DNA Related Biological Terms

The DNA of plant plastids, including chloroplasts.

A DNA molecule produced by replication of a parent DNA molecule.

A section of DNA that has been inserted into a vector molecule, such as a plasmid or a phage chromosome, and then replicated to form many identical copies. See also clone

1. A method of identifying people based on the analyses of a persons satalite DNA (satalite DNA are small tandem repeats which make up a significant proportion of a cell's DNA and that is unique for each person)2. The largely individual-specific autoradiographic banding pattern produced when DNA is digested with a Restriction endonuclease that cuts outside a family of VNTRs, and a Southern blot of the electrophoretic gel is probed with a VNTR-specific probe.

DNA glycosylase is a kind of endonuclease initiating excision repair at various damaged or improper Bases in DNA. DNA glycosylase recognizes and removes damaged bases from DNA by cleaving the base–sugar (N-glycosylic) bond and downstream base excision repair enzymes restore the correct nucleotide. Abscisic acid (ABA), a plant hormone, can be an inducer for DNA glycosylase. ABA functions in many plant developmental processes, including seed and bud dormancy, the control of organ size, and stomatal closure. It can also regulate numerous aspects of plant growth, development, and stress responses. MUTYH gene can encode a DNA glycosylase involved in oxidative DNA damage repair. Besides, GAPDH encodes a member of the glyceraldehyde-3-phosphate dehydrogenase protein family. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. The encoded protein has additionally been identified to have uracil DNA glycosylase activity in the nucleus.

Known DNA sizes used to determine the size of an unknown DNA sample. The DNA ladder usually contains regularly spaced sized samples which when run on an agarose gel looks like a "ladder".

Introduction DNA ligase is an essential enzyme in molecular biology that catalyzes the formation of phosphodiester bonds between adjacent nucleotides, effectively sealing breaks in the DNA backbone. It plays a critical role in cellular processes such as DNA replication, repair, and recombination. In laboratory settings, DNA ligase is widely used for recombinant DNA technology, including cloning, gene assembly, and the construction of DNA libraries. By joining DNA fragments, the enzyme ensures the integrity and continuity of double-stranded DNA molecules. Mechanism of Action Substrate Recognition DNA ligase acts on nicks (single-strand breaks) or blunt and cohesive ends (sticky ends) within DNA molecules. The enzyme recognizes the 3'-hydroxyl (OH) group of one nucleotide and the 5'-phosphate (P) group of the adjacent nucleotide as its substrates. Cofactor Requirement DNA ligase activity requires cofactors to mediate the formation of the phosphodiester bond: ATP: Used by eukaryotic and viral DNA ligases (e.g., T4 DNA ligase). NAD+: Required by bacterial ligases, such as E. coli DNA ligase. Formation of an Enzyme-AMP Intermediate ATP or NAD+ is hydrolyzed, leading to the formation of a covalent ligase-AMP intermediate. The AMP group is transferred to the 5'-phosphate of the DNA, activating it for ligation. Phosphodiester Bond Formation The 3'-OH group of the adjacent nucleotide attacks the activated 5'-phosphate, forming a phosphodiester bond. AMP is released, completing the ligation process and restoring the integrity of the DNA backbone. Ligation of Blunt vs. Sticky Ends Sticky Ends: Ligase readily joins complementary overhanging ends (cohesive ends), such as those generated by restriction enzymes. Blunt Ends: Ligation of blunt-ended fragments is less efficient, as there are no overhangs to stabilize the interaction between fragments. Higher concentrations of ligase or longer incubation times are often required. Applications Molecular Cloning DNA ligase is used to join DNA fragments, such as a gene of interest, into plasmid vectors for transformation and gene expression studies. T4 DNA Ligase: The most widely used ligase in molecular cloning, capable of ligating both sticky and blunt-ended fragments. Construction of Recombinant DNA Molecules The enzyme enables the assembly of multiple DNA fragments, facilitating the construction of complex plasmids or recombinant genes. Ligation-Mediated PCR (LM-PCR) DNA ligase is employed in LM-PCR to join adapters or linkers to fragmented DNA, enabling efficient amplification for sequencing or gene mapping. DNA Repair Studies DNA ligase enzymes are used in research to investigate repair mechanisms involving the joining of DNA breaks, such as in homologous recombination or non-homologous end joining (NHEJ). Next-Generation Sequencing (NGS) Library Preparation Ligases are essential in preparing NGS libraries by joining sequencing adapters to fragmented DNA, allowing for efficient sequencing of genomic material. Synthetic Biology and Gene Assembly DNA ligase is used in Gibson Assembly, a technique for seamless joining of DNA fragments. In this process, exonucleases generate complementary overhangs, which are then sealed by DNA ligase without the need for restriction enzymes. Types of DNA Ligases T4 DNA Ligase Source: Derived from the T4 bacteriophage, it is the most commonly used ligase in molecular biology. Cofactor: ATP. Activity: Joins both sticky and blunt-ended DNA fragments efficiently. E. coli DNA Ligase Cofactor: NAD+ Usage: Mainly used in research involving DNA repair and bacterial plasmid ligation. Mammalian DNA Ligase I, III, and IV These ligases are involved in different DNA repair pathways: Ligase I: Plays a role in Okazaki fragment ligation during DNA replication. Ligase III: Functions in base excision repair. Ligase IV: Critical for non-homologous end joining (NHEJ) during double-strand break repair. Limitations and Challenges Blunt-End Ligation Inefficiency: Ligation of blunt-ended DNA fragments can be challenging and requires higher enzyme concentrations or extended incubation. Incomplete Ligation: If the DNA fragments are not properly phosphorylated, ligation may fail. Pre-treatment with a kinase enzyme (e.g., T4 polynucleotide kinase) may be necessary. Self-Ligation of Vectors: During cloning, vectors without inserts may re-circularize, leading to false-positive results. Dephosphorylation of the vector can help reduce self-ligation. GenScript Services and Products GenScript offers a variety of products and services related to DNA ligase, including: T4 DNA Ligase : High-efficiency ligase for routine molecular cloning and recombinant DNA work. Quick Ligation Kits : Fast ligation kits designed for time-sensitive cloning projects. Custom Vector Construction Services : Seamless assembly of DNA fragments into expression vectors. Oligonucleotide and Vector Design Services : Optimize primers and vectors for cloning using ligase-based methods. Conclusion DNA ligase is a cornerstone enzyme in molecular biology, facilitating the joining of DNA fragments for cloning, repair, and sequencing applications. The ability to ligate both sticky and blunt-ended DNA fragments makes T4 DNA ligase the enzyme of choice for most laboratory workflows. Advances in synthetic biology and genome editing have expanded the utility of DNA ligase beyond traditional cloning, enabling seamless gene assembly and complex recombinant DNA construction.

DNA markers are used to identify resistance genes and their introgression and pyramiding into new cultivars. A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. DNA markers have been developed for many disease resistance genes. Various DNA marker-based methods have been applied for the assessment of genetic variability and analysis of genetic relatedness.

A multisubunit enzyme which plays a role in synthesizing new DNA strands using a DNA template by catalysing the formation of phosphodiester bonds; several such enzymes exist.

One of two or more alternate forms (alleles) of a chromosomal locus that differ in nucleotide sequence or have variable numbers of repeated nucleotide units.