4.4 DNA damage and repair mechanisms
5 min read•august 16, 2024
DNA damage is a constant threat to our genetic material. From everyday cellular processes to environmental factors, our DNA faces numerous challenges. This section explores the various types of DNA damage and the intricate repair mechanisms cells employ to maintain genomic integrity.
Understanding DNA damage and repair is crucial for grasping how cells preserve their genetic information. These processes play vital roles in preventing mutations, cancer, and , highlighting the importance of DNA maintenance in overall cellular health.
DNA Damage Types and Causes
Endogenous and Exogenous Sources of DNA Damage
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- DNA damage occurs through endogenous sources (cellular processes) or exogenous sources (environmental factors) leading to various DNA lesions
- Endogenous sources include reactive oxygen species from cellular metabolism and spontaneous hydrolysis of DNA
- Exogenous sources encompass ultraviolet (UV) radiation, ionizing radiation, and chemical mutagens (cigarette smoke)
Chemical Modifications and Structural Alterations
- Base modifications alter the chemical structure of nucleotides potentially causing mutations
- Oxidation transforms guanine to 8-oxoguanine, which can mispair with adenine
- Alkylation adds methyl or ethyl groups to bases (O6-methylguanine)
- Deamination converts cytosine to uracil, changing base-pairing properties
- Single-strand breaks (SSBs) and double-strand breaks (DSBs) disrupt the DNA backbone
- SSBs often result from oxidative damage or aborted topoisomerase activity
- DSBs can be caused by ionizing radiation or certain chemotherapeutic agents (etoposide)
- Pyrimidine dimers form by UV radiation distorting the DNA helix
- Cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts are common UV-induced lesions
- These dimers interfere with replication and transcription by blocking polymerase progression
Complex DNA Lesions and Replication Errors
- DNA-protein crosslinks occur when proteins become covalently bound to DNA
- Induced by certain chemotherapeutic agents (cisplatin) or ionizing radiation
- Interfere with DNA metabolism and can lead to replication fork collapse
- Interstrand crosslinks (ICLs) form covalent bonds between opposite DNA strands
- Caused by bifunctional alkylating agents (nitrogen mustards) or psoralen plus UV light
- Prevent strand separation during replication and transcription, highly toxic to cells
- Incorrect nucleotide incorporation during DNA replication leads to base mismatches
- Can result from polymerase errors or presence of damaged or modified bases
- If left unrepaired, mismatches can lead to point mutations in subsequent replication cycles
DNA Repair Mechanisms
Excision Repair Pathways
- (BER) removes and replaces damaged bases
- DNA glycosylases recognize and excise specific types of damaged bases (uracil-DNA glycosylase removes uracil)
- Short-patch BER replaces a single nucleotide, while long-patch BER replaces 2-10 nucleotides
- (NER) removes bulky DNA lesions
- Global genomic NER (GG-NER) surveys the entire genome for helix-distorting lesions
- Transcription-coupled NER (TC-NER) specifically repairs lesions in actively transcribed genes
- NER involves damage recognition, dual incision, excision of a 24-32 nucleotide patch, gap-filling synthesis, and ligation
Double-Strand Break Repair
- (HR) uses a homologous template for accurate DSB repair
- Primarily active in S and G2 phases when sister chromatids are available
- Involves end resection, strand invasion, DNA synthesis, and resolution of Holliday junctions
- Non-homologous end joining (NHEJ) directly ligates broken DNA ends without a template
- Active throughout the cell cycle, but can introduce small insertions or deletions
- Key proteins include Ku70/80, DNA-PKcs, and IV
Specialized Repair Mechanisms
- Direct reversal repair mechanisms reverse specific types of DNA damage
- Photolyase uses light energy to directly reverse pyrimidine dimers (not present in placental mammals)
- O6-methylguanine-DNA methyltransferase (MGMT) removes alkyl groups from O6-position of guanine
- Translesion synthesis (TLS) allows replication to proceed past DNA lesions
- Utilizes specialized polymerases (Pol η, Pol κ, Pol ι, and Rev1) with lower fidelity but higher tolerance for damaged templates
- Can introduce mutations but prevents replication fork collapse and allows completion of DNA replication
Mismatch Repair for DNA Integrity
Mismatch Recognition and Repair Process
- (MMR) recognizes and corrects base-base mismatches and small insertion/deletion loops
- Eukaryotic MMR system involves MutS homologs (MSH) for mismatch recognition
- MSH2-MSH6 (MutSα) primarily recognizes base-base mismatches and small loops
- MSH2-MSH3 (MutSβ) recognizes larger insertion/deletion loops
- MutL homologs (MLH) coordinate repair activities
- MLH1-PMS2 (MutLα) is the primary MutL complex in eukaryotic MMR
- MMR distinguishes newly synthesized strand from template strand
- In bacteria, strand discrimination uses DNA adenine methylation (DAM) patterns
- In eukaryotes, strand discontinuities or PCNA orientation may guide strand discrimination
MMR Mechanism and Significance
- MMR process involves several steps:
- Mismatch recognition by MutS homologs
- Recruitment of MutL homologs and exonuclease (EXO1)
- Excision of error-containing region (up to 1-2 kb)
- Resynthesis of correct sequence by δ
- Ligation to complete the repair
- MMR enhances DNA replication fidelity by reducing error rate 50-1000 fold
- Plays crucial role in preventing mutations and maintaining genomic stability
- Defects in MMR genes associated with microsatellite instability
- Leads to increased cancer susceptibility (hereditary nonpolyposis colorectal cancer, HNPCC)
Additional Roles of MMR
- MMR contributes to cell cycle regulation and checkpoint activation
- Can trigger cell cycle arrest in response to certain types of DNA damage
- Involved in signaling in response to excessive DNA damage
- Participates in antibody diversification processes (somatic hypermutation and class switch recombination)
- Contributes to triplet repeat expansion, relevant in certain neurodegenerative diseases (Huntington's disease)
Consequences of Unrepaired DNA Damage
Genomic Instability and Cellular Dysfunction
- Accumulation of unrepaired DNA damage leads to mutations and
- Point mutations can alter protein function or expression (activating oncogenes or inactivating tumor suppressors)
- Chromosomal aberrations (translocations, deletions, amplifications) can disrupt gene dosage and regulation
- Persistent DNA damage triggers cell cycle arrest through checkpoint activation
- ATM and ATR kinases initiate signaling cascades in response to DNA damage
- activation leads to expression of p21, causing G1/S arrest
- Prolonged arrest can result in cellular senescence or apoptosis
Impaired Cellular Processes and Tissue Function
- Unrepaired DNA lesions block transcription, reducing or altering gene expression
- Can disrupt cellular processes and protein function across various pathways
- Accumulation of damaged proteins due to transcription errors can overwhelm protein quality control systems
- DNA damage in stem cells impairs tissue regeneration and contributes to aging
- Reduced stem cell pool and diminished differentiation capacity affect organ function
- Contributes to age-related decline in various tissues (hematopoietic system, skin, intestinal epithelium)
Genetic Disorders and Cancer Susceptibility
- Inherited defects in DNA repair pathways associated with various genetic disorders
- Xeroderma pigmentosum extreme UV sensitivity and skin cancer predisposition (NER defect)
- Cockayne syndrome developmental abnormalities and premature aging (TC-NER defect)
- Fanconi anemia bone marrow failure and cancer predisposition (ICL repair defect)
- Increased cancer susceptibility major consequence of impaired DNA repair
- Accumulated mutations can lead to hallmarks of cancer (sustained proliferation, resistance to cell death)
- Lynch syndrome (hereditary nonpolyposis colorectal cancer) results from MMR defects
Neurodegeneration and Developmental Abnormalities
- DNA damage accumulation in neurons linked to neurodegeneration and cognitive decline
- Neurons have limited capacity for replacement in adult brain, making them vulnerable to accumulated damage
- Oxidative DNA damage implicated in Alzheimer's and Parkinson's diseases
- Exposure to DNA-damaging agents coupled with inadequate repair can lead to developmental issues
- Fetal alcohol syndrome involves DNA damage from ethanol metabolism
- Maternal smoking during pregnancy increases risk of birth defects and childhood cancers
Key Terms to Review (18)
Aging: Aging refers to the gradual biological process of becoming older, characterized by the accumulation of cellular and molecular damage over time. This process impacts various biological systems, leading to a decline in function and an increased risk of diseases. The relationship between aging and DNA damage is critical, as the ability of cells to repair damaged DNA diminishes with age, contributing to the overall aging process and associated health issues.
Apoptosis: Apoptosis is a programmed cell death mechanism that occurs in multicellular organisms, allowing for the orderly and controlled elimination of cells. This process is crucial for maintaining tissue homeostasis, development, and responding to cellular stress or damage, linking it closely to DNA repair mechanisms, cellular organelles, and the genetics of cancer.
Base excision repair: Base excision repair is a cellular mechanism that corrects DNA damage by removing and replacing damaged or non-canonical bases within the DNA strand. This process is vital for maintaining genomic integrity, as it addresses small-scale lesions caused by oxidative stress, alkylation, or deamination, preventing these changes from leading to mutations during DNA replication.
Brca1: BRCA1 is a gene that provides instructions for producing a protein involved in the repair of DNA damage, particularly double-strand breaks. Mutations in the BRCA1 gene are linked to an increased risk of breast and ovarian cancer, highlighting its critical role in maintaining genomic stability and preventing tumor formation.
Carcinogenesis: Carcinogenesis is the process by which normal cells transform into cancer cells through a series of genetic and epigenetic changes. This transformation often involves DNA damage, mutations, and alterations in cellular signaling pathways that disrupt normal cell functions. Understanding this process is crucial as it highlights the significance of DNA repair mechanisms in preventing cancer development.
Cell cycle checkpoint: A cell cycle checkpoint is a regulatory mechanism in the cell cycle that ensures the proper progression of cell division by monitoring and verifying critical events. These checkpoints act as control points where the cell assesses its internal and external conditions, such as DNA integrity and cell size, before moving on to the next phase of the cycle. They play a crucial role in preventing the division of damaged or unprepared cells, thereby maintaining genomic stability and preventing diseases like cancer.
Crispr-cas9: CRISPR-Cas9 is a revolutionary gene-editing technology that enables precise modifications to DNA within organisms, utilizing a guide RNA to direct the Cas9 enzyme to specific genomic locations. This tool has transformed the fields of genetics and molecular biology, allowing for advances in functional genomics, therapeutic interventions, and agricultural applications.
Dna ligase: DNA ligase is an essential enzyme that facilitates the joining of DNA strands together by catalyzing the formation of phosphodiester bonds. This process is crucial during DNA replication and repair, where it seals nicks in the sugar-phosphate backbone of DNA, ensuring the integrity and continuity of the genetic material. Without DNA ligase, proper replication and repair processes would be severely hindered, leading to potential mutations and genomic instability.
Dna polymerase: DNA polymerase is an essential enzyme that synthesizes new DNA strands by adding nucleotides to a growing DNA chain during replication and repair processes. This enzyme plays a critical role in ensuring the accuracy and efficiency of DNA replication, facilitating various applications such as amplification in laboratory techniques, addressing DNA damage, and functioning in both prokaryotic and eukaryotic organisms.
Double-strand break: A double-strand break (DSB) is a type of DNA damage where both strands of the DNA helix are severed, resulting in a complete disruption of the DNA molecule. DSBs can be caused by various factors such as ionizing radiation, chemical agents, or during normal cellular processes like replication. These breaks pose significant challenges to the cell, as they can lead to chromosomal instability and are associated with cancer if not repaired correctly.
Gel electrophoresis: Gel electrophoresis is a laboratory technique used to separate and analyze macromolecules, such as DNA, RNA, and proteins, based on their size and charge. This method is crucial for various applications in molecular biology, including the examination of recombinant DNA constructs, the evaluation of PCR products, the assessment of DNA damage, and the study of the structural properties of nucleic acids.
Genomic instability: Genomic instability refers to the increased frequency of mutations within the genome of a cell, which can lead to alterations in DNA sequence, structure, or chromosome number. This phenomenon is significant because it can contribute to various diseases, particularly cancer, by promoting tumorigenesis and making cells more prone to further genetic changes. Understanding genomic instability is essential in studying how DNA damage and repair mechanisms fail, leading to cellular dysfunction and disease progression.
Homologous recombination: Homologous recombination is a biological process that enables the exchange of genetic material between two similar or identical strands of DNA, often occurring during meiosis and DNA repair. This mechanism is crucial for maintaining genetic diversity in sexually reproducing organisms and plays a significant role in repairing double-strand breaks in DNA, ensuring genomic stability.
Mismatch repair: Mismatch repair is a cellular process that corrects errors that occur during DNA replication, specifically the mispairing of nucleotides. This repair mechanism enhances the fidelity of DNA replication by identifying and repairing mismatched bases, which helps prevent mutations from being propagated in daughter cells. It plays a crucial role in maintaining genomic stability and ensuring accurate transmission of genetic information.
Mutagenesis: Mutagenesis is the process by which genetic mutations are generated, often as a result of exposure to mutagens, which can be physical agents like radiation or chemical agents. This process is significant in various biological contexts, including the regulation of gene expression, the maintenance of genetic integrity, and the understanding of DNA structure and properties. Mutagenesis plays a critical role in evolution, cancer development, and the adaptation of organisms to their environments.
Nucleotide excision repair: Nucleotide excision repair is a crucial DNA repair mechanism that removes damaged segments of DNA, allowing for the restoration of the original sequence. This process is vital for fixing various types of DNA damage, including those caused by ultraviolet (UV) light and chemical mutagens, ensuring genomic stability and preventing mutations from being passed on during cell division.
P53: p53 is a crucial tumor suppressor protein that plays a vital role in preventing cancer by regulating the cell cycle and facilitating DNA repair mechanisms. It acts as a guardian of the genome, responding to various cellular stresses, such as DNA damage, by either halting the cell cycle for repair or initiating apoptosis if the damage is irreparable. The functionality of p53 is essential in maintaining cellular integrity and preventing the proliferation of cells with damaged DNA.
Single-strand break: A single-strand break (SSB) is a form of DNA damage characterized by the disruption of one of the two strands of the DNA helix, resulting in a break that can potentially compromise the integrity of genetic information. SSBs can arise from various sources, including environmental factors like radiation and chemicals, as well as normal cellular processes such as replication and transcription. These breaks are significant because they can lead to further mutations or double-strand breaks if not repaired promptly.