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Endonuclease III: an endonuclease from Escherichia coli that introduces single polynucleotide chain scissions in ultraviolet-irradiated DNA.

An endonuclease that makes single polynucleotide chain scissions in UV-irradiated DNA has been purified from Escherichia coli. The activity has the following properties: (1) unirradiated DNA is attacked very little if at all; (2) single-stranded DNA is not attacked, whether irradiated or not; (3) there is no requirement for divalent cations, and the activity is not affected by addition of EDTA; (4) the pH optimum is approximately 7; (5) the activity is inhibited by 1 M NaCl, single-stranded DNA, transfer RNA, and unirradiated double-stranded DNA; (6) the sedimentation coefficient, S20, W, is approximately 2.6; (7) it is a basic protein. The enzyme is tentatively named E. coli endonuclease III. The physiological function of the endonuclease has not yet been established.

Centrifugation, Density Gradient↗

Polynucleotide phosphorylase can participate in decay of mRNA in Escherichia coli in the absence of ribonuclease II.

In a mutant strain defective in polynucleotide phosphorylase, under conditions where the enzyme becomes limiting, it is possible to demonstrate that chemical as well as functional half lives of mRNA become longer if the strain is also missing ribonuclease II. These results allow to unify in a simple model a variety of observations about turnover of RNA in a variety of bacteria.

Escherichia coli↗

RNA processing by RNase III is involved in the synthesis of Escherichia coli polynucleotide phosphorylase.

The synthesis of Escherichia coli polynucleotide phosphorylase (PNPase) was examined in a mutant strain defective in the RNA processing enzyme RNase III (Rnc-). We found that the specific activity and the synthesis rate of PNPase were increased in the Rnc- strain by more than three times that in an Rnc+ strain. Such increased synthesis of PNPase was not observed in a mutant strain transformed with a plasmid carrying the rnc+ gene. Quantitative analysis of RNA showed that the transcripts from the pnp gene, which encodes PNPase, were degraded more slowly in the Rnc- strain than in the Rnc+ strain. These results indicate that processing of the transcripts by RNase III is intimately involved in controlling the expression of pnp by affecting the stability of its messenger RNA.

DNA Restriction Enzymes↗

A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins.

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a 'c-value paradox' becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence 'motif' that is variable within certain limits. Noncoding sequences of the chickens ovalbumin gene furnish an appropriate example of a sequence motif. GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organisms, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.

Animals↗

The effects of gamma-irradiation on the hydration characteristics of DNA and polynucleotides. III. A comparative NMR study of frozen and liquid solutions.

The effects of gamma-irradiation and changes in the macromolecular structure on the water proton resonance spectra observed in frozen and liwuid solutions have been compared for the DNA and polynucleotide solutions, using H2O or mixed H2O/D2O solvents. The results indicate that in order to obtain information concerning the role of hydration water in mediating the overall radiation damage, the NMR studies must be performed in the frozen state.

Cold Temperature↗

The binding and reactions of nucleotides and polynucleotides on iron oxide hydroxide polymorphs.

The iron oxide hydroxide minerals goethite and akaganéite were likely constituents of the sediments present in, for instance, geothermal regions of the primitive earth. They may have adsorbed organics and catalyzed the condensation processes which led to the origins of life. The binding to and reactions of nucleotides and oligonucleotides with these minerals was investigated. The adsorption of adenosine, 5'-AMP, 3'-AMP, 5'-UMP, and 5'-CMP to these minerals was studied. Adenosine did not bind to goethite and akaganéite. The adsorption isotherms for the binding of the nucleotides revealed that they all had close to the same affinity for the mineral. Binding to goethite was about four times stronger than to akaganéite. There was little difference in the adsorption of each nucleotide suggesting the binding was between the negative charge on the phosphate group and the positive charges on the mineral surface. The absence of binding of adenosine is consistent with this explanation. Binding decreases as the pH increases due to the titration of the positive (acidic) centers on the minerals. Two times as many moles of polynucleotides were bound to these minerals as compared to the mononucleotides. Watson-Crick hydrogen bonding of adenosine and 5'-AMP to poly(U) complexes with goethite and akaganéite was observed. There was no interaction of uridine with the poly(U)-goethite complex as expected if Watson-Crick hydrogen bonding is taking place. Neither goethite nor akaganéite catalyzed the oligomerization of the phosphorimidazolide of adenosine (ImpA). The template directed synthesis of oligomers of 5'-GMP on the poly(C) bound to goethite was observed. Higher molecular weight oligomers were observed when the poly(C) was bound to goethite than was found in the absence of the mineral.

Adenosine↗

De Novo Synthesis of DNA-Like Molecules by Polynucleotide Phosphorylase In Vitro

In the presence of Mg2+ ions, polynucleotide phosphorylase (PNPase, EC 2.7.7.8) is known to synthesize RNA-like polymers using ribonucleoside-5'-diphosphate (NDP) substrates but to be unable to utilize deoxyribonucleoside substrates. Our experiments show that when MgCl2 is replaced by FeCl3, PNPase becomes able to synthesize deoxyheteropolymers using deoxyribonucleoside-5'-diphosphates (dNDPs). The deoxyheteropolymer formed from the four dNDPs is degraded by pancreatic DNase, but not by RNase, and is readily used as a template by DNA-dependent DNA polymerase. Synthesis of this DNA-like polymer is accomplished de novo without the help of any primer or preexisting template. What is more, dA/dG and dC/dT ratios of polymers synthesized by different bacterial PNPases closely match ratios found in DNA of the bacterial species the enzyme came from.

Journal Article↗

New ribosome-inactivating proteins with polynucleotide:adenosine glycosidase and antiviral activities from Basella rubra L. and bougainvillea spectabilis Willd.

New single-chain (type 1) ribosome-inactivating proteins (RIPs) were isolated from the seeds of Basella rubra L. (two proteins) and from the leaves of Bougainvillea spectabilis Willd. (one protein). These RIPs inhibit protein synthesis both in a cell-free system, with an IC50 (concentration causing 50% inhibition) in the 10(-10) M range, and by various cell lines, with IC50S in the 10(-8)-10(-6) M range. All three RIPs released adenine not only from rat liver ribosomes but also from Escherichia coli rRNA, polyadenylic acid, herring sperm DNA, and artichoke mottled crinkle virus (AMCV) genomic RNA, thus being polynucleotide:adenosine glycosidases. The proteins from Basella rubra had toxicity to mice similar to that of most type 1 RIPs (Barbieri et al., 1993, Biochim Biophys Acta 1154: 237-282) with an LD50 (concentration that is 50% lethal) < or = 8 mg.kg-1 body weight, whilst the RIP from Bougainvillea spectabilis had an LD50 > 32 mg.kg-1. The N-terminal sequence of the two RIPs from Basella rubra had 80-93% identity, whereas it differed from the sequence of the RIP from Bougainvillea spectabilis. When tested with antibodies against various RIPs, the RIPs from Basella gave some cross-reactivity with sera against dianthin 32, and weak cross-reactivity with momordin I and momorcochin-S, whilst the RIP from Bougainvillea did not cross-react with any antiserum tested. An RIP from Basella rubra and one from Bougainvillea spectabilis were tested for antiviral activity, and both inhibited infection of Nicotiana benthamiana by AMCV.

3T3 Cells↗

Isolation and characterization of four type-1 ribosome-inactivating proteins, with polynucleotide:adenosine glycosidase activity, from leaves of Phytolacca dioica L.

Four type-1 (single-chain) ribosome-inactivating proteins (RIPs), with isoelectric points between 9.5 and 9.7, were isolated from leaves of Phytolacca dioica L. The purification procedure furnished the four proteins with an overall yield of about 16% and separated them from a protein of 29,407 +/- 2 Da, as determined by electrospray mass spectrometry, whose N-terminal amino acid sequence differed from that of pokeweed (Phytolacca americana L.) leaf chitinase (PLC-B) by only one amino acid (R17I). The four RIPs (PD-L1 to PD-L4) inhibited protein synthesis by a rabbit reticulocyte lysate with 50% inhibition at the picomolar level, and produced the beta-fragment, diagnostic of the specific enzymatic action of RIPs, on yeast ribosomes. Comparison of their N-terminal sequences, up to residue 45, showed that PD-L1 is identical to PD-L2 [designated the isoleucine (Ile) form from the N-terminal residue] and PD-L3 is identical to PD-L4 [designated the valine (Val) form from the N-terminal residue] and that there are 35 identical residues between the two forms. Furthermore, the Val form presents the same number of identical residues as PD-S2, an RIP isolated from the seeds of the same plant. With the exception of PD-L4, the purified RIPs gave a positive reaction when stained for sugars on SDS-PAGE gels and, when analyzed by electrospray mass spectrometry, had M(r) values of 32,715 +/- 1 (PD-L1), 31,542 +/- 1 (PD-L2), 30,356 +/- 1 (PD-L3) and 29,185 +/- 1 Da (PD-L4). The 1171 kDa difference in M(r), within the same RIP form, could be due to glycosylation. Like leaf saporins and many other RIPs, the four RIPs released several adenines from poly(A), herring sperm DNA and rRNA 16S + 23S, thus acting as polynucleotide:adenosine glycosidases. This property was less pronounced in PD-L1 and PD-L3 than in PD-L2 and PD-L4, respectively. The proteins PD-L1 and PD-L4 showed 3.7% reactivity with the antiserum anti-dianthin 32 and no reactivity with antisera to PAP-R saporin-S6, momordin 1 and even PD-S2, an RIP isolated from the seeds of the same plant. Protein PD-L4 showed 12.5% cross-reactivity with anti-PD-L1, while the opposite cross-reactivity was 100%.

Amino Acid Sequence↗

Ionophorous polymers. Interaction with polynucleotides and effects on RNA-directed DNA polymerase activity.

Poly(vinylbenzo-18-crown-6), a water-soluble polymer endowed with ion-binding crown moieties as pendent groups, forms insoluble complexes with polyadenylate in the presence of K+; the corresponding monomeric benzo-18-crown-6, does not form a precipitate under the same conditions. In the presence of Na+ and Mn2+ which in aqueous solution complex weakly to crown compounds, no coprecipitation of the crown polymer and polyadenylate occurs; nevertheless, the crown polymer strongly binds to immobilized polyadenylate even under these conditions. The interactions of crown polymer with the poly-nucleotide result in a loss of templating ability of the latter. Using RNA-dependent DNA polymerase of murine leukemia virus it was found that (1) enzymatic action is efficiently inhibited even in the absence of ions which coprecipitate crown polymer and template, (2) inhibition is reversed by addition of excess polynucleotide and (3) monomeric crown does not inhibit the reaction.

Binding Sites↗

An efficient synthesis of polyguanylic acid by a thermophilic polynucleotide phosphorylase.

Polyguanylic acid (poly(G)) was synthesized from GDP in a yield of 60-75% by Thermus thermophilus polynucleotide phosphorylase (polyribonucleotide: orthophosphate nucleotidyltransferase, EC 2.7.7.8) at 70 degrees C, pH 8.5 in the presence of Mg2+. The yield was dependent on the ratio of GDP to Mg2+, but was independent of the concentrations of enzyme or substrate. The maximal rate of GDP polymerization was obtained when the ratio of GDP to Mg2+ was 3:1. However, by prolonged incubation, the higher initial ratio of over 4:1 was preferred because of the rapid consumption of GDP in the reaction mixture. Poly(G) prepared by 1 h incubation was heterogeneous in size from 5 S to over 23 S, but by prolonged incubation of 19 h the size of product converged to 9 S as judged by sucrose density gradient centrifugation. Its chain length was determined by terminal nucleoside analysis to be 200 nucleotides long.

Bacteria↗

Polynucleotides. XLIV. Synthesis and properties of poly (2-azaadenylic acid) and poly(2-azainosinic acid).

Chemically synthesized 2-azaadenosine 5'-diphosphate (n2ADP) and 2-azainosine 5'-diphosphate (n2IDP) were polymerized to yield poly(2-azaadenylic acid), poly(n2A), and poly(2-azainosinic acid), poly(n2I), using Escherichia coli polynucleotide phosphorylase. In neutral solution, poly(n2A) and poly(n2I) had hypochromicities of 32 and 5.5%, respectively. Poly(n2A) formed an ordered structure, which had a melting temperature (Rm) of 20 degrees C at 0.15 M salt concentration. Upon mixing with poly(U), poly(n2A) formed a 1 : 2 complex with Tm of 41 degrees C at 0.15 M salt concentration. Poly(n2A) and poly(n2I) formed three-stranded complexes with poly(I), and poly(A), respectively. Poly(n2A) . 2poly(I), poly(A) . 2poly(n2I), and poly(n2A) . 2poly(n2I) complexes had Tm values of 23, 48, and 31 degrees C at 0.15 M salt concentration, respectively. Poly(n2I) formed a double-stranded complex with poly(C), but its Tm was very low.

Circular Dichroism↗

A method for the synthesis of oligonucleotide by single addition of 2'-O-(o-nitrobenzyl)nucleoside 5'-diphosphates using polynucleotide phosphorylase.

Two hexanucleotides A-U-G-U-G-A and C-A-A-U-U-G were synthesized from the chemically synthesized trimers C-A-A and A-U-G by addition of 2'-O-(o-nitrobenzyl)nucleoside diphosphates using polynucleotide phosphorylase isolated from either Escherichia coli or Micrococcus luteus. In each reaction the preference of the enzyme was tested. The o-nitrobenzyl group was removed after addition of the mononucleotide and the deblocked product was isolated by chromatography on DEAE-Sephadex in high yields.

Adenosine Diphosphate↗

The existence of unique B structures in polynucleotides with alternating purine-pyrimidine sequences.

The infrared spectra of the sodium salts of calf-thymus DNA, poly(dA-dC).poly(dG-dT), poly(dA-dT) and poly(dG-dC) were measured for the samples as highly hydrated, nonoriented gels. The bands from the sugar-phosphate vibrational modes show that poly(dG-dC) assumes a B-family structure which is different from the B structures of the other samples. Poly(dG-dC) most likely assumes a wrinkled B structure. The other samples retain a smooth B structure. An alternating purine-pyrimidine sequence is not a sufficient condition for the formation of wrinkled B structure in a polynucleotide.

DNA↗

Osmium-labeled polynucleotides: reaction of osmium tetraoxide, with poly-1,N6-ethenoadenylic acid.

Osmium tetraoxide, in the presence of ligands such as pyridine and bipyridine, adds across the etheno bridge of 1,N6-etheno-9-methyladenine and poly-1,N6-ethenoadenylic acid. The Os:P ratio in the labeled polynucleotide was approximately equal to 1 when bipyridine was used as the stabilizing ligand. A similar study with polycytidylic acid, which had been partially modified with chloroacetaldehyde so that some bases were converted to 3,N4-ethenocytosine, gave an OS:P ratio of approximately equal to 1.3. Calf-thymus DNA, in which the adenine and cytosine bases were modified by chloroacetaldehyde, gave an Os:P ratio of approximately equal to 1 after 24 h. These results suggest that 3,N4-ethenocytosine will add two Os labels.

Adenosine Triphosphate↗

Some properties of the irreversible complexes of nitracrine (ledakrin, C-283) with polynucleotides.

In the presence of sulfhydryl compounds an anticancer drug nitracrine (NA), 1-nitro-9-aminoalkylacridine derivative forms strong, probably covalent complexes with DNA. It has been found that it binds with similar efficiency to RNA and DNA exhibiting a certain preference for single-stranded structure. At NA/polynucleotide ratio of 0.15 and nucleic acids concentration 100 microgram/ml the numbers of drug molecules bound per 10(3) nucleotides were about 10--13 for native calf thymus DNA, 19--28 for denatured DNA and 23--36 for RNA. Some base specificity to guanine is observed both in polydeoxyribo- and polyribonucleotides. The complexes of NA with DNA and double-stranded synthetic polynucleotides exhibit decreased transcriptional template activity in bacterial RNA synthesis in vitro system except poly(A) synthesis on poly(dA) x poly(dT) which is insensitive to the drug. The drug binding in vitro leads to cross-link formation in DNA as shown by means of ultraviolet spectrophotometry and hydroxylapatite chromatography of heat-denatured NA-DNA complexes. The amount of the double bonds introduced by the drug is however relatively low as compared with cross-linking of irradiated 8-methoxy-psoralen-DNA (MOP-DNA) complexes.

Aminoacridines↗

The incorporation of O6-methyldeoxyguanosine monophosphate and O4-methyldeoxythymidine monophosphate into polynucleotide templates leads to errors during subsequent in vitro DNA synthesis.

O4-MedTMP and O6-MedGMP may be incorporated from their 5'-triphosphates into polynucleotides by DNA polymerases. Once incorporated O6-MedGMP leads to errors during further cycles of DNA synthesis with a mutagenic efficiency of 0.3-0.7, the value depending upon the relative dNTP concentrations in the assay. In contrast O4-MedTMP leads to very few errors following its incorporation into DNA. The results demonstrate that O6-MedGMP, once incorporated into DNA, should be destined to give rise to DNA base changes during the second round of DNA synthesis.

DNA Replication↗

Interaction of ellipticine and an indolo[2,3b]-quinoxaline derivative with DNA and synthetic polynucleotides.

The non-covalent DNA interaction of the anticancer drug ellipticine (Scheme I, 1a) as well as an indolo[2,3-b]-quinoxaline derivative (Scheme I, 3b) with a dimethylaminoethyl side chain has been studied by light absorption, linear dichroism (LD) and fluorescence. Compound 3b (Scheme I) has antitumorigenic as well as antiviral activity. Both compounds bind to DNA or synthetic polynucleotides such as poly(dA-dT).(dA-dT) and poly(dG-dC).(dG-dC) by intercalation. In contrast to ellipticine, compound 3b (Scheme I) exhibits a significant binding specificity for alternating AT sequences. Its fluorescence is strongly enhanced in AT sequences and quenched in GC sequences. Fluorescence titrations evaluated as Scatchard plots show that both ellipticine and compound 3b (Scheme I) bind to the nucleic acids according to a non-cooperative neighbor exclusion model.

Alkaloids↗