JavaScript NENÍ povolen !

Prosím povolte JavaScript.

* Zobrazit nápovědu

Reset

MeSH: Single-Strand Specific DNA and RNA Endonucleases-metabolism

8 záznamů v PubMed Filtry

Článek

Characteristics and application of S1-P1 nucleases in biotechnology and medicine

Koval, Tomáš
Autor Koval, Tomáš Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic. Electronic address: tomas.koval@ibt.cas.cz
Dohnálek, Jan
Autor Dohnálek, Jan Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic. Electronic address: jan.dohnalek@ibt.cas.cz

Biotechnology advances. 2018 May-Jun ; 36 (3) : 603-612. [epub] 20171214

Biotechnol Adv
ISSN 1873-1899 | 0734-9750
Zdroj

3'-nucleases/nucleotidases of the S1-P1 family (EC 3.1.30.1) are single-strand-specific or non-specific zinc-dependent phosphoesterases present in plants, fungi, protozoan parasites, and in some bacteria. They participate in a wide variety of biological processes and their current biotechnological applications rely on their single-strand preference, nucleotide non-specificity, a broad range of catalytic conditions and high stability. We summarize the present and potential utilization of these enzymes in biotechnology and medicine in the context of their biochemical and structure-function properties. Explanation of unanswered questions for bacterial and trypanosomatid representatives could facilitate development of emerging applications in medicine.

Článek

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition

PloS one. 2016 ; 11 (12) : e0168832. [epub] 20161230

PLoS One
ISSN 1932-6203
Zdroj

The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.

Článek

Salmonella enterica subsp. enterica serovar Enteritidis harbours ColE1, ColE2, and rolling-circle-like replicating plasmids

Canadian journal of microbiology. 2004 Feb ; 50 (2) : 107-12.

Can J Microbiol
ISSN 0008-4166
Zdroj

Using DNA hybridization, at least three distinct groups of low molecular mass plasmids were identified in Salmonella enterica subsp. enterica serovar Enteritidis. After sequencing representative plasmids from each group, we concluded that they belonged to ColE1, ColE2, and rolling-circle-like replicating plasmids. Plasmid pK (4245 bp) is a representative of widely distributed ColE1 plasmids. Plasmid pP (4301 bp) is homologous to ColE2 plasmids and was present predominantly in single-stranded DNA form. The smallest plasmids pJ (2096 bp) and pB (1983 bp) were classified as rolling-circle-like replicating plasmids. Both encoded only a single protein essential for their own replication, and they must have existed in an unusual molecular structure, as (i) they were capable of hybridization without denaturation, (ii) their DNA could be linearized with S1 nuclease, and (iii) even after such treatment, the ability to hybridize without denaturation did not disappear.

Článek

Two superhelix density-dependent DNA transitions detected by changes in DNA adsorption/desorption behavior

Biochemistry. 1998 Apr 07 ; 37 (14) : 4853-62.

ISSN 0006-2960
Zdroj

The adsorption behavior of covalently closed circular plasmid DNA at the mercury/water interface was studied by means of AC impedance measurements. The dependence of the differential capacitance (C) of the electrode double layer on the potential (E) was measured in the presence of adsorbed DNA. It was found that the C-E curves of supercoiled DNA at native and highly negative superhelix densities (sigma), relaxed covalently closed circular DNA, and nicked DNA differed from each other. A detailed study of topoisomer distributions ranging from -sigma of 0 to 0.11 revealed two supercoiling-dependent transitions, at about -sigma = 0.04 (transition TI) and 0.07 (transition TII). Transition TI was detected by measuring the height of the adsorption/desorption peak 1 (at about -1.2 V against the saturated calomel electrode) and the decrease of capacitance (DeltaC) at -0.35 V. This transition may be due to a sudden change in the ability of the DNA to respond to the alternating voltage, probably caused by changes in the DNA tertiary and/or secondary structure. Transition TII was detected by measuring peak 3* (at about -1.3 V), which was absent in topoisomers with -sigma less than 0.05. This transition is due to changes in the DNA adsorption/desorption behavior related to increased accessibility of bases at elevated negative superhelix density. Opening of the duplex at highly negative superhelix density was also detected by the single-strand selective probe of DNA structure, osmium tetroxide, 2, 2'-bipyridine. Our results suggest that electrochemical techniques provide sensitive experimental analysis of changes in DNA structure.

MeSH
adsorpce MeSH
elektrochemie MeSH
endonukleasy specifické pro jednořetězcové nukleové kyseliny metabolismus MeSH
hydrolýza MeSH
konformace nukleové kyseliny MeSH
plazmidy MeSH
superhelikální DNA chemie metabolismus MeSH
Publikační typ
časopisecké články MeSH
práce podpořená grantem MeSH
Názvy látek
endonukleasy specifické pro jednořetězcové nukleové kyseliny MeSH
superhelikální DNA MeSH

Článek

In vitro and in vivo transcription from a computer predicted promoter

Gene. 1997 Mar 18 ; 187 (2) : 281-7.

ISSN 0378-1119
Zdroj

A fragment (172 bp) of B. subtilis phage phi29 DNA, which does not contain a functional promoter for phage transcription, has been shown to direct transcription in the promoter-probe plasmid pPV33. The promoter candidate found in this fragment by the computer method of acceptability is compared with cryptic promoters selected by this computer method. It is characterized in vitro by electron microscopic visualization of RNA polymerase binding and 'run off' transcription, and in vivo by high resolution S1 mapping.

Článek

Complex of osmium tetroxide with 1,10-phenanthroline binds covalently to double-stranded DNA

Journal of biomolecular structure & dynamics. 1995 Dec ; 13 (3) : 537-46.

J Biomol Struct Dyn
ISSN 0739-1102
Zdroj

Complex of osmium tetroxide with 1,10-phenanthroline (Os,phen) reacts with double-stranded B-DNA in contrast to osmium tetroxide, pyridine and other osmium structural probes which show a strong preference for single-stranded DNA (ssDNA) (Palecek, E. in Abelson, J.N., and Simon, M.I. (eds), Lilley, D.M.J., and Dahlberg, J.E., (volume eds.), Methods in Enzymology, Vol. 212, DNA Structures, part B., Academic Press, 139-155 (1992)). Modification of negatively supercoiled DNA (scDNA) with Os,phen changes the DNA electrophoretic mobility inducing the DNA relaxation at lower degrees of modification followed by formation of positive supercoils at higher modification extents. Electrophoretic mobility of the Os,phen-modified DNA fragments in agarose gel is almost unchanged while a strong retardation of the same fragments is observed in polyacrylamide gels. Os,phen-modified DNA is hypersensitive to nuclease S1. Cleavage of this DNA by restriction enzymes is selectively inhibited showing a preference of Os,phen for TA and AT dinucleotide steps. DNA modification by Os,phen is inhibited by low and moderate concentrations of MgCl2. The covalent binding of Os,phen to double-stranded DNA (dsDNA) is preceded by noncovalent interactions (probably intercalation) inducing DNA structural changes; the shape of the Os,phen-modified DNA molecule appears to be severely deformed.

Článek

Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing

Journal of biomolecular structure & dynamics. 1988 Oct ; 6 (2) : 261-75.

J Biomol Struct Dyn
ISSN 0739-1102
Zdroj

Structural distortions on the boundary between right-handed and left-handed segments in the superhelical plasmid pPK2 (a derivative of pUC19 containing (dC-dG)n segments cloned into polylinker) were studied by means of chemical probes. Strong osmium tetroxide, pyridine (Os,py) modification of DNA at native superhelical density (sigma) was found in four thymines surrounding the (dC-dG)13 segment. These results correlated with restriction cleavage inhibition (due to modification): BamHI cleavage was strongly inhibited, unlike the neighbouring XbaI and SalI (weak or no inhibition). In the (dC-dG)8 segment considerably weaker modification of the B-Z junctions was observed, accompanied by weak inhibition of BamHI cleavage, while the neighbouring SmaI and KpnI were not affected. Os,py modification of DNA at native sigma was not detected by nuclease S1 cleavage at and (dC-dG)n segment. However, this enzyme recognized and cleaved at the B-Z junction, osmium modified at more negative sigma. The results obtained with the glyoxal and diethyl pyrocarbonate modification support the idea of very narrow B-Z junctions at native sigma.

Článek

B-Z junctions in supercoiled pRW751 DNA contain unpaired bases or non-Watson-Crick base pairs

Journal of biomolecular structure & dynamics. 1987 Oct ; 5 (2) : 297-306.

J Biomol Struct Dyn
ISSN 0739-1102
Zdroj

Structural distortions on the boundary between right-handed and left-handed DNA segments in negatively supercoiled plasmid pRW751 (a derivative of pBR322 containing (dC-dG)13 and (dC-dG)16 segments) were studied by means of osmium tetroxide, pyridine and glyoxal. These two probes react preferentially with single-stranded DNA, but only the latter requires non-paired bases for the reaction. Nuclease S1 and testing of the inhibition of BamHI cleavage (whose recognition sequences GGATCC lie on the "outer" boundaries between the (dC-dG)n and the pBR322 nucleotide sequence) were used to detect the site-specific chemical modification in pRW751. As a result of glyoxal treatment BamHI cleavage was strongly inhibited in topoisomeric samples whose superhelical density was sufficiently negative to stabilize the (dC-dG)n segments in the left-handed form. Osmium tetroxide, pyridine modification resulted in a similar inhibition of BamHI cleavage and in a formation of nuclease S1 sensitive sites. The results suggest that the "outer" B-Z junctions in pRW751 contain one or few non-paired bases or non-Watson-Crick base pairs.

* Zobrazit nápovědu

Upřesnit dle MeSH