates then the pieces are reunited randomly, resulting into the formation of two copies of DNA from one single copy. The new DNA molecules are hybrids which contain new DNA in patches. This method of DNA replication could not be accepted since it cannot be proven scientifically.

Conservative Replication

According to this model of DNA replication, two DNA molecules are formed from parental DNA. One copy has both parental strands and the other contains both the newly synthesized strands. This method is also not accepted as it cannot be proven experimentally.

Semiconservative Replication

This model of DNA replication was proposed by Watson and crick and according to it, both strands of parental DNA separate from each other. Each old strand synthesizes a new strand, thus each of the two resulting DNA molecules has one parental and one new strand. This is the most accepted model of DNA replication as there are several evidences backing it up.

Mechanism of DNA Replication

The semi-conservative model of DNA replication consists of six important phases: unwinding, binding of RNA primase, elongation, removal of primers, termination, and DNA repair.

The first stage of the process of DNA replication is the unwinding of the old strands of the parent DNA molecule. This involves the breaking of hydrogen bonds between bases of the two anti-parallel strands. The splitting occurs in places of the chains which are rich in A-T. This is because there are only two bonds between adenine and thymine whereas there are three hydrogen bonds between cytosine and guanine. The two strands of the double helix are first separated by enzymes. Then, each strand acts as a template for the synthesis of a new complimentary DNA molecule. The initiation point where the splitting starts is called the origin of replication. The resultant structure is called the replication fork.

The second stage which is the synthesis of RNA primer is essential for the initiation of DNA replication. RNA primer is synthesized by DNA template near the origin with the help of RNA primase. RNA primase attracts nucleotides which bind to the DNA nucleotides of the 3’-5’ strand due to hydrogen bonds between the bases. The RNA nucleotides are the starters for the binding of DNA nucleotides.

The third stage (elongation) proceeds in both directions, 5’-3’ and 3’-5’ template. The 3’-5’ proceeding daughter strand that uses a 5’-3’ template is called the leading strand because the DNA polymerase ‘a’ can read the template and continuously add nucleotides. The 3’-5’ template cannot be read by DNA polymerase ‘a’. The replication of this template is called lagging strand; in which the RNA primase add more RNA primers. DNA polymerase ‘a’ reads the template and lengthens the bubbles. The gap between two RNA primers is called Okazaki fragments. The RNA primers are necessary for DNA polymerase ‘a’ to bind nucleotides to the 3’ end of them. The daughter strand is elongated with the binding of more DNA nucleotides.

The RNA primers are removed or degraded by DNA polymerase which adds complimentary nucleotides to the gaps. DNA ligase enzyme adds phosphates in the remaining gaps of the phosphate-sugar backbone. Each new double helix is comprised of one old and one new chain. This is called semi-conservative replication.

The termination process takes place when the DNA polymerase reaches an end of the strands. After removal of the RNA primer, it’s impossible for DNA polymerase to seal the gaps because there is no primer. As a result, the end of the parental strand where the last primer binds is not replicated. This ends of the linear DNA consist of noncoding DNA that contains repeat sequences called telomeres. A part of this is removed in every cycle of DNA replication.

DNA repair is the final stage of DNA replication and is where the possible errors caused during the replication process are repaired by DNA repair mechanism. Enzymes like nucleases also play an important role of removing the wrong nucleotides and the DNA polymerase fills the gaps.

Models for Replication of Prokaryotic DNA

Prokaryotes such as bacteria have circular DNA hence replication in them differs from that of eukaryotes who have linear DNA molecules. Suggested models for replication of circular DNA include: Cairns model and rolling circle model.

The Cairns model of DNA replication was proposed in 1963, and explains mechanism of DNA replication in double stranded circular DNA of bacteria. According to this model, circular DNA replication occurs in steps:

Unwinding of DNA in which the double stranded circular DNA starts separation at the origin. Two points are established. As the growing points move apart, the unwinding of the DNA double strand takes place.

Initiation of replication; at the point of origin, bidirectional replication is initiated. Both strands of DNA are replicated leading to further unwinding of the DNA double strand, resulting to the formation of a torque.

Super twisting: the torque leads to super twisting of DNA strand. As a result, super twisting, one of the strands is cut making the parental strands to rotate freely. The cut is made by a swiveling protein which relieves the strain.

Sealing of broken points: the breaks are sealed by swiveling proteins and thus the replication is over (‘Cairns model’, n.d.)

Rolling circle model of DNA replication was proposed in 1968. This model explains mechanism of DNA replication in in single stranded circular DNA of viruses. It involves:

Synthesis of new strand: first the chromosome becomes double stranded by synthesis of a negative strand. The original strand is positive and the negative strand is synthesized inside the positive parental strand.

Cut in outer strand: the negative or inner strand remains a close circle and the positive strand is nicked at a specific site by endonuclease enzyme. This enzyme recognizes a particular sequence at this point thus a linear strand with 3’- and 5’- is created.

Formation of tail: the original positive strand comes out in the form of a tail of a single linear strand as a consequence of rolling circle.

Synthesis of new strand: the synthesis of new strands takes place along the parental strand at the tail end in 3’-5’ direction.

Cutting of tail: the tail is then cut off into a linear segment by endonuclease. The linear segment becomes circular by joining two end with the help of a ligase enzyme. As a result, a new circular molecule is formed which becomes a new rolling circle and replicates further (Gilbert and Dressler, 1968).

Conclusion

In conclusion, DNA replication is a crucial process involving a series of phases in all living organisms such as the unwinding of the DNA molecule, formation of RNA primers, elongation, removal of primers, termination and DNA repair; that ensures the continuous transmission of genetic information from one generation to the next. Moreover, there are various models which accurately explain the process of DNA replication including dispersive, conservative and semi-conservative models. In addition, some evidences of the semi-conservative model of DNA replication include Taylors experiment, cairns experiment, and Meselson experiment. DNA replication in prokaryotic organisms occurs via two models, that is: the rolling circle model and the Cairns’ model.