DNA Damage and Repair Mechanisms

Types of DNA Damage

DNA is constantly exposed to damaging agents that can alter its structure and integrity. The nature of these structural changes determines which repair systems are activated to maintain genomic stability.

• Minor Changes: Do not grossly distort the overall DNA structure. These can be detected during transcription or replication when DNA strands are separated.

• Major Distortion: Causes physical impediment to replication or transcription, such as bulky adducts or crosslinks.

• Strand Breaks: Single-strand breaks (SSB) are typically repaired by ligation, while double-strand breaks (DSB) are more severe and can lead to extensive DNA loss if not properly repaired.

Overview of DNA Repair Systems

Cells employ multiple repair pathways to correct different types of DNA damage. The main systems include:

• I. Direct Reversal: Repairs damage without DNA synthesis. Example: photoreactivation of pyrimidine dimers.

• II. Excision Repair: Damaged DNA is removed and resynthesized using the complementary strand as a template. Subtypes include:

  • Base Excision Repair (BER)

  • Nucleotide Excision Repair (NER)

  • Mismatch Excision Repair (MMR)

• III. Recombination Repair: Uses the homologous chromosome as a template for accurate repair, especially for DSBs.

• IV. Non-Homologous End Joining (NHEJ): Directly joins broken DNA ends; error-prone and can lead to mutations.

• V. Translesion Synthesis: DNA synthesis occurs without a template, allowing replication past lesions but is highly error-prone.

Direct Reversal Repair

Some organisms, such as bacteria and lower eukaryotes, can directly reverse certain types of DNA damage using specific enzymes.

• Photoreactivation: Photolyase enzyme uses light energy to break the bonds of pyrimidine dimers caused by ultraviolet (UV) irradiation.

• Dark Repair: Refers to repair mechanisms that do not require light.

Example:

UV-induced thymine dimers are reversed by photolyase in the presence of visible light in bacteria, but not in mammals.

Excision Repair Pathways

Excision repair involves removal of damaged DNA followed by resynthesis using the undamaged strand as a template.

• Base Excision Repair (BER): Removes small, non-helix-distorting base lesions. DNA glycosylases recognize and remove damaged bases, followed by endonuclease cleavage and DNA polymerase filling.

• Nucleotide Excision Repair (NER): Removes bulky, helix-distorting lesions such as pyrimidine dimers. Involves recognition, excision of a short single-stranded DNA segment, and resynthesis.

  • In E. coli: UvrA, UvrB, and UvrC proteins coordinate lesion recognition and excision.

  • In mammals: XP genes (XPA, XPB, XPC, etc.) are involved; defects cause Xeroderma Pigmentosum, leading to extreme UV sensitivity.

• Mismatch Excision Repair (MMR): Corrects base mispairings that escape proofreading during DNA replication. The system distinguishes the newly synthesized strand (often by nicks or methylation status) and excises the incorrect segment.

Table: Comparison of Excision Repair Pathways

Double-Strand Break (DSB) Repair

DSBs are among the most lethal forms of DNA damage. Two main pathways exist:

• Homologous Recombination Repair (HRR): Uses a homologous chromosome or sister chromatid as a template for accurate repair. Predominant in S and G2 phases of the cell cycle.

• Non-Homologous End Joining (NHEJ): Directly ligates broken DNA ends without a template. Can occur throughout the cell cycle but is error-prone.

Equation:

Generalized repair synthesis:

Translesion Synthesis

When replication machinery encounters unrepaired lesions, specialized DNA polymerases can synthesize DNA across the damage. This process is error-prone and can introduce mutations.

• Translesion Polymerases: Can bypass bulky lesions but lack proofreading activity.

Transposable Elements

Definition and Types

Transposable elements (TEs) are DNA sequences capable of moving to new positions within the genome. They contribute to genetic diversity and genome evolution.

• Class I: Retrotransposons

  • Move via an RNA intermediate (copy-and-paste mechanism).

  • Encode reverse transcriptase.

  • Examples: LINEs, SINEs, LTR retrotransposons.

• Class II: DNA Transposons

  • Move via a DNA intermediate (cut-and-paste mechanism).

  • Encode transposase enzyme.

Table: Major Transposable Element Types in Human Genome

Structure and Mechanism

• Terminal Inverted Repeats (TIRs): Flank DNA transposons and are recognized by transposase.

• Target Site Duplications: Created during integration due to staggered cuts in the target DNA.

• Autonomous vs. Non-autonomous: Autonomous elements encode the necessary enzymes for transposition; non-autonomous elements rely on enzymes from other TEs.

Transposition Mechanisms

• Cut-and-Paste (DNA Transposons): The transposon is excised and inserted into a new site, leaving behind a double-strand break.

• Copy-and-Paste (Retrotransposons): The element is transcribed into RNA, reverse transcribed into DNA, and inserted elsewhere, increasing copy number.

Example:

LINE-1 elements in humans are active retrotransposons that can cause insertional mutations.

Genomic Impact and Applications

• TEs can disrupt gene function by inserting into coding or regulatory regions.

• They contribute to genome rearrangements, duplications, and deletions via recombination between TE copies.

• TEs are used as tools in genetic engineering and mutagenesis studies.

Summary Table: DNA Repair Pathways and Transposable Elements

Additional info: Some explanations and table entries were expanded for clarity and completeness based on standard genetics curriculum.