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.

• 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).

• Binary Fission

  • The starting point of replication, the origin, is close to the binding site of the chromosome at the plasma membrane .
  • Replication of the DNA is bidirectional, moving away from the origin on both strands of the loop simultaneously.
  • As the new double strands are formed, each origin point moves away from the cell wall attachment toward the opposite ends of the cell.
  • FtsZ and tubulin are homologous structures derived from common evolutionary origins.
  • While both proteins are found in extant organisms, tubulin function has evolved and diversified tremendously since evolving from its FtsZ prokaryotic origin.

• 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.

• Evolution of Viruses

  • Although biologists have accumulated a significant amount of knowledge about how present-day viruses evolve, much less is known about how viruses originated in the first place.
  • One possible hypothesis, called devolution or the regressive hypothesis, proposes to explain the origin of viruses by suggesting that viruses evolved from free-living cells.
  • A third hypothesis posits a system of self-replication similar to that of other self-replicating molecules, probably evolving alongside the cells they rely on as hosts; studies of some plant pathogens support this hypothesis.
  • As technology advances, scientists may develop and refine further hypotheses to explain the origin of viruses.
  • These researchers hope to one day better understand the origin of viruses, a discovery that could lead to advances in the treatments for the ailments they produce.

• The DNA Double Helix

  • The two strands of the helix run in opposite directions, so that the 5′ carbon end of one strand faces the 3′ carbon end of its matching strand.
  • This antiparallel orientation is important to DNA replication and in many nucleic acid interactions.
  • Only certain types of base pairing are allowed.
  • During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.
  • Most of the time when this happens the DNA is able to fix itself and return the original base to the sequence.

• Gene Duplications and Divergence

  • Replication slippage is an error in DNA replication, which can produce duplications of short genetic sequences.
  • During replication, DNA polymerase begins to copy the DNA, and at some point during the replication process, the polymerase dissociates from the DNA and replication stalls.
  • Replication slippage is also often facilitated by repetitive sequence but requires only a few bases of similarity.
  • Duplication creates genetic redundancy and if one copy of a gene experiences a mutation that affects its original function, the second copy can serve as a 'spare part' and continue to function correctly.
  • This leads to a neutral "subfunctionalization" model, in which the functionality of the original gene is distributed among the two copies.

• DNA Repair

  • Most mistakes during replication are corrected by DNA polymerase during replication or by post-replication repair mechanisms.
  • Most of the mistakes during DNA replication are promptly corrected by DNA polymerase which proofreads the base that has just been added .
  • Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as mismatch repair .
  • In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has been completed.
  • In mismatch repair, the incorrectly-added base is detected after replication.

• Strategies Used in Sequencing Projects

  • The chain termination method involves DNA replication of a single-stranded template with the use of a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single unit, of DNA.
  • Every time a ddNTP is incorporated in the growing complementary strand, it terminates the process of DNA replication, which results in multiple short strands of replicated DNA that are each terminated at a different point during replication.
  • When the reaction mixture is processed by gel electrophoresis after being separated into single strands, the multiple, newly-replicated DNA strands form a ladder due to their differing sizes.
  • Reading the gel on the basis of the color of each band on the ladder produces the sequence of the template strand .
  • Originally, shotgun sequencing only analyzed one end of each fragment for overlaps.