Biomaterial Database

Specific nicking of DNA at apurinic sites by peptides containing aromatic residues. 1981

J Pierre, and J Laval

Tripeptides containing aromatic residues between basic ones, such as Lys-Trp-Lys and Lys-Tyr-Lys can nick supercoiled or relaxed DNAs containing apurinic/apyrimidinic sites (AP-sites). The nicking, which is ionic strength-dependent, occurs at AP-sites, since native PM2 DNA is not hydrolyzed. The nicking activity of the tripeptides at AP-sites occurs in total darkness. An activation energy of 21 +/- 2 kcal . mol-1 has been calculated for the incision of PM2 DNA by Lys-Trp-Lys. Tripeptides without aromatic residues, such as Lys-Ala-Lys-O-Methyl and Lys-Lys-Lys, can nick apurinic DNA, although with a much lower efficiency. Relaxed depurinated PM2 DNA is a poor substrate for the tripeptide, indicating that single-stranded regions are better recognition sites. The nicking of the DNA backbone probably occurs by beta elimination, since reduced AP-sites do not act as substrate. The termini generated are 3'-hydroxyl and 5'-phosphoryl.

UI	MeSH Term	Description	Entries
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D008239	Lysine	An essential amino acid. It is often added to animal feed.	Enisyl,L-Lysine,Lysine Acetate,Lysine Hydrochloride,Acetate, Lysine,L Lysine
D009842	Oligopeptides	Peptides composed of between two and twelve amino acids.	Oligopeptide
D002621	Chemistry	A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.
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
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
D004279	DNA, Viral	Deoxyribonucleic acid that makes up the genetic material of viruses.	Viral DNA
D001080	Apurinic Acid	Hydrolysate of DNA in which purine bases have been removed.	Acid, Apurinic
D013329	Structure-Activity Relationship	The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.	Relationship, Structure-Activity,Relationships, Structure-Activity,Structure Activity Relationship,Structure-Activity Relationships
D014364	Tryptophan	An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.	Ardeydorm,Ardeytropin,L-Tryptophan,L-Tryptophan-ratiopharm,Levotryptophan,Lyphan,Naturruhe,Optimax,PMS-Tryptophan,Trofan,Tryptacin,Tryptan,Tryptophan Metabolism Alterations,ratio-Tryptophan,L Tryptophan,L Tryptophan ratiopharm,PMS Tryptophan,ratio Tryptophan