Phage Deoxyribonucleic Acid Research Articles

Purification of DNA Nanoparticles Using Photocleavable Biotin Tethers.

The number of applications of self-assembled deoxyribonucleic acid (DNA) origami nanoparticles (DNA NPs) has increased drastically, following the development of a variety of single-stranded template DNA (ssDNA) that can serve as the scaffold strand. In addition to viral genomes, such as M13 bacteriophage and lambda DNAs, enzymatically produced ssDNA from various template sources is rapidly gaining traction and being applied as the scaffold for DNA NP preparation. However, separating fully formed DNA NPs that have custom scaffolds from crude assembly mixes is often a multistep process of first separating the ssDNA scaffold from its enzymatic amplification process and then isolating the assembled DNA NPs from excess precursor strands. Only then is the DNA NP sample ready for downstream characterization and application. In this work, we highlight a single-step purification of custom sequence- or M13-derived scaffold-based DNA NPs using photocleavable biotin tethers. The process only requires an inexpensive ultraviolet (UV) lamp, and DNA NPs with up to 90% yield and high purity are obtained. We show the versatility of the process in separating two multihelix bundle structures and a wireframe polyhedral architecture.

The human oral phageome

Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.

Dynamics of polystyrene beads linking to DNA molecules under single optical tweezers: A numerical study using full normalized Langevin equation

The dynamics of a polystyrene bead linking to a [Formula: see text]-phage deoxyribonucleic acid (DNA) molecule under single optical tweezers using CW laser beam is analyzed by the full normalized Langevin equation with elastic and Brownian forces. The obtained results show that the stable time and stable position of polystyrene bead depend on its beginning position, laser beam waist, and laser beam power. The oscillation of polystyrene beads at stable position is observed with different parameters of optical tweezers. Finally, the conditions to stabilize the bead and to stretch the [Formula: see text]-phage DNA by single laser beam optical tweezers are discussed.

Measurement of the interaction forces at various pH levels by using AFM for the interpretation of DNA adsorption on silanized surfaces

Various surfaces have been used for deoxyribonucleic acid (DNA) immobilization, one example being a silanized surface. This is useful for determining DNA lengths and, thus, locating specific gene sequences in DNA by using fluorescence microscopy and scanning probe microscopy. In this study, we deposited DNA by using the molecular combing method and, we used fluorescence microscopy to study how the chain lengths of n-alkylsilanes affected the surface density of DNA deposited on the silanized surfaces in a tris-ethylenediaminetetraacetic acid (TE) buffer. The forces between a cleaned silicon-nitride (Si3N4) tip and each substrate surface in aqueous buffers at various pH levels (1.0 ~ 9.0) were also studied by using atomic force microscopy to measure the force-distance curves. We explain why the density of lambda bacteriophage DNA (λ-DNA) deposited by using the molecular combing method at pH 8 was lower on the silanized surface with the shorter alkyl chain than it was on the silanized surface with the longer alkyl chain in terms of the electrical double layer (EDL) and the adhesive force.

Observation of stretched single DNA molecules by Kelvin probe force microscopy

Lambda bacteriophage deoxyribonucleic acid (DNA) molecules stained with YOYO-1 were deposited and stretched on chemically modified Si(1 0 0) wafer and cover glass substrates. The Si(1 0 0) wafer with a natural oxide layer and the cover glass surface were first chemically modified by vapor phase chemisorption with mixed two organosilanes. DNA molecules were then aligned on the substrate surfaces by chemical and physical adsorption from an aqueous solution during molecular combing. The aligned DNA molecules were observed by Kelvin probe force microscopy and intermittent contact-mode atomic force microscopy (AFM) as well as fluorescence microscopy. Interaction between the stretched DNA molecules and the chemically modified Si(1 0 0) substrate surface was examined using these AFMs.

Hopping conductivity in nucleotide base stacks*

AbstractThe frequency‐dependent complex hopping conductivities of single nucleotide base stacks and base pair stacks were calculated on the following basis: (1) The determination of the density of states of these disordered systems with the help of the matrix block negative counting method. (2) Using the inverse iteration technique, the Anderson localization of the one‐electron functions belonging to the physically interesting levels were computed. (3) With the help of the latter quantities the hopping frequencies corresponding to the relative motion of the base pairs with respect to each other (acoustic phonons) were determined. (4) Finally, using a random‐walk theory the frequency‐dependent complex conductivities [σ(ω)] were computed. The |σ(ω)|−ω curves show a saturation at ω≈1010 s−1. The |σ(ω)|'s have the values in the base pairs case (taking into account the role of the sugar–phosphate backbone, basis set, and correlation effects) are a few times 1 Ω−1 cm−1 for ω>1010 s−1. This room temperature result is in excellent agreement with the energy loss (in a resonant cavity) experiment on lambda phage deoxyribonucleic acid (DNA) of Gruner and co‐workers. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

N<SUP>4</SUP>-アミノシチジンによる突然変異の機構

N4-Aminocytidine is strongly mutagenic towards E. coli, S. typhimurium, B. subtilis and coliphages phi X174 and M13mp2. It also causes mutations in mammalian cell lines and somatic cell mutations in D. melanogaster. The sequence analysis of deoxyribonucleic acid (DNA) from mutated phages revealed that N4-aminocytidine induces both adenine-thymine (AT) to guanine-cytosine (GC) and GC to AT transitions. No transversions are detectable. When E. coli and the mammalian cells were cultured in the presence of [3H]-N4-aminocytidine, [3H]-N4-aminodeoxycytidine was found in their DNA. It is likely that N4-aminocytidine is metabolized within the cells into N4-aminodeoxy-cytidine 5'-triphosphate (dCamTP), which is then incorporated into DNA, thereby causing base-pair transitions. To prove this hypothesis, we studied the incorporation of dCamTP into polynucleotides in the in vitro DNA synthesis catalyzed by E. coli DNA polymerase I large fragment (Klenow enzyme) and DNA polymerase alpha from a mouse cell line. Both polymerases catalyze incorporation of dCamTP into DNA efficiently in place of dCTP opposite guanine, and less efficiently, but to a significant extent, in place of dTTP opposite adenine. These observations prove the erroneous nature of dCamTP as a substrate for DNA synthesis. DNA containing N4-aminocytosine was prepared by the incorporation of dCamTP into single-stranded phage DNA annealed to complementary oligonucleotides. The DNA was transfected to E. coli cells. The analysis of progeny phages indicates that N4-aminocytosine residue in DNA causes A to G or G to A mutation in the position opposite to the site where N4-aminocytosine should be incorporated.

21] Site-specific mutagenesis to modify the human tumor necrosis factor gene

Publisher Summary The development of oligonucleotide-directed site-specific mutagenesis on single-stranded phage template has provided a powerful new technique in the study of structure-function relationships of proteins. This chapter describes a simplified procedure for oligonucleotide-directed site-specific mutagenesis on M13 single-stranded phage deoxyribo nucleic acid (DNA) templates. The rationale behind this approach is to make use of the DNA repair mechanism present in the E. coli host to repair the gapped M13 phage DNA into the covalently closed circular form before replication of the DNA molecules. The mutagenesis procedure described in this chapter provides a rapid method for the modification of cloned genes. It takes advantage of the ability of E. coli to efficiently repair gapped circular DNA molecules, to shorten the overall time of the mutagenesis, from initiation of the mutagenesis reaction to the identification of the mutant phage plaque. Although this faster method is less efficient in the conversion of parent DNA to mutant DNA molecules, the ability to use the same oligonucleotide primer as a probe to identify the mutant phage plaques effectively compensates for this inefficiency.

5] Purification and assay of type II DNA methylases

Publisher Summary This chapter discusses the purification and assay of type II deoxyribonucleic acid (DNA) methylases. Bacterial Type II DNA modification methylases can be readily prepared, because their sequence specificities are well defined and are generally stable monomers. Purification procedures for several Type II modification methylases are available. Generally, purifications have been based upon DNA protection assays. Specific DNA methylases are detected in those chromatographic fractions, which protect bacteriophage DNA from cleavage by a particular restriction endonuclease. A more sensitive method has been successfully used on a commercial scale for the purification of over 20 different DNA methylases. In this assay, a synthetic duplex oligonucleotide is self-ligated (polymerized) to an acid-precipitable form. A specific DNA methylase may then be measured radiometrically by the incorporation of 3 H-labeled S-adeno. It is useful to employ a combination of techniques during a particular DNA methylase purification: (1) electrophoretic protection assays, (2) specific [ 3 H]SAM, polymerized oligonucleotide linker incorporation assays, and (3) less specific [ 3 H]SAM, phage DNA incorporation assays. Generally, the most sensitive and specific linker assay is used in crude or early chromatographic fractions. Partially characterized DNA methylase fractions may then be assayed using less discriminating procedures. The chapter discusses the assay of DNA methylases, including polymerized oligonucleotide linker assay, the trichloroacetic acid (TCA) precipitation of reaction samples, DNA protection assay, and other related concepts. The chapter also presents a summary of DNA methylase purification.

Influence of local nucleotide sequence on substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro.

Three highly purified DNA polymerases, Escherichia coli polymerase I (enzyme A) and the polymerases induced by wild-type T4 phage and by T4 phage mutant L141 (antimutator phenotype), have been examined with respect to their tendency to incorporate the deoxyribonucleotide of 2-aminopurine [(AP)] for deoxyadenylate at specific sites in deoxyribonucleic acid (DNA). Using phi X174 phage DNA as a template and selected phi X174 restriction fragments as specific primers, we synthesized short sequences of phi X174 DNA in vitro by the polymerase of interest, with the 5'-triphosphate of 2-aminopurine deoxyriboside and dATP at equimolar concentration. The relative incorporation of (AP) at the various adenine sites was determined by providing the newly synthesized DNA fragment with a specific terminal radioactive label, subjecting the DNA fragment to thermal depurination as a DNA cleavage reaction highly selective for (AP), and analyzing the resulting radioactive fragments by denaturing gel electrophoresis, autoradiography, and microdensitometry. The L141 polymerase shows very pronounced site-dependent variations in (AP) incorporation. For the wild-type T4 polymerase, the pattern of (AP) incorporation follows the biases seen for the L141 enzyme, although in a less pronounced form. Sequence preferences for (AP) incorporation are least marked for E. coli polymerase I (enzyme A); in several instances, they run counter to the sequence biases observed with the T4 enzymes. For the enzyme showing the most pronounced sequence effects, L141 polymerase, the extent of (AP) incorporation was determined at 57 different sites. No simple principle governing the sequence dependence of (AP) incorporation could be deduced from these results.

New nalidixic acid resistance mutations related to deoxyribonucleic acid gyrase activity.

In Escherichia coli K-12 mutants which had a new nalidixic acid resistance mutation at about 82 min on the chromosome map, cell growth was resistant to or hypersusceptible to nalidixic acid, oxolinic acid, piromidic acid, pipemidic acid, and novobiocin. Deoxyribonucleic acid gyrase activity as tested by supercoiling of lambda phage deoxyribonucleic acid inside the mutants was similarly resistant or hypersusceptible to the compounds. The drug concentrations required for gyrase inhibition were much higher than those for cell growth inhibition but similar to those for inhibition of lambda phage multiplication. Transduction analysis with lambda phages carrying the chromosomal fragment of the tnaA-gyrB region suggested that one of the mutations, nal-31, was located on the gyrB gene.

Identification of deoxyribonucleic acid restriction fragments of beta-converting corynebacteriophages that carry the gene for diphtheria toxin.

Deoxyribonucleic acid fragments bearing the gene for diphtheria toxin have been identified in restriction enzyme digests of deoxyribonucleic acids from beta-converting and gamma-nonconverting corynebacteriophages. A combination of physical and genetic evidence has established that the Bam HI band C fragment of beta phage deoxyribonucleic acid, which carries the specific phage attachment site (Buck and Groman, J. Bacteriol. 148:131-142, 1981), also carries most, and probably all, of the gene for diphtheria toxin. A detailed restriction map of this tox-bearing Bam HI fragment has been developed, and the locations and orientation of the tox gene and the attP site within this fragment have been established.

Genetic elements novel for Corynebacterium diphtheriae: specialized transducing elements and transposons.

It was shown in an accompanying paper (Buck and Groman, J. Bacteriol. 148: 131-142, 1981) that gamma-tsr-1 phage stocks produced by heat induction of lysogens are a mixture of two phages which differ in the content of their deoxyribonucleic acid (DNA). This difference is evidenced by the appearance of "heterogeneous" (HET) fragments in restriction enzyme digests of gamma-tsr-1 phage DNA. It was estimated that 20 to 80% of the phage in these lysates produced HET fragments. The appearance of HET fragments correlated with the appearance of a DNA insertion (DI-1) in the gamma phage genome as revealed in heteroduplexes of DNA from gamma-tsr-1 and beta corynebacteriophages. The HET fragments were seen in DNA from heat-induced lysates, but not in DNA from phage stocks produced by lytic infection. By DNA-DNA hybridization analysis it was shown that a fraction of gamma-tsr-1 phages from heat-induced lysates carried an insertion of bacterial DNA in the vegetative phage attachment site (attP), and that this insertion was responsible for the formation of HET fragments. Since the phage produced by this event carried a complete phage genome plus a small segment of bacterial DNA, they were called transducing elements. On the basis of these facts it was concluded that heat-induced gamma-tsr-1 prophage was excised at an abnormal site at a very high frequency. Abnormal excision was highly specific, and the change in excision specificity occurred simultaneously with the spontaneous mutation of the phage to heat inducibility. From this and other data it was postulated that a mutation in the immune repressor was reponsible for an alteration in the specificity of the normal excision process. This distinguishes the mechanism of formation of gamma-tsr-1 transducing elements from that employed by other phages. A second DNA insertion (DI-2) in the tox (diphtheria toxin) gene of gamma-tsr-1 and gamma-tsr-2 was also identified as an insertion of bacterial DNA. The DI-2 insertion had a stem-and-loop structure similar to that seen in heteroduplexes visualizing transposons or insertion elements. It seems likely that gamma wild-type phage, which is mutant for tox, was originally tox(+), but that transposition of bacterial DNA into the gene inactivated it.

Cloning of sporulation gene spoOB of Bacillus subtilis and its genetic and biochemical analysis.

A specialized transducing phage carrying a sporulation gene (spoOB) was constructed from Bacillus subtilis temperate phage rho 11 by in vitro and in vivo recombinations. Transformation experiments showed that the spoOB gene resides on a 1.4-megadalton fragment generated by EcoRI endonuclease treatment of the phage deoxyribonucleic acid (DNA). Mutants of this phage which lost transducing activity were isolated and used for genetic complementation tests and the analysis of protein(s) coded by the 1.4-megadalton fragment. The spoOB locus was shown to be composed of one cistron. Sodium dodecyl sulfate-polyacrylamide gel analysis of proteins synthesized in ultraviolet-irradiated cells infected with these phages showed that the 1.4-megadalton fragment codes at least one protein, of molecular weight 39,000, which is synthesized in both vegetative and sporulating cells. A cleavage map of the phage DNA was constructed by use of restriction endonucleases, EcoRI, BamHI, and SalI, and the site of integration of the 1.4-megadalton fragment was determined. Expression and function of the spoOB gene are discussed.

Isolation of Bacillus subtilis genes from a charon 4A library.

A library of Bacillus subtilis chromosomal deoxyribonucleic acid (DNA) was constructed, using lambda charon 4A as a cloning vector. Partially cleaved Bacillus subtilis DNA was prepared by partial methylation with EcoRI methylase, followed by complete EcoRI endonuclease digestion. More than 95% of the phage particles carried B. subtilis DNA inserts. When this library was screened for transforming activity, using competent cells, 70% of the genetic markers tested were found in a sample of 1,710 plaques. Cloned genetic loci were found to be about 100-fold more efficient in transforming activity than chromosomal DNA. Intact phage particles containing the pheA locus were found to be able to transform competent recipients with approximately the same efficiency as phage DNA. Transformation by intact particles was insensitive to deoxyribonuclease.

Transformation of a Bacillus subtilis L-form with bacteriophage deoxyribonucleic acid.

A stable L-form, sal-1, of Bacillus subtilis was transformed with deoxyribonucleic acid (DNA) from bacteriophages phi 25 and phi 29 to determine whether exogenous DNA can be introduced into this organism. The viral transformation (transfection) was successful with the use of polyethylene glycol. In the presence of the fusogen, bacteriophage phi 25 DNA initiated a single cycle of infection. When compared with transfection of competent cells of Bacillus subtilis, the appearance of viral particles was delayed and their production occurred over a longer time period. L-form cells were best able to support intracellular replication of phi 25 viral particles when in balanced growth in a rich medium. The addition of polyethylene glycol also induced infection of sal-1 with whole bacteriophage phi 25 particles which could not otherwise infect the L-form and enhanced infection by intact phi 29 particles. Primary recombination was shown to be required for polyethylene glycol-mediated phi 25 transfection, but not phi 29 transfection or for whole bacteriophage phi 25 infection mediated by polyethylene glycol. Successful transfection of sal-1 suggests that the L-form may be amenable to genetic modification with exogenous DNA.

Regulation of polar morphogenesis in Caulobacter crescentus.

Deoxyribonucleic acid (DNA) phage phi CbK-resistant nonmotile mutants of Caulobacter crescentus CB15 were examined for their formation of polar surface structures (a stalk, a single flagellum, pili, and DNA phage receptors). These mutants were devoid of pili and DNA phage receptors and simultaneously defective either in both stalk formation and flagellar activity (stalk-defective type) or in the formation of normal flagella (flagella-defective type). DNA phage phi Cr30-mediated transductions revealed that stalk-defective mutants were of a single genetic type, whereas flagella-defective mutants were grouped into two different genetic types, I and II. To investigate how membrane proteins change in the above morphology mutants, cell envelopes pulse-labeled with L-[35S]methionine were analyzed by two-dimensional gel electrophoresis. No gross change of membrane proteins was observed in the stalk-defective mutant CB15 pdr-803, except a 49,000-molecular-weight (49K) protein which was found reduced. However, a 27K, two 28.5K, and a 70.5K protein were missing from the membrane of the flagella-defective type I mutant CB15 pdr-813. These proteins are most likely to be flagella-related protein, flagellins A and B, and hook protein, respectively. In another flagella-defective type II mutant, CB15 pdr-816, the 27K and two 28.5K proteins were similarly absent but the 70.5K protein was consistently present in the membrane. The synthesis of flagellin was next assayed radioimmunologically in the above 35S-labeled mutants. Stalk-defective CB15 pdr-803 synthesized flagellin normally, compared to the wild-type strain. Flagellins A (26K) and B (28K) formed multiple spots in isoelectric focusing. A 29K protein was also detected in the flagellin-specific radioactivity from the cytoplasm. Flagella-defective type I CB15 pdr-813 synthesized flagellin only at a basal level. Thus transcription or translation of flagellin appeared to be repressed in this mutant. Another flagella-defective type II strain, CB15 pdr-816, however, synthesized flagellin at an apparently enhanced rate compared with the wild type. Flagellin synthesized in CB15 pdr-816 was flagellin A and a smaller 22K flagellin. Flagellin B was not synthesized in the mutant. It then follows that flagellin B is not a precursor of flagellin A and the 22K flagellin. Flagella-defective type II CB15 pdr-816, without flagellin B, formed a stub structure with a hook attached to one end instead of normal flagella. In the wild-type membrane, flagellin B was the major flagellin, whereas flagellin A was major in the cytoplasm and the flagellar filament. It is suggested from these results that flagellin B is important in the assembly of normal flagella.

Molecular cloning of Escherichia coli K-12 hexuronate system genes: exu region

Lambda transducing bacteriophages carrying the exu region (min 66) of Escherichia coli K-12 (lambda pexu) were previously isolated. A restriction map of these phages is presented. Starting from the lambda pexu phage deoxyribonucleic acid, various endonuclease-generated exu fragments were subcloned into multicopy plasmid vectors, using in vitro recombination techniques. The precise location of the exu genes, relative to the endonuclease sites, was determined. Plasmids carrying uxaC and uxaA genes overproduced the corresponding enzymes 30- to 40-fold. When these plasmids were expressed in an in vitro protein-synthesizing system, two polypeptides of 50,500 and 53,000 molecular weights appeared and were identified as the uxaC and uxaA gene products. A 2.6-kilobase-pair deoxyribonucleic acid fragment was shown to code for a functional exuR repressor which controls the expression of the exu region. Plasmids containing this fragment overproduced the regulatory protein. It was possible to localize the operator region, uxaCo, which overlapped a PstI endonuclease site, and to confirm the transcriptional direction of the uxaC-uxaA operon from uxaC to uxaA.

Recombination of uracil-containing lambda bacteriophages.

Controlled incorporation of uracil into the deoxyribonucleic acid (DNA) of lambda bacteriophages was achieved by growth on dut ung thy mutants of Escherichia coli. The frequency of substitution of uracil for thymine, estimated by alkaline sucrose sedimentation of phage DNA treated in vitro with uracil DNA glycosylase, ranged from 0.17 to 1.9%. The corresponding ratio between the plating efficiencies on wild-type (Ung+) and glycosylase-deficient (Ung-) bacteria ranged from 0.70 to 0.05. If a single-hit dependence of plating efficiency on uracil content is assumed, the probability that any given uracil residue is lethal is approximately 1% (about one-fifth the probability for a pyrimidine dimer). The effect of uracil on recombination was studied in experiments with lambda tandem duplication phages (ethylenediaminetetraacetic acid [EDTA] sensitive), which are converted to single-copy phages (EDTA resistant) by general recombination. For repressed infections (of homoimmune lysogens), recombination was measured by a two-stage assay (DNA extraction, transfection of spheroplasts, and EDTA treatment). The frequencies observed for uracil-containing phages (2 to 4%) were 5 to 10 times higher than control values. However, comparisons with ultraviolet irradiated phages indicated that uracil residues promoted recombination less than 1/100 as efficiently as ultraviolet-induced lesions. Recombination of uracil-containing phages during repressed infections was negligible in recA and partially reduced in recB bacteria. Recombination was very low in ung cells, suggesting that excision repair was responsible for the stimulation. Interestingly, uracil-stimulated recombination was elevated about twofold in xth bacteria.

Mechanism of Haemophilus influenzae transfection by single and double prophage deoxyribonucleic acid.

Whole phages HP1 and HP3, vegetative-phage deoxyribonucleic acid (DNA), and single and tandem double prophage DNA were exposed to ultraviolet radiation and then assayed on a wild-type (DNA repair-proficient) Haemophilus influenzae Rd strain and on a repair-deficient uvr-1 strain. Host cell reactivation (DNA repair) was observed for whole-phage and vegetative-phage DNA but not for single and double prophage DNA. Competent (phage-resistant) Haemophilus parainfluenzae cells were normally transfected with H. influenzae-grown phage DNA and with tandem double prophage DNA but not at all with single prophage DNA. CaCl2-treated H. influenzae suspensions could be transfected with vegetative phage DNA and with double prophage DNA but not with single prophage DNA. These observations support the hypothesis that transfection with single prophage DNA occurs through prophage DNA single-strand insertion into the recipient chromosome (at the bacterial att site) followed by DNA replication and then prophage induction.