origin of replication

Examples of origin of replication in the following topics:

• DNA Replication in Eukaryotes

  • There are specific chromosomal locations called origins of replication where replication begins.
  • Because two helicases bind, two replication forks are formed at the origin of replication; these are extended in both directions as replication proceeds creating a replication bubble.
  • Eukaryotic chromosomes have multiple origins of replication, which initiate replication almost simultaneously.
  • Each origin of replication forms a bubble of duplicated DNA on either side of the origin of replication.
  • A replication fork is formed by the opening of the origin of replication; helicase separates the DNA strands.

• DNA Replication in Prokaryotes

  • There are specific nucleotide sequences called origins of replication where replication begins.
  • In E. coli, which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences.
  • The origin of replication is recognized by certain proteins that bind to this site.
  • Two replication forks at the origin of replication are extended bi-directionally as replication proceeds.
  • A replication fork is formed when helicase separates the DNA strands at the origin of replication.

• Chromosomes and DNA Replication in the Archaea

  • The circular chromosomes contain multiple origins of replication, using DNA polymerases that resemble eukaryotic enzymes.
  • DNA replication, similar in all systems, involves initiation, elongation, and termination.
  • The replication of DNA, beginning at the origins of replication present on the circular chromosomes, requires initiator proteins.
  • The recruitment of additional proteins by way of the initiator proteins allows the separation of the circular DNA and results in the formation of a bubble.
  • The DNA replication system in Archaea, similar to all systems, requires a free 3'OH group before synthesis is initiated.

• Telomere Replication

  • As DNA polymerase alone cannot replicate the ends of chromosomes, telomerase aids in their replication and prevents chromosome degradation.
  • Every RNA primer synthesized during replication can be removed and replaced with DNA strands except the RNA primer at the 5' end of the newly synthesized strand.
  • After sufficient rounds of replication, all the telomeric repeats are lost, and the DNA risks losing coding sequences with subsequent rounds.
  • Once the 3' end of the lagging strand template is sufficiently elongated, DNA polymerase adds the complementary nucleotides to the ends of the chromosomes; thus, the ends of the chromosomes are replicated.
  • A simplified schematic of DNA replication where the parental DNA (top) is replicated from three origins of replication, yielding three replication bubbles (middle) before giving rise to two daughter DNAs (bottom).

• Inhibiting Nucleic Acid Synthesis

  • Other antimicrobial drugs interfere with DNA replication, the biological process that occurs in all living organisms and copies their DNA and is the basis for biological inheritance.
  • In a cell, DNA replication begins at specific locations in the genome, called "origins. " Uncoiling of DNA at the origin, and synthesis of new strands, forms a replication fork.
  • DNA replication, like all biological polymerization processes, proceeds in three enzymatically catalyzed and coordinated steps: initiation, elongation and termination.
  • Any of the steps in the process of DNA replication can be targeted by antimicrobial drugs.
  • Portions of the enzyme were made transparent so as to make the path of RNA and DNA more clear.

• Basics of DNA Replication

  • In conservative replication, the two original DNA strands,  known as the parental strands, would re-basepair with each other after being used as templates to synthesize new strands; and the two newly-synthesized strands, known as the daughter strands, would also basepair with each other; one of the two DNA molecules after replication would be "all-old" and the other would be "all-new". 
  • In dispersive replication, after replication both copies of the new DNAs would somehow have alternating segments of parental DNA and newly-synthesized DNA on each of their two strands.
  • This suggested either a semi-conservative or dispersive mode of replication.
  • The three suggested models of DNA replication.
  • Grey indicates the original parental DNA strands  or segments and blue indicates newly-synthesized daughter DNA strands or segments.

• The Secondary & Tertiary Structures of DNA

  • Once the double stranded DNA is exposed, a group of enzymes act to accomplish its replication.
  • Because of the directional demand of the polymerization, one of the DNA strands is easily replicated in a continuous fashion, whereas the other strand can only be replicated in short segmental pieces.
  • Separation of a portion of the double helix takes place at a site called the replication fork.
  • As replication of the separate strands occurs, the replication fork moves away (to the left in the diagram), unwinding additional lengths of DNA.
  • In contrast, the replication fork moves toward the 3'-end of the original green strand, preventing continuous polymerization of a complementary new red strand.

• Mu: A Double-Stranded Transposable DNA Bacteriophage

  • It can then use transposition to initiate its viral DNA replication.
  • Once the viral DNA is inserted into the bacteria, the Mu's transposase protein/enzyme in the cell recognizes the recombination sites at the ends of the viral DNA (gix-L and gix-R sites) and binds to them, allowing the process of replicating the viral DNA or embedding it into the host genome.
  • Mu phage transposition is the best known example of replicative transposition.
  • Replicative transposition is a mechanism of transposition in molecular biology, proposed by James A.
  • Shapiro in 1979, in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element.

• Selection

  • The use of the word cloning refers to the fact that the method involves the replication of a single DNA molecule starting from a single living cell to generate a large population of cells containing identical DNA molecules.
  • This will generate a population of organisms in which recombinant DNA molecules are replicated along with the host DNA.
  • This single cell can then be expanded exponentially to generate a large amount of bacteria, each of which contain copies of the original recombinant molecule.
  • Molecular cloning is similar to polymerase chain reaction (PCR) in that it permits the replication of a specific DNA sequence.
  • The fundamental difference between the two methods is that molecular cloning involves replication of the DNA in a living microorganism, while PCR replicates DNA in an in vitro solution, free of living cells.

• Elements of Life

  • There is no "standard model" of the origin of life.
  • A fundamental question is about the nature of the first self-replicating molecule.
  • Since replication is accomplished in modern cells through the cooperative action of proteins and nucleic acids, the major schools of thought about how the process originated can be broadly classified as "proteins first" and "nucleic acids first. " The principal thrust of the "nucleic acids first" argument is as follows:
  • The polymerization of nucleotides into random RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis).
  • Biologist John Desmond Bernal coined the term biopoiesis for this process,and suggested that there were a number of clearly defined "stages" that could be recognized in explaining the origin of life: