DNA Repair

Table of Contents

Introduction | Base Excision Repair | Nucleotide Excision Repair | Homologous Recombination | Non-homologous End-joining | Direct Reversal of DNA Method | Antibodies

Introduction

DNA repair refers to a collection of processes by which cells identify and correct damaged DNA. In human cells, normal metabolic activities and environmental factors cause DNA damage. Lesions resulting from DNA damage cause structural changes that can prevent gene transcription and induce harmful mutations in the cells genome. The rate of DNA repair is dependent of many factors, including cell type, cell age and the extracellular environment. The DNA repair ability of a cell is vital to the integrity of its genome, and thus to its normal function. A cell that has accumulated a large amount of DNA damage or that can no longer effectively repair damage can enter one of three stages: senescence, apoptosis, or unregulated cell division, which can lead to the formation of a malignant tumor.

Eukaryotic and prokaryotic cells possess multiple mechanisms to repair DNA and control damage to their genomes. These include base excision repair (BER) and nucleotide excision repair (NER) that excise and replace damaged nucleotide bases and helix-distorting lesions, respectively. Many of the proteins involved in NER are also active in the related transcription-coupled repair (TCR). In addition, mismatch repair (MMR) proteins act to replace mismatched nucleotides and repair insertion/deletion loops. Furthermore, there are two types of double-stranded DNA break repair, homologous recombination (HR) and non-homologous end-joining (NHEJ).

Base Excision Repair

Base excision repair is a crucial mechanism for fixing DNA damage and preventing the spread of mutations. This process involves a specific series of enzyme activities. DNA glycosylases/AP lyases are the first enzymes to identify and remove damaged bases, creating an abasic (AP) DNA site by breaking beta-N glycosidic bonds. Repair can then proceed through either the short patch (1 nucleotide) or long patch (2-10 nucleotides) pathways, depending on the initial base removal events. Endonucleases recognize the AP site, nick the damaged DNA, and recruit DNA polymerases to fill in the gap. Finally, DNA ligase seals the new DNA strand to complete the base excision repair process. R&D Systems offers a range of high-quality base excision repair products, including DNA glycosidases, endonucleases, polymerases, and more.

Nucleotide Excision Repair

Nucleotide excision repair (NER) is an important DNA repair mechanism by which the cell repairs DNA damage occurring to bases. Base damage can be caused by a variety of sources including chemicals and UV light. NER is the mechanism by which the cell can prevent unwanted mutations by removing the majority of UV-induced DNA damage (mostly in the form of thymine dimers and 6-4-photoproducts). The importance of this repair mechanism is evidenced by the severe human diseases that result from in-born genetic mutations of NER proteins, including Xeroderma pigmentosum and Cockayne's syndrome. NER recognizes bulky distortions in the shape of the DNA double helix. Recognition of these distortions leads to the removal of a short single-stranded DNA segment that includes the lesion, creating a single-stranded gap in the DNA. This gap is subsequently filed in by DNA polymerase, using the undamaged strand as a template.

Homologous Recombination

Homologous recombination (HR) is one mechanism used in the repair of double-strand breaks (DSB) in DNA. In the process of HR, a DSB is repaired by copying the missing information from the sister chromatid or homologous chromosome, resulting in the exact restoration of DNA.

Non-homologous End-joining

Non-homologous end-joining (NHEJ) is one mechanism used in the repair of DNA double-strand breaks (DSB). NHEJ is referred to as 'non-homologous' because the broken ends are directly ligated without the need for a homologous template, as is necessary for homologous recombination. NHEJ is evolutionarily conserved throughout all kingdoms of life and is the predominant DSB repair pathway in many organisms. This mechanism typically utilizes short homologous DNA sequences (microhomologies) to guide repair. Microhomologies in the single-stranded overhangs that are often present on the ends of DSB are used to promote restorative repair. When these overhangs are compatible, NHEJ almost always repairs the break accurately with no sequence loss. Imprecise repair leading to the loss of nucleotides can also occur, but is much less common. The NHEJ pathway is also responsible for fusing the ends of chromosomes that have undergone telomere failure.

Direct Reversal of DNA as a Method to Repair Damage

Direct reversal of DNA damage is one repair mechanism used to restore damaged DNA. Although this is the most energy efficient method, few types of damaged DNA are repaired in this way. The formation of pyrimidine dimmers, the major type of damage caused by UV light, distorts the double helix and blocks transcription or replication past the damaged site. The process of photoreactivation causes direct reversal of the dimerized reaction, thus the original pyrimidine bases are restored. Direct reversal of O6 adducts caused by chemotherapy agents is accomplished in mammalian cells by the protein O6-methylguanine DNA methyltransferase (MGMT). Some tumors overexpress MGMT and are resistance to alkylator therapy.

Antibodies for Molecules Involved in DNA Damage Detection/Repair

Antibodies are a common tool in DNA repair, with hundreds of subgroups that mark specific proteins. 

p53 Antibodies

p53 is a tumor-suppressing protein, which plays an important role in the development of cancer cells. It is sited at the junction of a network of signaling pathways. Depending on its interaction with other proteins, it can either prevent or initiate programmed cell death. Its disruption is implicated in a wide range of cancers.

53BP1 Antibodies

The tumor binding protein 53BP1 plays a critical role in tumor suppression in the p53 pathway. It is also thought to be involved with DNA repair. Different 53BP1 antibodies are specific to particular residues on the 53BP1 protein. 

FANCD2 Antibodies

FANCD2 antibodies interact with FANCD proteins, which are implicated in Fanconi anaemia - a genetic disease. FANCD is essential for cellular repair after cancer therapy. Disruption of this pathway leads to increased cell sensitivity and progressive bone marrow failure.

PARP Antibodies

PARP is involved in DNA repair following environmental stress. It is cleaved by a number of caspase proteins in vitro, including Caspase-3. PARP cleavage is a useful marker in cells subjected to apoptosis.

Rad51 Antibodies

The RAD51 protein plays a major role in the repair of double strand DNA breakages. It reacts with the BRCA1 and BRCA2 proteins, and this interaction is thought to be important to DNA damage cell response. RAD51 alteration, and inactivation of BRCA2, are linked to breast cancer development. RAD51 antibodies are used in studies of both proteins.

• Mini-review: DNA Damage Response
• Regulation of the Cell Cycle and DNA Damage-Induced Checkpoint Activation Poster
• Article: Gene Expression in the Aging Brain
• DNA Damage and Repair Kits & Reagents
• DNA Modifying Enzymes