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PubMed1990

Replication, transcription and nuclease digestion of the unusual X-DNA double helix of poly(amino2dA-dT).

The alternating copolymer poly(amino2dA-dT) isomerizes into the unusual X-DNA double helix at low-salt aqueous conditions (Vorlicková et al., J. Biomolec. Struct. Dyn. 6, 503-510 (1988)). This observation allowed us to start studies on how the X-DNA is recognized, copied and hydrolyzed by various enzymes. In the present paper X-DNA replication, transcription and digestion by various polymerases and nucleases, respectively, are examined and compared to appropriate controls. It is found that X-DNA is a poor primer-template for DNA synthesis by the E. coli Klenow DNA polymerase (12% of the activity observed with B-DNA), the Micrococcus luteus DNA polymerase I (25%) and the AMV reverse transcriptase (51%). In contrast, X-DNA is a better template by 74% than B-DNA for calf thymus DNA polymerase alpha. For transcription by E. coli RNA polymerase enzyme poly(amino2dA-dT) did not serve as a template at all in either B or X conformation. Poly(amino2dA-dT) in its B form proved to be much more stable than poly(dA-dT) against hydrolysis by pancreatic DNase and snake venom phosphodiesterase. Formation of the X conformation in poly(amino2dA-dT) decreased this large difference in nuclease stability.

DNA Replication↗

PubMed2002

Mitochondrial factors modulate the activity of endonuclease G, the major nuclease of Mammalian mitochondria.

Endonuclease G (Endo G), a sugar-nonspecific nuclease preferring single-stranded DNA (ssDNA), is responsible for major nuclease activity in mitochondria. If the enzyme provides an important nicking function for mitochondrial DNA (mtDNA) in vivo, then mitochondrial factors likely exist which modulate the enzyme's activity and prevent cleavage at single-stranded moieties of mtDNA. In the present paper, we report that specific membrane phospholipids, polyamines and single-stranded DNA-binding protein (SSB) appear to exert such effects in vitro. Phosphatidylcholine and phosphatidylethanolamine, the major constituents of the mitochondrial inner membrane, stimulated purified Endo G activity 5- to 10-fold. Spermine at 5-100 microM also stimulated activity about 4-fold. However, at more than 500 microM, the spermine largely inhibited the degradation of ssDNA and duplex DNA. Escherichia coli SSB, which has physicochemical properties analogous to those of mitochondrial SSB (mtSSB), markedly inhibited the degradation of phiX174 ssDNA by Endo G, indicating the possible involvement of mtSSB in vivo in protection of single-stranded regions of mtDNA from nucleolytic attacks.

Animals↗

PubMedDate not supplied

DNA adduct levels in fish from pristine areas are not detectable or low when analysed using the nuclease P1 version of the 32P-postlabelling technique.

In order to understand and apply DNA adduct formation in fish liver as a biomarker for aquatic pollution, information concerning the natural background levels in noncontaminated organisms, caused by endogenous compounds, is of fundamental importance. In this study, DNA adducts were analysed in liver of 11 fish species from arctic and sub-arctic areas in the northern Atlantic using the nuclease P1 version of the 32P-postlabelling technique. The collected fish were assumed not to have been influenced by anthropogenic pollution apart from possible long-range transported pollutants. As polycyclic aromatic hydrocarbons (PAHs) are thought to be fundamental in forming the type of DNA adducts detected by the method used, biliary PAH metabolite levels were measured in a selection of the investigated species. In all investigated individuals, the levels of PAH metabolites were undetectable. Controlled on-site exposure experiments with benzo[a]pyrene (polar cod) and laboratory experiments with crude oil (polar cod and Atlantic cod) were conducted. DNA adducts were formed in both these species. The field-sampled fish showed undetectable levels of DNA adducts or levels just above the detection limit. The present study supports the assumption that when DNA adducts are detected by the nuclease P1 version of the 32P-postlabelling method in fish liver, it can be interpreted as DNA damage caused by pollutants.

Animals↗

PubMed1967

Streptococcal nucleases. II. Characterization of DNAse D.

Preparations of streptococcal DNAse D with high specific activity and free of other streptococcal nucleases have been obtained by zone electrophoresis and column chromatography. Antisera prepared by injecting rabbits with such preparations specifically neutralize the activity of this enzyme. As with DNAse B, preparations of DNAse D regularly exhibit ribonuclease activity. For both B and D enzymes, the order of substrate preference is thymus DNA, yeast RNA, bacterial RNA; but the specific activity of the D enzyme is higher than that of the B enzyme with respect to thymus DNA and lower with respect to bacterial RNA. Both the deoxyribonuclease and the ribonuclease activities exhibited by preparations of both enzymes are inhibited by bacterial RNA, but approximately 100-fold greater concentrations of bacterial RNA are required to achieve inhibition of the deoxyribonuclease activity of the D enzyme equivalent to the inhibition of the B enzyme. The deoxyribonuclease activity of the D enzyme is also inhibited by yeast RNA, but even larger amounts are required. These observations indicate that the D enzyme is immunologically distinct from the other streptococcal nucleases and that it differs quantitatively from the B enzyme with respect to relative specific activities on different substrates and behavior in the presence of the bacterial ribonucleic acid inhibitor.

Citrates↗

PubMed1994

Inhibition of HIV type 1 reverse transcriptase assay by nucleases produced by contaminating mycoplasmas.

Mycoplasmal contamination of HIV-1-infected cells has been found to induce reduction of reverse transcriptase (RT) activity; however, the exact mechanism of this phenomenon was not clearly elucidated. Our results indicate that the apparent reduction in RT activity is due to a calcium-dependent nuclease(s) that is (are) produced by contaminating mycoplasmas. The interference with the RT assay was found to be due to the degradation of products of the RT activity. Addition of EGTA at a 1 mM concentration was sufficient to remove the inhibitory effect. The particular HIV-1-producing cell line that was under study was found to be contaminated with Mycoplasma fermentans and Mycoplasma pirum and the latter was isolated in pure culture. Nuclease activity was also observed with pure cultures of mycoplasmas from different species. The activity was found to be of the endonuclease type because it was active with both supercoiled and linear DNAs.

Cell Line↗

PubMed1994

Resistance to degradation by nucleases of (2'S)-2'-deoxy-2'-C-methyloligonucleotides, novel potential antisense probes.

An oligonucleotide must fulfill two main requirements to become a potential antisense probe: effective hybridization properties with the complementary sequence and stability toward nucleases. In this article the degradation pattern of a new class of potential antisense fragment, (2'S)-2'-deoxy-2'-C-methyloligonucleotides, is analyzed. The results described here show that the modification introduced in these oligonucleotides confers an enhanced stability toward purified nucleases, human sera, and HeLa cell extracts.

Base Sequence↗

PubMed2004

A human telomerase-associated nuclease.

Ciliate and yeast telomerase possess a nucleolytic activity capable of removing DNA from the 3' end of a single-stranded oligonucleotide substrate. The nuclease activity is thought to assist in enzyme proofreading and/or processivity. Herein, we report a previously uncharacterized human telomerase-associated nuclease activity that shares several properties with ciliate and yeast telomerases. Partially purified human telomerase, either from cell extracts or recombinantly produced, demonstrated an ability to remove 3' nontelomeric nucleotides from a substrate containing 5' telomeric DNA, followed by extension of the newly exposed telomeric sequence. This cleavage/extension activity was apparent at more than one position within the telomeric DNA and was influenced by sequences 5' to the telomeric/nontelomeric boundary and by substitution with a methylphosphonate moiety at the telomeric/nontelomeric DNA boundary. Our data suggest that human telomerase is associated with an evolutionarily conserved nucleolytic activity and support a model in which telomerase-substrate interactions can occur distal from the 3' primer end.

Exodeoxyribonucleases↗

PubMed2003

DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.

The Vibrio vulnificus nuclease, Vvn, is a non-specific periplasmic nuclease capable of digesting DNA and RNA. The crystal structure of Vvn and that of Vvn mutant H80A in complex with DNA were resolved at 2.3 A resolution. Vvn has a novel mixed alpha/beta topology containing four disulfide bridges, suggesting that Vvn is not active under reducing conditions in the cytoplasm. The overall structure of Vvn shows no similarity to other endonucleases; however, a known 'betabetaalpha-metal' motif is identified in the central cleft region. The crystal structure of the mutant Vvn-DNA complex demonstrates that Vvn binds mainly at the minor groove of DNA, resulting in duplex bending towards the major groove by approximately 20 degrees. Only the DNA phosphate backbones make hydrogen bonds with Vvn, suggesting a structural basis for its sequence-independent recognition of DNA and RNA. Based on the enzyme-substrate and enzyme-product structures observed in the mutant Vvn-DNA crystals, a catalytic mechanism is proposed. This structural study suggests that Vvn hydrolyzes DNA by a general single-metal ion mechanism, and indicates how non-specific DNA-binding proteins may recognize DNA.

Amino Acid Sequence↗

PubMed1982

Influence of disulfide-reducing agents on fractionation of the chromatin complex by endogenous nucleases and deoxyribonuclease I in aging mice.

Age-related alterations in chromatin were evaluated by a fractionation procedure involving limited digestion of liver cell nuclei from young adult and old mice with endogenous nucleases and deoxyribonuclease I. The results suggest that in the chromatin the bulk of the nuclear deoxyribonucleic acid (DNA) may be folded or compacted into domains or loops and associated at a few points with a nuclear protein skeleton structure represented by the final pellet fraction which is resistant to deoxyribonuclease I. Disulfide bonds appear to play a role in the linkage of regions of DNA with this nuclear protein skeleton structure. The amount of DNA that could be released from the pellet fraction by disulfide-reducing agents was significantly greater with old than with young adult mice. In addition, the amount of chromatin material released into the first soluble fraction decreased and that in the second soluble fraction increased with age. Treatment of the nuclei with disulfide-reducing agents did not correct this particular age-related change. Previous results had shown a similar alteration with age of chromatin subjected to digestion by micrococcal nuclease. The combined results suggest the existence of a supranucleosomal alteration in chromatin structure during aging.

Aging↗

PubMed1974

Mung bean nuclease: mode of action and specificity vs synthetic esters of 3'-nucleotides.

Mung bean nuclease hydrolyzes synthetic esters of 3'-nucleotides to nucleosides and phosphate esters; esters of 2'-nucleotides, and 2'--> 5' internucleotide linkages, are resistant. Esters of ribonucleotides are cleaved at 100-fold the rate for deoxyribonucleotides, the increased rate being due to presence of the 2'-hydroxyl and not to differences in conformation. Introduction of a 5'-substituent leads to a 3-fold increase in rate. The rates of hydrolysis vary up to 10-fold with the nature of the base, in the order adenine > hypoxanthine > uracil; and up to 6-fold with the nature of the ester radical. This form of cleavage of esters of 3'-nucleotides is also characteristic for nuclease-3'-nucleotidase activities from potato tubers and wheat, suggesting that one type of enzyme is responsible for all these activities.

Esterification↗

PubMed1982

Accurate transcription of cloned Xenopus rRNA genes by RNA polymerase I: demonstration by S1 nuclease mapping.

We have demonstrated faithful transcriptional initiation of cloned Xenopus rRNA genes upon injection into Xenopus oocytes. This observation has been made possible by the use of an S1 nuclease assay that is both sensitive and quantitative. In order to detect rRNA synthesis from the injected template above the large background of rRNA endogenously present in oocytes, the divergence of ribosomal DNA sequences between two Xenopus species was utilized. Cloned X. laevis ribosomal DNA was injected into the nuclei of X. borealis oocytes. Total oocyte RNA was then isolated and hybridized to a radioactive DNA probe that over laps the 5' end of X. laevis rRNA; endogenous rRNA of the X. borealis oocytes does not hybridize to the probe. RNA/DNA hybrids were treated with S1 nuclease and protected fragments were sized by polyacrylamide gel electrophoresis. RNA made from the injected rDNA protects the same region of probe as does authentic X. laevis precursor rRNA. Thus, transcription appears to initiate on the cloned, microinjected X. laevis rDNA at the same site as is used in vivo. This synthesis is not impaired by coinjection of an amount of alpha-amanitin sufficient to inhibit RNA polymerase II and III; therefore the reaction is mediated by RNA polymerase I. The amount of transcription may be reproducibly quantitated and we have varied a number of parameters in order to maximize transcriptional expression of the injected rDNA. Eight independently isolated X. laevis rDNA clones as well as several subcloned initiation regions of these genes are all accurately transcribed at approximately equal efficiency. This assay should facilitate analysis of several aspects of rRNA transcription, including deleniation of the Xenopus RNA polymerase I promoter location.

Animals↗

PubMed1983

Nuclease-hypersensitive sites in the chromatin domain of the chicken lysozyme gene.

We have examined the chromatin structure of a 22 kilobase-pair chromosomal region containing the lysozyme gene in laying hen. Nuclease-hypersensitive sites were probed with DNAase I by using an indirect end-labeling technique. Eight DNAase I-hypersensitive sites could be mapped in the flanking regions of the gene in oviduct cells, in which the gene is expressed. The same sensitive sites were detected by utilization of an endogenous nuclease activity present in oviduct nuclei. Only one hypersensitive site was detected in the chromatin from erythrocytes, in which the gene is not expressed. The 3'-terminus of the lysozyme gene is highly exposed in nuclei from both tissues. Of special interest is the hypersensitive site at the 5'-terminus of the actively transcribed gene since it maps at the region of multiple initiation sites of transcription and the putative control regions of steroid hormones. DNAase I-hypersensitive chromatin structures also at a greater distance from the gene may take part in the control of gene expression.

Animals↗

PubMed1983

Nuclease mapping of the secondary structure of the 49-nucleotide 3' terminal cloacin fragment of Escherichia coli 16s RNA and its interactions with initiation factor 3.

Escherichia coli translational initiation factor 3 (IF3) may be crosslinked to the 3' end of 16S RNA in 30S ribosomal subunits. In order to determine the sequence to which IF3 may bind in vivo, samples of 5'-32P labelled 3' terminal 49-nucleotide fragment of 16S RNA were incubated 5 min. at 37 degrees in 40 mM Tris-HOAc, pH 7.4, 100 mM NaCl, 1 mM Mg (OAc)2, 1 mM ZnSO4, with or without IF3, then reacted a further 5 min with nuclease S1, RNase T1, or RNase A. Base pairing between the 5' and 3' legs of the fragment occurs in the absence of IF3, but is disrupted by IF3 binding. IF3 appears to protect some residues near the 5' end of the fragment (U1495, A1499, A1500, A1502, and A1503) from nuclease S1, and potentiates S1 attack on others (G1494, G1497, C1501, G1504, G1505, U1506, G1517, G1529, G1530, and C1533). A series of equimolar reactions at increasing dilution imply an association constant range of 1.4-7.0 X 10(7) M-1.

Bacteriocins↗

PubMed1984

Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment.

We have determined the nucleotide sequences around two alternative sites cleaved in supercoiled PM2 DNA by single-strand-specific mung bean nuclease in different ionic environments. In 10 mM Tris-HC1 (pH 7.0, 37 degrees C), the major site is a dA+dT-rich sequence which maps with a known early denaturation region at 0.75 map units. About 30 cleavages occurred in a 135 bp region. Cleavages were largely excluded at (dA)n . (dT)n (n = 3-7) sequences. Cleavage patterns of this type have not been previously observed in dA+dT-rich sequences. With the addition of 0.1 M NaC1 the major alternative site occurred in a hyphenated inverted repeat sequence 500 bp away (0.70 map units) and did not map to an early denaturation region. One major and 4 minor cleavages occurred in the region between the repeats, suggesting that a hairpin containing at most a 12 bp stem and 10 base loop is recognized. The basis for nuclease recognition of the dA+dT-rich sequence is not clear. The differences in the sequences and cleavage patterns at the alternative sites indicate that their secondary structures differ.

Bacteriophages↗

PubMed1984

Interactions between avian myeloblastosis reverse transcriptase and tRNATrp. Mapping of complexed tRNA with chemicals and nucleases.

The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. Results with nucleases and chemicals show that reverse transcriptase interacts preferentially with the D arm, the anticodon stem and the T psi stem. All these regions are located in the outside of the L-shaped structure of tRNA. This domain of interaction is different to that reported previously in the complex of beef tRNA with the cognate aminoacyl-tRNA synthetase (M. Garret et al.; Eur. J. Biochem. In press). Avian reverse transcriptase destabilizes the region of tRNA where most of the tertiary interactions maintaining the structure of tRNA are located.

Alkylation↗

PubMed1985

Selective protection of in vitro synthesized cDNA against nucleases by incorporation of phosphorothioate-analogues.

The conditions for the stepwise synthesis of single- (ss) and double-stranded (ds) cDNA using thio-analogues instead of dNTPs are described in this paper. RNA of paramyxovirus Sendai (strain 6/94) serves as template in these experiments. The increased resistance of this alpha S-modified cDNA against several nucleases, like S1-Nuclease, DNase I, Exonuclease III, snake venom Phosphodiesterase (PDE) and the combination of DNase I and PDE is demonstrated.

DNA↗

PubMed1987

S1 nuclease sensitivity of a double-stranded telomeric DNA sequence.

We examined structural properties of poly d(C4A2).d(T2G4), the telomeric DNA sequence of the ciliated protozoan Tetrahymena. Under conditions of high negative supercoiling, poly d(C4A2).d(T2G4) inserted in a circular plasmid vector was preferentially sensitive to digestion with S1 nuclease. Only the C4A2 strand was sensitive to first-strand S1 cutting, with a markedly skewed pattern of hypersensitive sites in tracts of either 46 or 7 tandem repeats. Linear poly d(C4A2).(T2G4) showed no preferential S1 sensitivity, no circular dichroism spectra indicative of a Z-DNA conformation, no unusual Tm, and no unusual migration in polyacrylamide gel electrophoresis. The S1 nuclease sensitivity properties are consistent with a model proposed previously for supercoiled poly d(CT).d(AG) (Pulleyblank et al., Cell 42:271-280, 1985), consisting of a double-stranded, protonated, right-handed underwound helix. We propose that this structure is shared by related telomeric sequences and may play a role in their biological recognition.

Base Sequence↗

PubMed1988

Mung bean nuclease exhibits a generalized gene-excision activity upon purified Plasmodium falciparum genomic DNA.

A novel set of reaction conditions for mung bean nuclease has been described in which Plasmodium genes were specifically excised as intact fragments from purified DNA. We have now determined that under the new conditions mung bean nuclease cleaves precisely at sites outside of the coding region of every P. falciparum gene for which the extent of the protein coding region in genomic DNA is known. We conclude that this enzyme activity is probably a general one for P. falciparum genes. Introns are not specifically cleaved, although one gene contained a cleavage site within an intron. There is no direct relationship between dA.dT-richness and sites of cleavage under these conditions. Also contrary to the expectations of a model based on cleavage at denaturation bubbles, there was no general relationship between the concentration of the DNA denaturant, formamide, and the size of the resulting gene-containing fragments. Thus, the data strongly suggest the involvement of an altered DNA structure near gene boundaries in determining the recognition sites for this enzyme activity.

Animals↗