Biomaterial Database

[Cleavage of bacteriophage PM2 DNA by S1 nuclease]. 1978

E M Gonikberg

The kinetics of cleavage of superhelical PM2 DNA by the single strand-specific S1 nuclease is studied at various salt concentrations (0.01--1 MNaCl) by electrophoresis in neutral and alkaline agarose gels. Cleavage of different DNA forms (superhelical DNA I, relaxed circular DNA II and linear DNA III) is described by the kinetic equations of the first order, and respective rate constants k1, k2, and k3 are determined at all salt concentrations used. It is shown that a high salt concentration (not lower than 0.2 MNaCl) is necessary for high specificity of S1 nuclease action on DNA regions with impaired base pairing. Examination of the S1 nuclease preparation action on superhelical PM2 DNA may be used as a convenient and reliable assay of its specificity.

UI	MeSH Term	Description	Entries
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D011549	Pseudomonas	A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.	Chryseomonas,Pseudomona,Flavimonas
D003851	Deoxyribonucleases	Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.	DNAase,DNase,Deoxyribonuclease,Desoxyribonuclease,Desoxyribonucleases,Nucleases, DNA,Acid DNase,Alkaline DNase,DNA Nucleases,DNase, Acid,DNase, Alkaline
D004269	DNA, Bacterial	Deoxyribonucleic acid that makes up the genetic material of bacteria.	Bacterial DNA
D004270	DNA, Circular	Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)	Circular DNA,Circular DNAs,DNAs, Circular
D004277	DNA, Single-Stranded	A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.	Single-Stranded DNA,DNA, Single Stranded,Single Stranded DNA
D004278	DNA, Superhelical	Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.	DNA, Supercoiled,DNA, Supertwisted,Supercoiled DNA,Superhelical DNA,Supertwisted DNA
D004587	Electrophoresis, Agar Gel	Electrophoresis in which agar or agarose gel is used as the diffusion medium.	Electrophoresis, Agarose Gel,Agar Gel Electrophoresis,Agarose Gel Electrophoresis,Gel Electrophoresis, Agar,Gel Electrophoresis, Agarose