DNA Related Biological Terms

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. DNA can be damaged by many types of mutagens, including ultraviolet light, radiation, and chemicals, as well as by errors that occur during DNA replication. The repair of DNA is vital for the maintenance of genomic integrity and for the prevention of mutations, which can lead to cancer and other diseases. Here are the key aspects of DNA repair: 1. Types of DNA Damage: DNA damage can occur in various forms, such as single-strand breaks, double-strand breaks, cross-links, and chemical modifications of bases. 2. DNA Repair Mechanisms: There are several types of DNA repair mechanisms, each addressing different types of damage:     o Direct Reversal: Certain forms of damage are directly reversible, with specialized enzymes correcting alterations without breaking the DNA strand.     o Base Excision Repair (BER): Removes small, non-helix-distorting base lesions from the genome.     o Nucleotide Excision Repair (NER): Repairs bulky, helix-distorting base damage, such as thymine dimers caused by UV light.     o Mismatch Repair (MMR): Corrects errors introduced during DNA replication and recombination that result in mispaired (mismatched) nucleotides.     o Homologous Recombination (HR): Repairs double-strand breaks using a homologous sequence as a template, typically using the sister chromatid.     o Non-Homologous End Joining (NHEJ): Joins the ends of a double-strand break without the need for a homologous template, often resulting in small deletions or insertions. 3. Importance in Preventing Diseases: Effective DNA repair mechanisms are critical in preventing mutations that can lead to diseases such as cancer. Deficiencies in DNA repair mechanisms can increase the risk of genomic instability. 4. Cell Cycle and DNA Repair: The cell cycle has checkpoints to detect and repair DNA damage before the cell proceeds to the next phase. For example, before a cell enters mitosis, it checks for DNA damage and, if necessary, halts the cycle to allow for repair. 5. Aging and DNA Repair: The capacity for DNA repair may decrease with aging, contributing to the aging process and the increased risk of cancer in older individuals. 6. Therapeutic Implications: Understanding DNA repair pathways is crucial in developing certain cancer treatments. For example, some chemotherapeutic agents target rapidly dividing cells by inducing DNA damage, which cancer cells are less capable of repairing. DNA repair is a complex and vital process, maintaining the stability of an organism's genome and protecting it against the onset of various diseases. Research in DNA repair not only helps in understanding the fundamental processes of cellular biology but also aids in the development of medical therapies and cancer treatments.

(= DNA fingerprinting (DNA profiling))

(= exonuclease footprinting (DNase footprinting))

double-stranded DNA. (see also double helix (Watson-Crick model))

A method for identification of a protein-binding region in a double-stranded DNA fragment. One 5'-end of the DNA fragment is labelled with 32P and the DNA-fragment-protein complex is treated with a 3'-exonuclease to digest from the 3'-end until it meets the region protected by the DNA-binding protein. The labelled strand is characterized subsequently by its size to indicate the distance of the site of the binding protein from the 5'-end of the fragment. The technique is suitable for localization of a binding site to a specific region of a large DNA fragment, whereas footprinting gives the exact sequence of the binding site of a smaller fragment. (see also footprinting)Revzin, A. (ed.) (1993) footprinting of Nucleic Acid-Protein Complexes, Academic Press, San Diego Learn more about restriction enzymes.

Automated DNA sequencing using single-lane sequencing; adaptable to automated data collection.

see quadruplex DNA

Genomic DNA refers to the genetic material that in eukaryotes is found organized into multiple chromosomes within a nucleus, while in prokaryotes is organized as circular DNA residing within the cytoplasm. In eukaryotic cells, genomic DNA includes protein-coding (exons) and non-coding sequences (introns); in contrast, prokaryotes’ genomic DNA only contains exon sequences. Different molecular biology applications (e.g., Sanger, Next-generation sequencing) require the isolation of genomic DNA from whole blood or tissues. Isolation of genomic DNA from whole blood may be achieved through different methods (e.g., solution-based or solid-phase DNA extraction) involving several basic steps such as cell lysis, nucleoprotein denaturation, enzyme inactivation, contaminant removal (i.e., RNA, lipids, and proteins), and lastly DNA precipitation. Recommended reading: next generation sequencing

A form of triplex DNA characterized by Hoogstein base pairing.Yagil, G. (1991) Crit. Rev. Biochem. Mol. Biol. 26, 475-559; Frank-Kamenetskii, M.D. and Mirkin, S.M. (1995) Annu. Rev. Biochem. 64, 65-95; Vasquez, K.M. and Wilson, J.H. (1998) Trends Biochem. Sci. 23, 4-9

A branched double-stranded DNA structure, a chi-form in which each of four polynucleotide chains is complementary to and base-paired with the 3'-end of one polynucleotide and the 5'-end of another; unlike in a recombination intermediate, the junction cannot migrate (i.e. slide its branch point along the duplex) without breaking many more Watson-Crick base-pair hydrogen bonds as it advances than can re-form behind it. (see also Holliday model) Recommended reading: lipofectamine 2000 protocol