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Biochemistry May 1983Removal of purine bases from phi X174 single-stranded DNA leads to increased reversion frequency of amber mutations when this DNA is copied in vitro with purified DNA...
Removal of purine bases from phi X174 single-stranded DNA leads to increased reversion frequency of amber mutations when this DNA is copied in vitro with purified DNA polymerases. This depurination-induced mutagenesis is observed at three different genetic loci and with several different purified enzymes, including Escherichia coli DNA polymerases I and III, avian myeloblastosis virus DNA polymerase, and eukaryotic DNA polymerases alpha, beta, and gamma. The extent of mutagenesis correlates with the estimated frequency of bypass of the lesion and is greatest with inherently inaccurate DNA polymerases which lack proofreading capacity. With E. coli DNA polymerase I, conditions which diminish proofreading result in a 3-5-fold increase in depurination-induced mutagenesis, suggesting a role for proofreading in determining the frequency of bypass of apurinic sites. The addition of E. coli single-stranded DNA-binding protein to polymerase I catalyzed reactions with depurinated DNA had no effect on the extent of mutagenesis. Analysis of wild-type revertants produced during in vitro DNA synthesis by polymerase I or avian myeloblastosis virus DNA polymerase on depurinated phi X174 amber 3 DNA indicates a preference for insertion of dAMP opposite the putative apurinic site at position 587. These results are discussed in relation both to the mutagenic potential of apurinic sites in higher organisms and to studies on error-prone DNA synthesis.
Topics: Animals; Apurinic Acid; Avian Myeloblastosis Virus; Cattle; DNA Polymerase I; DNA Polymerase II; DNA Polymerase III; DNA Replication; DNA-Directed DNA Polymerase; Escherichia coli; HeLa Cells; Humans; Kinetics; Liver Neoplasms, Experimental; Mutation; Polynucleotides; Rats; Thymus Gland
PubMed: 6344919
DOI: 10.1021/bi00279a012 -
Chemico-biological Interactions 1988Styrene-7,8-oxide was reacted with guanosine and deoxyguanosine and four isomeric 7-alkylguanosines were isolated, two of each being substitutions through the alpha and...
Styrene-7,8-oxide was reacted with guanosine and deoxyguanosine and four isomeric 7-alkylguanosines were isolated, two of each being substitutions through the alpha and beta carbon of styrene oxide. The diastereomeric adducts imidazole ring-opened at an identical rate but the alpha- and beta-adducts differed (half-lives 90 and 56 min, respectively, pH 10, 24 degrees C). The 7-beta alkyl-deoxyguanosine derivatives ring-opened at a six times slower rate, which was similar to 7-methyldeoxyguanosine. The diastereomeric guanosine products also depurinated at the same rate but the beta-derivatives depurinated faster than the alpha-derivatives (t1/2 35 vs. 79 min, respectively, pH 1, 70 degrees C). The differences in the ring-opening and depurination of the alpha- and beta-isomers corresponded to their respective pK alpha values (7.31-7.32 vs. 7.16-7.19). The 7-alkyldeoxyguanosine derivatives of styrene oxide depurinated equally fast as 7-methyldeoxyguanosine. By contrast, the depurination of 7-alkylguanine was 15 times slower in the single-stranded DNA and 55 times slower in the double-stranded DNA.
Topics: Alkylation; Chromatography, High Pressure Liquid; DNA; Deoxyguanosine; Epoxy Compounds; Ethers, Cyclic; Guanosine; Half-Life; Imidazoles; Nucleosides; Purines; Stereoisomerism
PubMed: 3203402
DOI: 10.1016/0009-2797(88)90010-5 -
Depurination from DNA of 7-methylguanine, 7-(2-aminoethyl)-guanine and ring-opened 7-methylguanines.Chemico-biological Interactions 1989DNA was reacted with dimethyl sulphate and ethyleneimine to afford respective 7-methylguanine and 7-(2-aminoethyl)guanine derivatives. The substituted DNA was boiled in...
DNA was reacted with dimethyl sulphate and ethyleneimine to afford respective 7-methylguanine and 7-(2-aminoethyl)guanine derivatives. The substituted DNA was boiled in 0.1 M NaCl containing 10 mM phosphate buffer (pH 7.0), and the release of 7-alkylguanines, guanine and adenine was followed. The half-lives of depurination were 1.5 and 4.1 min for 7-(2-aminoethyl)guanine and 7-methylguanine, respectively. 7-Methylguanine was released some 60 times faster than guanine and adenine. When 7-methylguanine-containing DNA was treated in alkali to cause imidazole ring-opening, two products were liberated by boiling the DNA solution. These products were released with apparent half-lives of 69 and 34 min. These ring-opened products isomerized to each other completely within 1 h at 37 degrees C. The isomers had an identical ultraviolet spectrum and they displayed a pKa of 9.8. When silylated and analysed in gas chromatography-mass spectroscopy the two isomers had an identical molecular weight and fragmentation pattern, consistent with a structural assignment as N5-methyl-N5-formyl-2,5,6-triamino-4-oxopyrimidine. Only one of the isomers appeared to be present on DNA; the isomerization took place when the ring-opened product was released into solution.
Topics: Animals; Chromatography, High Pressure Liquid; DNA; Gas Chromatography-Mass Spectrometry; Guanine; Kinetics; Models, Chemical; Molecular Structure
PubMed: 2743474
DOI: 10.1016/0009-2797(89)90051-3 -
Nucleic Acids Research Aug 1996Fully protected CPG-immobilized monomer, dimer and trimer oligonucleotides were used to study depurination during the chemical synthesis of oligonucleotides....
Fully protected CPG-immobilized monomer, dimer and trimer oligonucleotides were used to study depurination during the chemical synthesis of oligonucleotides. Disappearance of the oligonucleotide during acid exposure time relative to an internal thymidine standard not subject to depurination was monitored by reverse phase HPLC analysis. Depurination half-times obtained for dichloroacetic acid (DCA) and trichloroacetic acid (TCA) in methylene chloride were found to be 3% DCA >> 15% DCA > 3% TCA. In order to understand the implications of depurination during DNA synthesis, the detritylation kinetics of model compounds DMT-dG-pT dimer and DMT-[17mer] mixed-base sequence were also measured. These results improve our ability to properly balance the contradictory goals of obtaining maximum detritylation with minimum depurination in oligonucleotide synthesis.
Topics: Adenosine; Base Sequence; Guanosine; Kinetics; Molecular Sequence Data; Oligodeoxyribonucleotides; Purines; Trityl Compounds
PubMed: 8760893
DOI: 10.1093/nar/24.15.3053 -
Infection and Immunity Jan 2007The plant toxin ricin is one of the most potent and lethal substances known. Ricin inhibits protein synthesis by removing a specific adenine from the highly conserved...
The plant toxin ricin is one of the most potent and lethal substances known. Ricin inhibits protein synthesis by removing a specific adenine from the highly conserved alpha-sarcin/ricin loop in the large rRNA. Very little is known about how ricin interacts with ribosomes and the molecular mechanism by which it kills cells. To gain insight to the mechanism of ricin-induced cell death, we set up yeast (Saccharomyces cerevisiae) as a simple and genetically tractable system to isolate mutants defective in cytotoxicity. Ribosomes were depurinated in yeast cells expressing the precursor form of the A chain of ricin (pre-RTA), and these cells displayed apoptotic markers such as nuclear fragmentation, chromatin condensation, and accumulation of reactive oxygen species. We conducted a large-scale mutagenesis of pre-RTA and isolated a panel of nontoxic RTA mutants based on their inability to kill yeast cells. Several nontoxic RTA mutants depurinated ribosomes and inhibited translation to the same extent as wild-type RTA in vivo. The mutant proteins isolated from yeast depurinated ribosomes in vitro, indicating that they were catalytically active. However, cells expressing these mutants did not display hallmarks of apoptosis. These results provide the first evidence that the ability to depurinate ribosomes and inhibit translation does not always correlate with ricin-mediated cell death, indicating that ribosome depurination and translation inhibition do not account entirely for the cytotoxicity of ricin.
Topics: Cell Death; Chemical Warfare Agents; Immunoblotting; Protein Biosynthesis; Purines; RNA, Ribosomal; Ribosomes; Ricin; Saccharomyces cerevisiae
PubMed: 17101666
DOI: 10.1128/IAI.01295-06 -
Toxins Apr 2017Both ricin and Shiga holotoxins display no ribosomal activity in their native forms and need to be activated to inhibit translation in a cell-free translation inhibition...
Both ricin and Shiga holotoxins display no ribosomal activity in their native forms and need to be activated to inhibit translation in a cell-free translation inhibition assay. This is because the ribosome binding site of the ricin A chain (RTA) is blocked by the B subunit in ricin holotoxin. However, it is not clear why Shiga toxin 1 (Stx1) or Shiga toxin 2 (Stx2) holotoxin is not active in a cell-free system. Here, we compare the ribosome binding and depurination activity of Stx1 and Stx2 holotoxins with the A1 subunits of Stx1 and Stx2 using either the ribosome or a 10-mer RNA mimic of the sarcin/ricin loop as substrates. Our results demonstrate that the active sites of Stx1 and Stx2 holotoxins are blocked by the A2 chain and the B subunit, while the ribosome binding sites are exposed to the solvent. Unlike ricin, which is enzymatically active, but cannot interact with the ribosome, Stx1 and Stx2 holotoxins are enzymatically inactive but can interact with the ribosome.
Topics: Ribosomes; Ricin; Shiga Toxin 1; Shiga Toxin 2
PubMed: 28398250
DOI: 10.3390/toxins9040133 -
Journal of Molecular Evolution Oct 2017The Alu element, the most prevalent SINE (short interspersed element) in the human genome, is one of the many RNA-encoding genes that evolved from the 7SL RNA gene....
The Alu element, the most prevalent SINE (short interspersed element) in the human genome, is one of the many RNA-encoding genes that evolved from the 7SL RNA gene. During analysis of the evolution of 7SL-derived RNAs, two distinct evolutionary intermediates capable of self-catalyzed DNA depurination (SDP) were identified. These SDP sequences spontaneously create apurinic sites that can result in increased mutagenesis due to their error-prone repair. This DNA self-depurination mechanism has been shown both in vitro and in vivo to lead to substitution and short frameshift mutations at a frequency that far exceeds their occurrence due to random errors in DNA replication. In both evolutionary intermediates, the same self-depurination sequence overlaps motifs necessary for successful transcription and SRP9/14 (signal recognition particle) binding; hence, mutations in this region could disrupt RNA activity. Yet, the 7SL-derived RNAs that arose from the elements capable of SDP show significant diversity in this region, and every new sequence retains the transcription and SRP9/14-binding motifs, even as it has lost the SDP sequence. While some (but not all) of the mutagenesis can be alternatively attributed to CpG decay, the very fact that the self-depurinating sequences are selectively discarded in all cases suggests that this was evolutionarily motivated to prevent further destructive mutagenesis by the SDP mechanism.
Topics: Alu Elements; DNA, Catalytic; Evolution, Molecular; Humans; Mutagenesis; Mutation; RNA, Small Cytoplasmic; Signal Recognition Particle
PubMed: 29103173
DOI: 10.1007/s00239-017-9811-y -
Mutation Research Aug 2015The human β-globin, δ-globin and ɛ-globin genes contain almost identical coding strand sequences centered about codon 6 having potential to form a stem-loop with a... (Comparative Study)
Comparative Study
The human β-globin, δ-globin and ɛ-globin genes contain almost identical coding strand sequences centered about codon 6 having potential to form a stem-loop with a 5'GAGG loop. Provided with a sufficiently stable stem, such a structure can self-catalyze depurination of the loop 5'G residue, leading to a potential mutation hotspot. Previously, we showed that such a hotspot exists about codon 6 of β-globin, with by far the highest incidence of mutations across the gene, including those responsible for 6 anemias (notably Sickle Cell Anemia) and β-thalassemias. In contrast, we show here that despite identical loop sequences, there is no mutational hotspot in the δ- or ɛ1-globin potential self-depurination sites, which differ by only one or two base pairs in the stem region from that of the β-globin gene. These differences result in either one or two additional mismatches in the potential 7-base pair-forming stem region, thereby weakening its stability, so that either DNA cruciform extrusion from the duplex is rendered ineffective or the lifetime of the stem-loop becomes too short to permit self-catalysis to occur. Having that same loop sequence, paralogs HB-γ1 and HB-γ2 totally lack stem-forming potential. Hence the absence in δ- and ɛ1-globin genes of a mutational hotspot in what must now be viewed as non-functional homologs of the self-depurination site in β-globin. Such stem-destabilizing variants appeared early among vertebrates and remained conserved among mammals and primates. Thus, this study has revealed conserved sequence determinants of self-catalytic DNA depurination associated with variability of mutation incidence among human β-globin paralogs.
Topics: Animals; Base Pair Mismatch; Base Sequence; Catalysis; Codon; Conserved Sequence; DNA; Evolution, Molecular; Guanine; Hemoglobinopathies; Humans; Molecular Sequence Data; Nucleic Acid Conformation; Point Mutation; Sequence Alignment; Sequence Homology, Nucleic Acid; Species Specificity; Vertebrates; beta-Globins; delta-Globins; gamma-Globins
PubMed: 26042536
DOI: 10.1016/j.mrfmmm.2015.05.001 -
Toxicon : Official Journal of the... Jul 2013The plant toxin ricin is highly toxic for mammalian cells and is of concern for bioterrorism. Ricin belongs to a family of functionally related toxins, collectively... (Review)
Review
The plant toxin ricin is highly toxic for mammalian cells and is of concern for bioterrorism. Ricin belongs to a family of functionally related toxins, collectively referred to as ribosome inactivating proteins (RIPs), which disable ribosomes and halt protein synthesis. Currently there are no specific antidotes against ricin or related RIPs. The catalytic subunit of ricin is an N-glycosidase that depurinates a universally conserved adenine residue within the sarcin/ricin loop (SRL) of the 28S rRNA. This depurination activity inhibits translation and its biochemistry has been intensively studied. Yet, recent developments paint a more complex picture of toxicity, with ribosomal proteins and cellular signaling pathways contributing to the potency of ricin. In particular, several studies have now established the importance of the ribosomal stalk structure in facilitating the depurination activity and ribosome specificity of ricin and other RIPs. This review highlights recent developments defining toxin-ribosome interactions and examines the significance of these interactions for toxicity and therapeutic intervention.
Topics: Animals; Apoptosis; Bioterrorism; Humans; RNA, Ribosomal, 28S; Ribosome Inactivating Proteins; Ribosomes; Ricin; Signal Transduction
PubMed: 23454625
DOI: 10.1016/j.toxicon.2013.02.001 -
Nucleic Acids Research Nov 1994Products formed from defined oligodeoxyribonucleotide tetramers (oligonucleotides) by depurination at pH 5.0 and 90 degrees C followed by chain breakage at the resulting...
Products formed from defined oligodeoxyribonucleotide tetramers (oligonucleotides) by depurination at pH 5.0 and 90 degrees C followed by chain breakage at the resulting apurinic sites (AP sites) were assigned by reversed phase HPLC. Through kinetic analysis, rate constants of depurination and subsequent chain breakage reactions were measured. Depurination of the oligonucleotides with purine bases locating at the terminal positions was several times faster than those with purines at the internal ones. The pKa values for the N7 of the G residues and the activation energies of the depurination were essentially independent of the position of the bases. The frequency factor was found to be responsible for the observed difference of the depurination rates. In contrast, the chain breakage by beta-elimination was several times faster for the AP sites formed at the internal positions than those at the 5'-terminal positions. It is suggested that an electron withdrawing phosphate group attached to the 5'-side of an AP site facilitates the chain cleavage.
Topics: Apurinic Acid; Chromatography, High Pressure Liquid; Guanine; Hot Temperature; Hydrogen-Ion Concentration; Kinetics; Magnetic Resonance Spectroscopy; Models, Chemical; Oligodeoxyribonucleotides
PubMed: 7800492
DOI: 10.1093/nar/22.23.4997