6+Repair+and+Recombination

DNA Repair Overview

DNA is relatively stable but can be damaged by various factors. Damage can arise from:

• Thermal Fluctuations: Frequent thermal changes can disrupt base pairing in DNA, potentially leading to mispairing during replication.

• Metabolic Accidents: Unintended oxidations from cellular metabolism can lead to various alterations in DNA structure, such as the formation of 8-oxoguanine, which can mispair with adenine during replication.

• Radiation: Ultraviolet (UV) radiation can lead to the formation of thymine dimers, causing distortions in the DNA helix, while X-ray radiation can cause breaks in the sugar-phosphate backbone of the DNA.

• Environmental Toxins: These agents, often categorized as mutagens or carcinogens, can cause mutations by chemically altering DNA bases or interfering with DNA replication.

It is important to differentiate DNA damage from replication errors, as the former indicates a physical alteration to the DNA molecule, while the latter refers to mistakes that occur during DNA synthesis.

DNA Damage Sources

• Thermal Fluctuations: These fluctuations frequently occur in the cellular environment, potentially disrupting the hydrogen bonds that hold DNA base pairs together.

• Metabolic Accidents: Reactive oxygen species (ROS) generated as byproducts of metabolism can oxidize DNA components, leading to structural changes that can result in mutations if not repaired.

• Radiation:

  • UV Radiation: Causes the formation of covalent linkages between adjacent thymine bases, resulting in thymine dimers that block DNA replication.

  • X-Ray Radiation: High-energy radiation can cause both single-strand breaks (SSBs) and double-strand breaks (DSBs), which are more critical as they affect both strands of the DNA helix.

• Environmental Toxins: Sources include chemicals found in tobacco smoke, certain dyes, and heavy metals. These compounds can interact with DNA and lead to various forms of damage, such as alkylation or cross-linking.

Mechanism of DNA Repair

Cells possess highly efficient mechanisms to identify and repair approximately 99.9% of DNA damage. This remarkable efficiency is due to a combination of specialized repair proteins and the use of template guidance, which ensures the correct sequence is restored following repair processes. Double-stranded DNA is utilized universally for this purpose due to its stability and ability to act as a template for accurate repair.

Common DNA Repair Mechanisms

1. Base Excision Repair (BER)

   • A critical pathway that repairs damaged bases within DNA.

   • DNA Glycosylases: Enzymes that identify specific damaged bases and cleave the bond between the base and the sugar, effectively flipping the damaged base out of the DNA strand. There are at least six distinct glycosylases, each with specificity for different types of base damage.

   • Following base removal, additional enzymes act:

     • AP Endonuclease: Cuts one side of the sugar-phosphate backbone after the base is excised, creating a single-stranded break.

     • Phosphodiesterase: Cleaves the remaining sugar-phosphate bond on the opposite side.

     • DNA Polymerase: Synthesizes a replacement base to fill the gap, using the undamaged strand as a template.

     • DNA Ligase: Seals the nicks in the sugar-phosphate backbone after the replacement base is inserted.

2. Nucleotide Excision Repair (NER)

   • Targets extensive, bulky distortions in the DNA structure caused by factors like UV-induced thymine dimers.

   • A multi-enzyme complex binds to the damaged DNA and makes cuts on either side of the lesion, removing a short single-stranded section.

   • A helicase unwinds the DNA, allowing DNA polymerase to synthesize a new strand from the remaining template, followed by sealing with DNA ligase.

3. Double-Strand Break Repair (DSBR)

   • Double-strand breaks are more dangerous than single-strand breaks since both strands of DNA are compromised, risking the loss of genetic material.

   • Non-Homologous End Joining (NHEJ): A repair pathway that rejoins the broken ends of DNA without requiring homology. While rapid, this method can lead to errors, often resulting in deletion mutations.

   • Homologous Recombination (HR): Preserves the original DNA sequence as it uses a sister chromatid as a template for repair and primarily occurs in S and G2 phases of the cell cycle. This process involves base pairing and exchange between homologous regions, playing a significant role in meiosis and maintaining genomic stability.

Evolution and Repair Processes

Connections Between Processes

• Transposition and Site-Specific Recombination: Include gene movement and integration into the genome without relying on sequence homology—common in various organisms, including bacteria and viruses, which rely on site recognition, cutting, excision, and insertion mechanisms.

• All forms of DNA manipulation, whether repair or recombination, use a set of conserved enzymes (e.g., endonucleases, exonucleases, helicases) that facilitate these processes, with the ability to maintain genomic integrity being crucial for cellular health and reproduction.

Importance of Mobile Genetic Elements (MGE)

• Mobile Genetic Elements account for about 45% of the human genome and significantly contribute to genetic variability.

• These MGEs can carry additional genes, leading to the potential for new traits or functions, and may also alter surrounding sequences, further enhancing genetic diversity and adaptability.

• Retroviruses and transposable elements, while behaving differently, also represent mechanisms of genomic alteration and stability, emphasizing the complexity of genetic dynamics in evolutionary contexts.