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Journal of Bacteriology Aug 1979The effects of caffeine and acriflavine on cell survival, single-strand deoxyribonucleic acid break formation, and postreplication repair in Escherichia coli wild-type...
The effects of caffeine and acriflavine on cell survival, single-strand deoxyribonucleic acid break formation, and postreplication repair in Escherichia coli wild-type WP2 and WP2 uvrA strains after ultraviolet irradiation was studied. Caffeine (0.5 mg/ml) added before and immediately after ultraviolet irradiation inhibited single-strand deoxyribonucleic acid breakage in wild-type WP2 cells. Single-strand breaks, once formed, were no longer subject to repair inhibition by caffeine. At 0.5 to 2 mg/ml, caffeine did not affect postreplication repair in uvrA strains. These data are consistent with the survival data of both irradiated WP2 and uvrA strains in the presence and absence of caffeine. In unirradiated WP2 and uvrA strains, however, a high caffeine concentration (greater than 2 mg/ml) resulted in gradual reduction of colony-forming units. At a concentration insufficient to alter survival of unirradiated cells, acriflavine (2 microgram/ml) inhibited both single-strand deoxyribonucleic acid breakage and postreplication repair after ultraviolet irradiation. These data suggest that although the modes of action for both caffeine and acriflavine may be similar in the inhibition of single-strand deoxyribonucleic acid break formation, they differ in their mechanisms of action on postreplication repair.
Topics: Acridines; Acriflavine; Caffeine; DNA Repair; DNA, Bacterial; Escherichia coli; Pyrimidine Dimers; Ultraviolet Rays
PubMed: 378983
DOI: 10.1128/jb.139.2.671-674.1979 -
Journal of Bacteriology Jun 1976The deoxyribonucleic acid of the dimorphic bacterium Caulobacter crescentus contains a component that renatures with rapid, unimolecular kinetics. This component was...
The deoxyribonucleic acid of the dimorphic bacterium Caulobacter crescentus contains a component that renatures with rapid, unimolecular kinetics. This component was present in both swarmer and stalked cells and exhibited the sensitivity to endonuclease S1 expected for hairpin loops. Double-stranded side branches between 100 and 600 nucleotide pairs in length were visible in electron micrographs of rapidly reassociating deoxyribonucleic acid isolated by hydroxyapatite chromatography. No extrachromosomal elements were found in spite of systematic attempts to detect their presence. These results indicate that the rapidly reassociating fraction derives from inverted repeat sequences within the chromosome and not from cross-links or plasmids. We estimate that there are approximately 350 inverted repeat regions per Caulobacter genome. The kinetic complexity of Caulobacter deoxyribonucleic acid, however, is no greater than that of other bacteria.
Topics: Bacteria; Base Sequence; DNA Restriction Enzymes; DNA, Bacterial; DNA, Circular; Nucleic Acid Renaturation; Nucleotides
PubMed: 947891
DOI: 10.1128/jb.126.3.1305-1315.1976 -
Scientific Reports Jan 2024The transcription factor binding site is a deoxyribonucleic acid sequence that binds to transcription factors. Transcription factors are proteins that regulate the...
The transcription factor binding site is a deoxyribonucleic acid sequence that binds to transcription factors. Transcription factors are proteins that regulate the transcription gene. Abnormal turnover of transcription factors can lead to uncontrolled cell growth. Therefore, discovering the relationships between transcription factors and deoxyribonucleic acid sequences is an important component of bioinformatics research. Numerous deep learning and machine learning language models have been developed to accomplish these tasks. Our goal in this work is to propose a GMean model for predicting unlabelled deoxyribonucleic acid sequences. The GMean model is a hybrid model with a combination of gated recurrent unit and K-mean clustering. The GMean model is developed in three phases. The labelled and unlabelled data are processed based on k-mers and tokenization. The labelled data is used for training. The unlabelled data are used for testing and prediction. The experimental data consists of deoxyribonucleic acid experimental of GM12878, K562 and HepG2. The experimental results show that GMean is feasible and effective in predicting deoxyribonucleic acid sequences, as the highest accuracy is 91.85% in predicting K562 and HepG2. This is followed by the prediction of the sequence between GM12878 and K562 with an accuracy of 89.13%. The lowest accuracy is the prediction of the sequence between HepG2 and GM12828, which is 88.80%.
Topics: Binding Sites; Protein Binding; Transcription Factors; Computational Biology; DNA
PubMed: 38291225
DOI: 10.1038/s41598-024-52933-4 -
Journal of Bacteriology Apr 1975Deoxyribonucleic acid (DNA)-cytosine methylation specified by the wild-type Escherichia coli K 12 mec+ gene and by the N-3 drug resistance (R) factor was studied in vivo...
Deoxyribonucleic acid (DNA)-cytosine methylation specified by the wild-type Escherichia coli K 12 mec+ gene and by the N-3 drug resistance (R) factor was studied in vivo and in vitro. Phage lambda and fd were propagated in the presence of L-[methyl-3H]methionine in various host bacteria. The in vivo labeled DNA was isolated from purified phage and depurinated by formic acid-diphenylamine treatment. The resulting pyrimidine oligonucleotide tracts were separated according to size and base composition by chromatography on diethylaminoethyl-cellulose in 7 M urea at pH 5.5 and 3.5, respectively. The distribution of labeled 5-methylcytosine in DNA pyrimidine tracts was identical for phage grown in mec+ and mec minus (N-3) cells. For phage lambda the major 5-methylcytosine containing tract was the tripyrimidine, C2T; for both fd-mec minus (N-3) DNA and fd-mec+DNA, C2T was the sole 5-methylcytosine-containing tract. When various lambda DNAs were methylated to saturation in vitro by crude extracts from mec+ and mec minus (N-3) cells, the extent of cytosine methylation was the same. This is in contrast to in vivo methylation where lambda-mec minus (N-3) DNA contains twice as many 5-methylcytosines per genome as lambda-mec+ DNA. Therefore, we suggest that the K12 met+ cytosine methylase and the N-3 plasmid modification methylase are capable of recognizing the same nucleotide sequences, but that the in vivo methylation rate is lower in mec+ cells.
Topics: Animals; Base Sequence; Cattle; Cell-Free System; Chromatography, DEAE-Cellulose; Coliphages; Cytosine; DNA; DNA Viruses; DNA, Viral; Escherichia coli; Extrachromosomal Inheritance; Methionine; Methylation; Methyltransferases; Pyrimidines; Thymus Gland; Tritium
PubMed: 1091619
DOI: 10.1128/jb.122.1.129-138.1975 -
Antimicrobial Agents and Chemotherapy Jul 1980The antibiotic aphidicolin inhibited in vitro deoxyribonucleic acid synthesis catalyzed by crude yeast extracts and by partially purified yeast deoxyribonucleic acid...
The antibiotic aphidicolin inhibited in vitro deoxyribonucleic acid synthesis catalyzed by crude yeast extracts and by partially purified yeast deoxyribonucleic acid polymerases. The mechanism of action of aphidicolin on yeast deoxyribonucleic acid polymerase I was noncompetitive with deoxyguanosine 5'-triphosphate, deoxyadenosine 5'-triphosphate, and deoxythymidine 5'-triphosphate and was of the mixed type with deoxycytidine 5'-triphosphate. The relative ratio of enzyme to the template-initiator complex was important for detecting the inhibitory effect of the antibiotic. The inhibition of in vitro deoxyribonucleic acid synthesis by aphidicolin was reversible, and the effect on yeast deoxyribonucleic acid polymerase might have been partially mediated by some supplementary factor(s).
Topics: Anti-Bacterial Agents; Aphidicolin; DNA; DNA Polymerase I; DNA Polymerase II; Deoxyribonucleotides; Diterpenes; Dose-Response Relationship, Drug; Kinetics; Nucleic Acid Synthesis Inhibitors; Saccharomyces cerevisiae
PubMed: 6774665
DOI: 10.1128/AAC.18.1.50 -
Journal of Bacteriology Jun 1964Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of some gram-negative bacteria....
Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of some gram-negative bacteria. J. Bacteriol. 87:1412-1422. 1964.-The deoxyribonucleic acid (DNA) base compositions and S values for a minimum of 134 coded properties were determined for representative cultures of the genera Pseudomonas, Xanthomonas, Aeromonas, Vibrio, Aerobacter, Escherichia, Alcaligenes, and Flavobacterium. Those cultures having a high degree of similarity by the criterion of numerical taxonomy were found to have similar DNA base compositions. The relative affinities of clusters of cultures suggest taxonomic relations. Eleven species of Xanthomonas might be a single species, and V. metschnikovii was shown to be more closely related to enteric bacteria than to other vibrios which, in turn, were found to be like pseudomonads. Aeromonas was found to be intermediate in similarity to enterics and pseudomonads and divisible into at least two, but possibly three, species. F. aquatile was unlike any of the other organisms studied, and its DNA also differed greatly in composition from other representatives of the genus.
Topics: Aeromonas; Alcaligenes; Bacteria; Base Composition; DNA; DNA, Bacterial; Electronic Data Processing; Enterobacter; Escherichia; Flavobacterium; Pseudomonas; Research; Vibrio; Xanthomonas
PubMed: 14188722
DOI: 10.1128/jb.87.6.1412-1422.1964 -
The Journal of Biological Chemistry Sep 1956
Topics: DNA; Lipid Metabolism; Liver; Liver Diseases; Liver Regeneration; Phospholipids; Phosphorus; X-Rays
PubMed: 13367014
DOI: No ID Found -
Angewandte Chemie (International Ed. in... Sep 2010DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent... (Review)
Review
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
Topics: Catalysis; DNA; RNA, Catalytic; Stereoisomerism
PubMed: 20669202
DOI: 10.1002/anie.200906345 -
Sensors (Basel, Switzerland) Sep 2022DNA (Deoxyribonucleic Acid) Cryptography has revolutionized information security by combining rigorous biological and mathematical concepts to encode original...
DNA (Deoxyribonucleic Acid) Cryptography has revolutionized information security by combining rigorous biological and mathematical concepts to encode original information in terms of a DNA sequence. Such schemes are crucially dependent on corresponding DNA-based cryptographic keys. However, owing to the redundancy or observable patterns, some of the keys are rendered weak as they are prone to intrusions. This paper proposes a Genetic Algorithm inspired method to strengthen weak keys obtained from Random DNA-based Key Generators instead of completely discarding them. Fitness functions and the application of genetic operators have been chosen and modified to suit DNA cryptography fundamentals in contrast to fitness functions for traditional cryptographic schemes. The crossover and mutation rates are reducing with each new population as more keys are passing fitness tests and need not be strengthened. Moreover, with the increasing size of the initial key population, the key space is getting highly exhaustive and less prone to Brute Force attacks. The paper demonstrates that out of an initial 25 × 25 population of DNA Keys, 14 keys are rendered weak. Complete results and calculations of how each weak key can be strengthened by generating 4 new populations are illustrated. The analysis of the proposed scheme for different initial populations shows that a maximum of 8 new populations has to be generated to strengthen all 500 weak keys of a 500 × 500 initial population.
Topics: Algorithms; DNA; Research Design
PubMed: 36236428
DOI: 10.3390/s22197332 -
Journal of Bacteriology Aug 1965Firshein, William (Wesleyan University, Middletown, Conn.). Influence of deoxyribonucleic acid degradation products and orthophosphate on deoxynucleotide kinase activity...
Firshein, William (Wesleyan University, Middletown, Conn.). Influence of deoxyribonucleic acid degradation products and orthophosphate on deoxynucleotide kinase activity and deoxyribonucleic acid synthesis in pneumococcus type III. J. Bacteriol. 90:327-336. 1965.-An oligodeoxynucleotide fraction derived from a deoxyribonuclease-treated calf-thymus deoxyribonucleic acid (DNA) can enhance the activity of deoxycytidylic acid (dCMP) and deoxyguanylic acid (dGMP) kinases in cell suspensions of type III pneumococci. High levels of orthophosphate can produce similar effects. For part of the incubation period, the activity of dCMP and dGMP kinases is very low or undetectable in unsupplemented-cell suspensions of pneumococci. In contrast, the remaining kinases, deoxyadenylic acid and thymidylic acid, which are present in ample amounts in control and supplemented cells throughout the incubation period, are unaffected by the addition of oligodeoxynucleotides and orthophosphate. The stimulation of kinase activity is amino acid-dependent and can be abolished by adding chloramphenicol. When the oligodeoxynucleotide fraction and orthophosphate are further supplemented with all eight of the naturally occurring deoxynucleosides and deoxynucleotides (which do not affect kinase activity), a preferential enhancement of DNA synthesis occurs in comparison with cell growth or protein synthesis. Addition of deoxynucleosides and deoxynucleotides to unsupplemented cells produces only a slight increase in DNA synthesis. The preferential enhancement of DNA synthesis can be prevented by adding chloramphenicol at a certain time during incubation.
Topics: Amino Acids; Carbon Isotopes; Chemical Phenomena; Chemistry; Chemistry Techniques, Analytical; Chloramphenicol; Culture Media; DNA; DNA, Bacterial; Deoxyribonucleases; Metabolism; Nucleosides; Nucleotides; Pharmacology; Phosphates; Phosphotransferases; Phosphotransferases (Phosphate Group Acceptor); Proteins; RNA; RNA, Bacterial; Radiometry; Research; Saccharomyces cerevisiae; Spectrophotometry; Streptococcus pneumoniae; Yeast, Dried
PubMed: 14329443
DOI: 10.1128/jb.90.2.327-336.1965