nucleotide excision repair

Examples of nucleotide excision repair in the following topics:

• DNA Repair

  • If it is the correct base, the next nucleotide is added.
  • The enzymes recognize the incorrectly-added nucleotide and excise it; this is then replaced by the correct base.
  • In another type of repair mechanism, nucleotide excision repair, enzymes replace incorrect bases by making a cut on both the 3' and 5' ends of the incorrect base .
  • Nucleotide excision repairs thymine dimers.
  • In normal cells, they are excised and replaced.

• DNA Replication in Prokaryotes

  • The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached.
  • DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.
  • It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide.
  • This means that it cannot add nucleotides if a free 3'-OH group is not available.
  • The replication fork moves at the rate of 1000 nucleotides per second.

• Bone Grafting

  • Bone grafting is a surgical procedure that replaces missing bone in order to repair bone fractures.
  • Bone grafting is a surgical procedure that replaces missing bone in order to repair bone fractures that are extremely complex, pose a significant health risk to the patient, or fail to heal properly .
  • In some cases bone may need to be surgically excised, such as cancer (osteosarcoma).
  • Bone grafting is also used to fuse joints to prevent movement, repair broken bones that have bone loss, and repair broken bone that has not yet healed.

• Nanoarchaeum and Aciduliprofundum

  • Its genome is only 490,885 nucleotides long; the smallest non-viral genome ever sequenced next to that of Candidatus Carsonella ruddii.
  • N. equitans genome consists of a single circular chromosome, and lacks almost all genes required for synthesis of amino acids, nucleotides, cofactors, and lipids, but encodes everything needed for repair and replication. 95% of its DNA encodes for proteins for stable RNA molecules.
  • Nanoarchaeum cannot synthesize most nucleotides, amino acids, lipids, and cofactors.
  • However, unlike many parasitic microbes, Nanoarchaeum has many DNA repair enzymes, as well as everything necessary to carry out DNA replication, transcription, and translation.

• Generalized Recombination and RecA

  • In homologous recombination, a type of genetic recombination, nucleotide sequences are exchanged between two similar molecules of DNA.
  • Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA.
  • Homologous recombination is a major DNA repair process in bacteria.
  • Double-strand DNA breaks in bacteria are repaired by the RecBCD pathway of homologous recombination .
  • This unzipping continues until RecBCD encounters a specific nucleotide sequence (5'-GCTGGTGG-3') known as a Chi site.

• Slipped-Strand Mispairing

  • This RecA-independent mechanism can transpire during either DNA replication or DNA repair and can be on the leading or lagging strand and can result in an increase or decrease in the number of short repeat sequences.
  • The short repeat sequences are 1 to 7 nucleotides and can be homogeneous or heterogeneous repetitive DNA sequences.
  • Start (ATG) is the start codon in which the ribosome initiates translation of nucleotide sequence into amino acids, and (-10 -35) is the promoter which is the binding site for the RNAP to initiate transcription of DNA into RNA.

• The Secondary & Tertiary Structures of DNA

  • Complementary primary nucleotide structures for each strand allowed intra-strand hydrogen bonding between each pair of bases.
  • Polymerization of nucleotides takes place by the phosphorylation reaction described by the following equation.
  • One of the benefits of the double stranded DNA structure is that it lends itself to repair, when structural damage or replication errors occur.
  • Inspection-repair enzymes detect such deformations, and use the undamaged nucleotide at that site as a template for replacing the damaged unit.
  • These repairs reduce errors in DNA structure from about one in ten million to one per trillion.

• Vectors for Genomic Cloning and Sequencing

  • Modern plasmids generally have many more features, notably including a "multiple cloning site" which includes nucleotide overhangs for insertion of an insert, and multiple restriction enzyme consensus sites to either side of the insert.
  • The vectors can be extracted from the bacteria, and the multiple cloning sites can be cut by restriction enzymes to excise the hundredfold or thousandfold amplified insert.

• Genome Evolution

  • Mutations can result in the addition or deletion of one or more nucleotide bases.
  • The "cut-and-paste" mechanism works by excising DNA from one place in the genome and inserting itself into another location in the code.
  • There are many mechanisms by which a functional gene can become a pseudogene including the deletion or insertion of one or multiple nucleotides.

• Chromosomes and DNA Replication in the Archaea

  • It is structurally similar to viral RNA dependent RNA polymerases, reverse transcriptases, cyclic nucleotide generating cyclases, and DNA polymerases involved in DNA replication and repair.