Publications

agarose gel electrophoresis reveals structural fluidity of a phage t3 dna packaging intermediate.	we find a new aspect of dna packaging-associated structural fluidity for phage t3 capsids. the procedure is (i) glutaraldehyde cross-linking of in vivo dna packaging intermediates for the stabilization of structure and then (ii) determining effective radius by two-dimensional agarose gel electrophoresis (2d-age). the intermediates are capsids with incompletely packaged dna (ipdna) and without an external dna segment; these intermediates are called ipdna-capsids. we initially increase the product ...	2012	22222979
a hypothesis for bacteriophage dna packaging motors.	the hypothesis is presented that bacteriophage dna packaging motors have a cycle comprised of bind/release thermal ratcheting with release-associated dna pushing via atp-dependent protein folding. the proposed protein folding occurs in crystallographically observed peptide segments that project into an axial channel of a protein 12-mer (connector) that serves, together with a coaxial atpase multimer, as the entry portal. the proposed cycle begins when reverse thermal motion causes the connector' ...	2010	21994710
the rnase protection assay.	a sensitive method for quantitation of mrna in gene transfer studies is mrna protection using end-labeled dna probes. in addition, this technique also provides structural information about the transcript under study (1). in vitro labeled antisense rnacan be used as an alternative to end-labeled dna probes (2,3. rna probes have attained wide popularity because of the ease of synthesis and high yield of probe in a labeling reaction. this has been made possible by the recent characterization of sin ...	1991	21416363
metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity.	the human oropharynx is a reservoir for many potential pathogens, including streptococcal species that cause endocarditis. although oropharyngeal microbes have been well described, viral communities are essentially uncharacterized. we conducted a metagenomic study to determine the composition of oropharyngeal dna viral communities (both phage and eukaryotic viruses) in healthy individuals and to evaluate oropharyngeal swabs as a rapid method for viral detection. viral dna was extracted from 19 p ...	2011	20547834
dna packaging-associated hyper-capsid expansion of bacteriophage t3.	evidence that in vivo bacteriophage t3 dna packaging includes capsid hyper-expansion that is triggered by lengthening of incompletely packaged dna (ipdna) is presented here. this evidence includes observation that some of the longer ipdnas in t3-infected cells are packaged in ipdna-containing capsids with hyper-expanded outer shells (he ipdna-capsids). in addition, artificially induced hyper-expansion is observed for the outer shell of a dna-free capsid. detection and characterization of he ipdn ...	2010	20122936
compensatory evolution for a gene deletion is not limited to its immediate functional network.	genetic disruption of an important phenotype should favor compensatory mutations that restore the phenotype. if the genetic basis of the phenotype is modular, with a network of interacting genes whose functions are specific to that phenotype, compensatory mutations are expected among the genes of the affected network. this perspective was tested in the bacteriophage t3 using a genome deleted of its dna ligase gene, disrupting dna metabolism.	2009	19445716
a likely pathway for formation of mobile group i introns.	mobile group i introns are rna splicing elements that have been invaded by endonuclease genes. these endonucleases facilitate intron mobility by a unidirectional, duplicative gene-conversion process known as homing [1]. survival of the invading endonuclease depends upon its ability to promote intron mobility. therefore, the endonuclease must either quickly change its cleavage specificity to match the site of intron insertion, or it must already be preadapted to cleave this sequence. here we show ...	2009	19200727
visualization of bacteriophage t3 capsids with dna incompletely packaged in vivo.	the tightly packaged double-stranded dna (dsdna) genome in the mature particles of many tailed bacteriophages has been shown to form multiple concentric rings when reconstructed from cryo-electron micrographs. however, recent single-particle dna packaging force measurements have suggested that incompletely packaged dna (ipdna) is less ordered when it is shorter than approximately 25% of the full genome length. the study presented here initially achieves both the isolation and the ipdna length-ba ...	2008	18952096
compensatory evolution in response to a novel rna polymerase: orthologous replacement of a central network gene.	a bacteriophage genome was forced to evolve a new system of regulation by replacing its rna polymerase (rnap) gene, a central component of the phage developmental pathway, with that of a relative. the experiment used the obligate lytic phage t7 and the rnap gene of phage t3. t7 rnap uses 17 phage promoters, which are responsible for all middle and late gene expression, dna replication, and progeny maturation, but the enzyme has known physical contacts with only 2 other phage proteins. t3 rnap wa ...	2007	17220516
transcriptional inhibition by an oxidized abasic site in dna.	2-deoxyribonolactone (dl) is an oxidized abasic site in dna that can be induced by gamma-radiolysis, ultraviolet irradiation, and numerous antitumor drugs. although this lesion is incised by ap endonucleases, suggesting a base-excision repair mechanism for dl removal, subsequent excision and repair synthesis by dna polymerase beta is inhibited due to accumulation of a protein-dna cross-link. this raises the possibility that additional repair pathways might be required to eliminate dl from the ge ...	2006	16485899
transcription arrest caused by long nascent rna chains.	the transcription process is highly processive. however, specific sequence elements encoded in the nascent rna may signal transcription pausing and/or termination. we find that under certain conditions nascent rna chains can have a strong and apparently sequence-independent inhibitory effect on transcription. using phage t3 rna polymerase (t3 rnap) and covalently closed circular (cccdna) dna templates that did not contain any strong termination signal, transcription was severely inhibited after ...	2004	15716026
characterization of bacteriophage t3 dna ligase.	dna ligases of bacteriophage t4 and t7 have been widely used in molecular biology for decades, but little is known about bacteriophage t3 dna ligase. here is the first report on the cloning, expression and biochemical characterization of bacteriophage t3 dna ligase. the polyhistidine-tagged recombinant t3 dna ligase was shown to be an atp-dependent enzyme. the enzymatic activity was not affected by high concentration of monovalent cations up to 1 m, whereas 2 mm atp could inhibit its activity by ...	2004	15113838
sonis reactivation of antiserum-neutralized bacteriophage t3.		1952	14938310
mutation affecting head antigen of bacteriophage t3.		1962	14490971
effect of cysteine and glycerol on capacity of irradiated cells of escherichia coli b for phage t3.		1964	14189808
effects of mitomycin and alpha-rays on the capacity of escherichia coli b for phage t3.		1963	13953928
genetic variants of phage t3.		1961	13726189
host range mutants and semitemperate mutants of bacteriophage t3.		1957	13443213
reproduction of bacteriophage t3 in protoplasts of escherichia coli, strain b.		1956	13373870
the influence of the host character of e. coli upon its lysis by bacteriophage. ii. the influence of host character on the acriflavine tolerance of bacteriophage t3.		1954	13221351
a genetic analysis of the factors controlling the h character in bacteriophage t3.		1953	13168960
induction of mutations in bacteriophage t3 by ultraviolet light.		1953	13116967
the action of aureomycin on the escherichia coli bacteriophage t3 system.		1953	13034738
preliminary crystallographic analysis of the bacteriophage p22 portal protein.	portal proteins are components of large oligomeric dsdna pumps connecting the icosahedral capsid of tailed bacteriophages to the tail. prior to the tail attachment, dsdna is actively pumped through a central cavity formed by the subunits. we have studied the portal protein of bacteriophage p22, which is the largest connector characterized among the tailed bacteriophages. the molecular weight of the monomer is 82.7 kda, and it spontaneously assembles into an oligomeric structure of approximately ...	2002	12372319
complete nucleotide sequence and likely recombinatorial origin of bacteriophage t3.	we report the complete genome sequence (38,208 bp) of bacteriophage t3 and provide a bioinformatic comparative analysis with other completely sequenced members of the t7 group of phages. this comparison suggests that t3 has evolved from a recombinant between a t7-like coliphage and a yersiniophage. to assess this, recombination between t7 and the yersinia enterocolitica serotype o:3 phage phiyeo3-12 was accomplished in vivo; coliphage progeny from this cross were selected that had many biologica ...	2002	12079351
luxs: its role in central metabolism and the in vitro synthesis of 4-hydroxy-5-methyl-3(2h)-furanone.	many bacteria produce extracellular molecules which function in cell-to-cell communication. one of these molecules, autoinducer 2 (ai-2), was first described as an extracellular signal produced by vibrio harveyi to control luciferase expression. subsequently, a number of bacteria have been shown to possess ai-2 activity in their culture supernatants, and bear the luxs gene product, which is required for ai-2 synthesis. in porphyromonas gingivalis, luxs and pfs, encoding a 5'-methylthioadenosine/ ...	2002	11932438
sea urchin mtdbp is a two-faced transcription termination factor with a biased polarity depending on the rna polymerase.	the sea urchin mitochondrial displacement (d)-loop binding protein mtdbp has been previously identified and cloned. the polypeptide (348 amino acids) displays a significant homology with the human mitochondrial transcription termination factor mterf. this similarity, and the observation that the 3' ends of mitochondrial rnas coded by opposite strands mapped in correspondence of mtdbp-binding sites, suggested that mtdbp could function as transcription termination factor in sea urchin mitochondria ...	2001	11713324
lowering s-adenosylmethionine levels in escherichia coli modulates c-to-t transition mutations.	deoxycytosine methylase (dcm) enzyme activity causes mutagenesis in vitro either directly by enzyme-induced deamination of cytosine to uracil in the absence of the methyl donor, s-adenosylmethionine (sam), or indirectly through spontaneous deamination of [5-methyl]cytosine to thymine. using a lac reversion assay, we investigated the contribution of the first mechanism to dcm mutagenesis in vivo by lowering the levels of sam. escherichia coli sam levels were lowered by reducing sam synthetase act ...	2001	11208790
structural analysis of the bacteriophage t3 head-to-tail connector.	the connector protein of bacteriophage t3, p8, has been overexpressed in escherichia coli. purification of the oligomers built by several copies of p8 reveals a mixed population of dodecamers and tridecamers. the percentages of these two types of oligomers differ in every culture growth, indicating that assembly of this protein depends upon the conditions of the expression system. those cultures that generated a majority of dodecamers allowed, after purification of the connectors, the two-dimens ...	2000	11042085
bacteriophage phiyeo3-12, specific for yersinia enterocolitica serotype o:3, is related to coliphages t3 and t7.	bacteriophage phiyeo3-12 is a lytic phage of yersinia enterocolitica serotype o:3. the phage receptor is the lipopolysaccharide o chain of this serotype that consists of the rare sugar 6-deoxy-l-altropyranose. a one-step growth curve of phiyeo3-12 revealed eclipse and latent periods of 15 and 25 min, respectively, with a burst size of about 120 pfu per infected cell. in electron microscopy phiyeo3-12 virions showed pentagonal outlines, indicating their icosahedral nature. the phage capsid was sh ...	2000	10960095
influence of s-adenosylmethionine pool size on spontaneous mutation, dam methylation, and cell growth of escherichia coli.	escherichia coli strains that are deficient in the ada and ogt dna repair methyltransferases display an elevated spontaneous g:c-to-a:t transition mutation rate, and this increase has been attributed to mutagenic o(6)-alkylguanine lesions being formed via the alkylation of dna by endogenous metabolites. here we test the frequently cited hypothesis that s-adenosylmethionine (sam) can act as a weak alkylating agent in vivo and that it contributes to endogenous dna alkylation. by regulating the exp ...	1999	10542178
stereospecific differences in repair by human cell extracts of synthesized oligonucleotides containing trans-opened 7,8,9, 10-tetrahydrobenzo[a]pyrene 7,8-diol 9,10-epoxide n2-dg adduct stereoisomers located within the human k-ras codon 12 sequence.	the potent environmental carcinogen benzo[a]pyrene (bap), following enzymatic activation to enantiomeric pairs of bay-region 7,8-diol 9, 10-epoxides (the benzylic 7-hydroxyl group and epoxide oxygen are cis for de-1 diastereomers and trans for de-2 diastereomers), reacts with dna to form covalent adducts predominately at the exocyclic amino groups of purines. specific adducts, corresponding to the trans opening of each of the four optically active bap de isomers at c-10 by the n 2-amino group of ...	1999	9888796
testing promoter activity in the trypanosome genome: isolation of a metacyclic-type vsg promoter, and unexpected insights into rna polymerase ii transcription.	in trypanosomes, most genes are arranged in polycistronic transcription units. individual mrnas are generated by 5'-trans splicing and 3' polyadenylation. remarkably, no regulation of rna polymerase ii transcription has been detected although many rnas are differentially expressed during kinetoplastid life cycles. demonstration of specific class ii promoters is complicated by the difficulty in distinguishing between genuine promoter activity and stimulation of trans splicing. using vectors that ...	1998	9709032
in vivo evidence that s-adenosylmethionine and fatty acid synthesis intermediates are the substrates for the luxi family of autoinducer synthases.	many gram-negative bacteria synthesize n-acyl homoserine lactone autoinducer molecules as quorum-sensing signals which act as cell density-dependent regulators of gene expression. we have investigated the in vivo source of the acyl chain and homoserine lactone components of the autoinducer synthesized by the luxi homolog, trai. in escherichia coli, synthesis of n-(3-oxooctanoyl)homoserine lactone by trai was unaffected in a fadd mutant blocked in beta-oxidative fatty acid degradation. also, cond ...	1998	9573148
transcription termination by bacteriophage t3 and sp6 rna polymerases at rho-independent terminators.	transcription termination of t3 and sp6 dna-dependent rna polymerases have been studied on the dna templates containing the threonine (thr) attenuator and its variants. the thr attenuator is from the regulatory region of the thr operon of escherichia coli. the dna template, encoding the thr attenuator, contains specific features of the rho-independent terminators. it comprises a dg + dc rich dyad symmetry, encoding a stem-and-loop rna, which is followed by a poly(u) region at the 3'-end. thirtee ...	1997	9476351
[a nested deletion method for cosmid dna using the bacteriophage t3 in vitro packaging system].		1997	9185481
a bacteriophage t3 promoter can be linked to a lethal gene without detectable toxicity for eukaryotic cells. interest for inducible transgenes.	the bacteriophage t3 promoter can be selectively transcribed by the corresponding rna polymerase in eukaryotic cells. a toxic gene can in principle be linked to this promoter in a "dormant" and innocuous transgene in a transgenic animal. in this scheme, the activating strain expresses the rna polymerase. when expression of the gene is needed in the progeny, the 2 lines are crossed. however, when a single molecule is sufficient to kill the cell--as with the diphtheria toxin--transcriptional "leak ...	1996	9091177
hypermutagenic in vitro transcription employing biased ntp pools and manganese cations.	in vitro dna-dependent rna transcription using bacteriophage t3 rna polymerase may be rendered hypermutagenic by employing biased nucleoside triphosphate (ntp) concentrations and manganese cations. using the e. coli r67 plasmid-encoded dihydrofolate reductase (dhfr) gene as target substitution rates approaching 4 x 10(-2) per base per reaction could be achieved, on a par with hypermutagenic reverse transcription. in all cases the majority of substitutions was that expected from the ntp pool bias ...	1997	9047346
in vitro transcripts from cloned cdnas of the lettuce infectious yellows closterovirus bipartite genomic rnas are competent for replication in nicotiana benthamiana protoplasts.	full-length cloned cdnas of lettuce infectious yellows closterovirus (liyv) rnas 1 and 2 were constructed and fused to the bacteriophage t3 rna polymerase promoter. to assess rna replication, nicotiana benthamiana protoplasts were inoculated with liyv virion rnas and liyv cdna-derived in vitro transcripts. analysis of protoplasts inoculated with liyv virion rnas or capped (m7gpppg) in vitro transcripts from liyv rna 1 and 2 cdnas showed accumulation of liyv genomic and putative subgenomic rnas ( ...	1996	8806497
an improved cosmid vector for the nested deletion method using the bacteriophage t3 dna packaging system.	we constructed a new cosmid vector suitable for the previously developed nested deletion method which used the in vitro dna packaging system of bacteriophage t3. the first step of this method is linearization of a cosmid clone to be packaged, and we previously introduced cleavage at the cos site using lambda-terminase, but optimization of the reaction conditions was required for complete digestion because of its instability. in the newly constructed vector, pat5, the sites of 4 different restric ...	1996	8724852
the gly74-->ser and ser3-->ala mutations in rhodobacter sphaeroides y thioredoxin: effects on active site reactivity and protein interaction.	in this study, we report the effects of two different substitutions in rhodobacter sphaeroides thioredoxin on two regions of the protein: the n-terminus end and the hydrophobic area implicated in protein/protein interactions. we have produced by site-directed mutagenesis r. sphaeroides thioredoxin single and double mutants in which the glycine residue at position 74 is changed to a serine and the serine at position 3 is changed to an alanine; the three mutant proteins have been purified. the two ...	1996	8654421
sequences homologous to yeast mitochondrial and bacteriophage t3 and t7 rna polymerases are widespread throughout the eukaryotic lineage.	although mitochondria and chloroplasts are considered to be descendants of eubacteria-like endo- symbionts, the mitochondrial rna polymerase of yeast is a nucleus-encoded, single-subunit enzyme homologous to bacteriophage t3 and t7 rna polymerases, rather than a multi-component, eubacterial-type alpha 2 beta beta' enzyme, as encoded in chloroplast dna. to broaden our knowledge of the mitochondrial transcriptional apparatus, we have used a polymerase chain reaction (pcr) approach designed to ampl ...	1996	8604305
conservative substitutions in the hydrophobic core of rhodobacter sphaeroides thioredoxin produce distinct functional effects.	the internal residue phe 25 in rhodobacter sphaeroides thioredoxin was changed to five amino acids (ala, val, leu, ile, tyr) by site-directed mutagenesis, and the mutant proteins were characterized in vitro and in vivo using the mutant trxa genes in an escherichia coli trxa- background. the substitution f25a severely impaired the functional properties of the enzyme. strains expressing all other mutations can grow on methionine sulfoxide with growth efficiencies of 45-60% that of the wild type at ...	1995	8580841
dna packaging atpase of bacteriophage t3.	a defined in vitro dna packaging system of phage t3, which is composed of purified proheads and two packaging proteins, the products of genes 18 and 19 (gp18 and gp19, respectively), displayed a dna-dependent atpase activity. atp was hydrolyzed to adp and pi. the atpase activity was stimulated by nonpackageable dna, such as single-stranded or circular dna, or rna (nonpac-atpase). among the inhibitors of dna packaging, actinomycin d specifically inhibited the atpase activity that was tightly coup ...	1993	8460483
[study of the activation mechanism of ecorii restriction endonuclease using synthetic dna duplexes].	efficiency of the cleavage of dna duplexes with one recognition site by ecorii restriction endonuclease decreases with the increase in substrate length. dna duplexes more than 215 base pairs long are practically not cleaved by this enzyme. it has been found that in the presence of substrates 11-14 base pairs long acceleration of hydrolysis of extended single-site substrates by ecorii enzyme is observed. the level of hydrolysis stimulation is dependent on the length and concentration of the secon ...	1993	8316237
analysis of functional domains of the packaging proteins of bacteriophage t3 by site-directed mutagenesis.	intracellular phage t3 dna is synthesized as a concatemer in which unit-length molecules are jointed together in head-to-tail fashion through terminally redundant sequences. the concatemeric dna is processed and packaged into the prohead with the aid of non-capsid proteins, gp18 and gp19. we have developed a defined system, composed of purified gp18, gp19 and proheads, and a crude system, composed of lysates of t3 infected cells, for in vitro packaging of t3 dna. the defined system displays an a ...	1994	8289246
reduced ethylene synthesis by transgenic tomatoes expressing s-adenosylmethionine hydrolase.	we have utilized a gene from bacteriophage t3 that encodes the enzyme s-adenosylmethionine hydrolase (samase) to generate transgenic tomato plants that produce fruit with a reduced capacity to synthesize ethylene. s-adenosylmethionine (sam) is the metabolic precursor of 1-aminocyclopropane-1-carboxylic acid, the proximal precursor to ethylene. samase catalyzes the conversion of sam to methylthioadenosine and homoserine. to restrict the presence of samase to ripening fruit, the promoter from the ...	1994	7999994
a functional chimeric dna primase: the cys4 zinc-binding domain of bacteriophage t3 primase fused to the helicase of bacteriophage t7.	two colinear bacteriophage t7 gene 4 proteins provide helicase and primase functions in vivo. t7 primase differs from t7 helicase by an additional 63 residues at the amino terminus. this terminal domain contains a zinc-binding motif which mediates an interaction with the basic primase recognition sequence 3'-ctg-5'. we have generated a chimeric primase in which the 81 amino-terminal residues are derived from the primase of phage t3 and the 484 carboxyl-terminal residues are those of phage t7 hel ...	1994	7991626
sequence-specific transcription arrest by peptide nucleic acid bound to the dna template strand.	the effects of pna (peptide nucleic acid) bound to double-stranded (ds) dna targets positioned downstream from phage t3 or t7 promoters in pbluescriptks+ derived plasmids on transcription by rna polymerases t3 or t7 have been studied. the dsdna targets a10, 5'-a5ga4 or 5'-a2ga2ga4, and the corresponding pnas t10, t5ct4 and t2ct2ct4 were used and the target-pna strand displacement complexes were performed in low-salt buffer, since pna does not bind efficiently to ds dna in higher salt than 50 mm. ...	1994	7958978
gene expression mediated by bacteriophage t3 and t7 rna polymerases in transgenic trypanosomes.	messenger rnas of higher eukaryotes share a functionally essential 5' monomethyl cap structure generated during a reaction that is linked exclusively to rna polymerase ii transcription. in unicellular parasites belonging to the kinetoplastida, however, mrnas acquire their 5' cap through a trans-splicing reaction which effectively uncouples pol ii transcription and capping. consequently functional mrnas can be produced by endogenous rna polymerase i. here we demonstrate the extension of this flex ...	1994	7937108
a novel tn10 tetracycline regulon system controlling expression of the bacteriophage t3 gene encoding s-adenosyl-l-methionine hydrolase.	to study the effects of in vivo dna methylation, we have developed an inducible system to control the intracellular concentration of s-adenosyl-l-methionine (adomet). the product of the bacteriophage t3 adomet hydrolase-encoding gene (amh), which degrades adomet to l-homoserine and 5'-methylthioadenosine, was employed to lower adomet concentrations in vivo. the amh gene was placed downstream from the inducible teta promoter of the tn10 tetracycline regulon substituting for most of the teta gene. ...	1994	7926842
structural and functional domains of the large subunit of the bacteriophage t3 dna packaging enzyme: importance of the c-terminal region in prohead binding.	during head assembly of phage t3, dna is packaged into a preformed protein shell, called the prohead, with the aid of non-capsid packaging proteins, the products of genes 18 and 19 (gp18 and gp19). we have developed a defined system, composed of purified gp18,gp19 and proheads for in vitro packaging of t3 dna. our previous results using the defined in vitro system indicate the sequential events in dna packaging: the packaging proteins, gp18 and gp19, bind dna and proheads, respectively. these co ...	1995	7844832
a novel method for generating nested deletions using the in vitro bacteriophage t3 dna packaging system.	to sequence a dna segment inserted into a cosmid vector under the directed sequencing strategy, we established a simple and rapid method for generating nested deletions which uses the in vitro packaging system of bacteriophage t3 dna. the principle is based on the previous finding that this system can translocate any linear double-stranded dna up to 40 kb into the phage capsid in a time-dependent manner and the encapsulated dna becomes dnase-resistant. for this purpose, we constructed a cosmid v ...	1994	7719924
the significance of distance and orientation of restriction endonuclease recognition sites in viral dna genomes.	studies on phage t3 and t7 have shown that these viruses avoid restriction not only by the phage-coded ocr (and s-adenosylmethionine hydrolase) protein functions or by the complete loss of specific recognition sites for certain restriction endonucleases from their genomes, but also that there are two additional modes: resistance towards ecop15 (which recognizes a non-symmetrical sequence) is achieved by an identical orientation of all the recognition sites in the virus genome (strand bias) and i ...	1995	7669344
analysis of the fine structure of the prohead binding domain of the packaging protein of bacteriophage t3 using a hexapeptide, an analog of a prohead binding site.	a large subunit of bacteriophage t3 packaging enzyme, a product of gene 19 (gp19, 586 amino acid residues), binds a prohead prior to dna translocation in dna packaging. its c-terminal region (571 to 576, region i) is of crucial importance for prohead binding. to elucidate the functional role(s) of region i in dna packaging, a hexapeptide (6pt3) corresponding to the region i sequence and its variants were synthesized and their effects on dna packaging in a defined in vitro system were examined. 6 ...	1995	7645255
versatile, multi-featured plasmids for high-level expression of heterologous genes in escherichia coli: overproduction of human and murine cytokines.	we describe the construction, expression characteristics and some applications of a versatile dual-promoter expression plasmid for heterologous gene expression in escherichia coli which contains both lambda pl and pt7 promoters. furthermore, the plasmid is optimized to allow the expression of mature coding sequences without compromising the strength of the highly efficient pt7 or of the t7g10 ribosome-binding site. the effect of the the naturally occurring rna loops at both the 5' and 3' ends of ...	1995	7590329
structure and assembly of bacteriophage t3 tails.		1981	7467129
incorporation of 5-substituted uracil derivatives into nucleic acids. the isolation and gamma-radiation-sensitivity of bacteriophage t3 containing the thymine analogue 5-vinyluracil.	bacteriophage t3 was produced in a form that contained 32% of its normal dna thymine residues replaced with 5-vinyluracil residues by infecting a thymine-requiring strain of escherichia coli with phage t3 in a medium containing 5-vinyluracil. when 2'-deoxy-5-vinyluridine was added to the medium instead, no incorporation was observed into the phage dna, and the presence of the deoxyribonucleoside severely decreased the number of viable phage particles produced. the analogue-containing phage, alth ...	1980	7406866
in vitro formation of the concatemeric dna of bacteriophage t3 and its biological activity in the in vitro packaging reaction.		1980	7361452
purification of gene 6 product of bacteriophage t3 and its role in vitro dna packaging.		1980	7352372
influence of dimethylsulfoxide on transcription by bacteriophage t3-induced rna polymerase.	dimethylsulfoxide (dmso) up to 25% (v/v) does not cause irreversible alterations of t3 dna at 42.5 degrees c as assayed by transcription with t3-specific rna polymerase. the optimal temperature for the formation of polyanion-resistant ternary complexes of the enzyme, t3 dna, and nascent rna chains is lowered by 12.5 degrees c in the presence of 20% (v/v) dmso. the same solvent concentration, however, decreased the temperature optimal for t3 rna chain elongation by only 2.5 degrees c, indicating ...	1981	7293245
phage t3 dna contains an exact copy of the 23 base-pair phage t7 rna polymerase promoter sequence.		1981	7265239
on the mechanism of inhibitory effect of violamycin antibiotics on the transcription by bacteriophage t3-induced rna polymerase.	the effect of three components of the anthracycline antibiotic violamycin on the transcription of bacteriophage t3 dna by bacteriophage t3-induced rna polymerase has been investigated in a cell-free system. the glycosides of violamycin bi possess the highest inhibitory activity, whereas those of violamycin bii and violamycin a show a reduced inhibitory effect. concentrations of violamycin bi depressing the incorporation of (3h)ump into rna chains have only a slight effect on the binding of the t ...	1981	7232204
nonenzymatic methylation of dna by the intracellular methyl group donor s-adenosyl-l-methionine is a potentially mutagenic reaction.	incubation of dna with s-adenosyl-l-methionine (sam) in neutral aqueous solution leads to base modification, with formation of small amounts of 7-methylguanine and 3-methyladenine. the products have been identified by high performance liquid chromatography of dna hydrolysates and by the selective release of free 3-methyladenine from sam-treated dna by a specific dna glycosylase. we conclude that sam acts as a weak dna-alkylating agent. several control experiments including extensive purification ...	1982	7188181
the synthesis and properties of some 5-substituted uracil derivatives.	the chemical syntheses of some 5-substituted uracil deorivatives, in particular 5-vinyl-2'-deoxyuridine, 5-ethynyl-2'-deoxyuridine and 4-(2-bromovinyl)-2'-deoxy-uridine are reviewed and their potential as radiation sensitizing agents, anti-cancer agents and antiviral agents is discussed. 5-ethynyl-2'-deoxyuridine is not incorporated into dna; is a thymidylate synthetase inhibitor and has a possible use as an anti-cancer drug. 5-vinyl-2'-dexyuridine can replace thymidine residues in dna of phage ...	1980	7019862
[serological characterization of bacteriophage t3 carrying different "non-classical" modifications].	the antigenic properties of bacteriophage t3 and a mutant t3/r7 which undergoes "non-classical" modification and restriction are compared. the "non-classical" modification of t3/r7 consists of a host-dependent, reversible change in the adsorption capacity of phage on different host strains. we have shown that this modification is connected with changes in the antigenic properties of phage components involved in phage absorption to the host cell. this means that, in contrast to the "classical" ho ...	1981	7019671
virus adaptation to host cells: the non-classical modification of phage t3.	bacterial virus t3 undergoes host-controlled modification which is not based on "classical" processes of dna modification and restriction. the adsorption and thus the growth of t3 on escherichia coli w cells (e. coli k12 derivative) decisively depends on the host strain on which the virus was previously propagated. depending on the modification conferred to the virus by its last host, its efficiency of plating (e.o.p.) on e. coli w varies by six orders of magnitude between 10(-7) and 10(-1). thi ...	1980	7008378
[detection of the host specificity system in shigellae].	the presence of dna host specific system in shigella sonnei 47843 bacteria has been demonstrated. phage ddiii grown on the cells of shigella stutzeri 2, in shigella sonnei 47843 cells is restricted by a factor of 105. phage t3 of eco b phenotype as well as ddiii phage is restricted in these cells. this circumstance means that the restriction-modification system of shigella sonnei 47843 differs in specificity from the well known system e. coli. the results obtained are the second case of host spe ...	1980	7000200
termination of transcription by escherichia coli ribonucleic acid polymerase in vitro. effect of altered reaction conditions and mutations in the enzyme protein on termination with t7 and t3 deoxyribonucleic acids.	both bacteriophage t7 and the related bacteriophage t3 have strong termination sites for bacterial rna polymerase located near 20% on the standard genome map. these termination sites are used with 90% efficiency in vivo, even in cells which contain a defective p protein. under normal reaction conditions in vitro, escherichia coli rna polymerase terminates with 90% efficiency at the t7 terminator site but shows little or no termination at the corresponding t3 locus. thus, the two templates form a ...	1980	6994805
isolation and sequence determination of 5'-terminal oligonucleotide fragments of rna transcripts synthesized by bacteriophage t3-induced rna polymerase from t3 dna.	the nucleotide sequence of the 5'-terminal oligonucleotides produced by pancreatic rnase digestion of bacteriophage t3 rna polymerase (ec 2.7.7.6) transcripts of t3 dna has been determined. the sequence determination is based upon a simple isolation procedure for the 5'-terminal oligonucleotides. this procedure involves treatment of pancreatic rnase digests of alpha 32p-labeled t3 rna polymerase transcripts with bovine brain exoribonuclease to remove oligonucleotides with free 5'-hydroxyl termin ...	1980	6933443
rabbit reticulocyte initiation factor 2 contains two polypeptide chains of molecular weights 48,000 and 38,000.	eukaryotic initiation factor 2 (eif-20) purified from rabbit reticulocyte lysates consists of equimolar amounts of two polypeptide chains of mr 48,000 and 38,000. determination of the molecular weight of the native factor gave a value which is consistent with a mr of 86,000 indicating that the factor is composed of one mr 48,000 and one mr 38,000 polypeptide. the purified factor exhibited all the binding activities characteristic of eif-2. the factor formed ternary complexes with met-trnafmet an ...	1980	6932024
studies on factors involved in in vitro packaging of phage t3 dna.		1981	6895788
bacteriophage t3 dna binding protein interaction with dna.		1981	6894046
purification of dna-binding proteins of bacteriophage t3 and heir role in in vitro packaging of phage t3 dna.		1980	6893505
[characterization of a cacl2-dependent transfection system of escherichia coli and t3 phage dna].	transfection by dna isolated from bacteriophage t3 was studied using escherichia coli 921/0 as host. the following conditions were found optimal: competent e. coli 921/0 were obtained by harvesting the bacteria at the onset of late exponential growth (5 x 10(8) cells/ml) and treating the latter with 0.05 m cacl2. hereafter, the microbes were suspended in 50 mm tris-hcl buffer (ph 7.2) and the concentration adjusted to 7 x 10(9) cells/ml. t3 dna was added and the suspension kept at 0 degrees c fo ...	1982	6760569
role of gene 8 product in morphogenesis of bacteriophage t3.	the product of gene 8 (gp8) of t3 phage is one of the minor head proteins located at the phage head-tail junction. to determine the role of gp8, an amber (8-) and four temperature-sensitive mutants (ts8) were characterized by sedimentation analysis, polyacrylamide gel electrophoresis, and extract complementation. neither dna-containing particles nor empty particles were formed in cells infected with 8-. in addition, prohead assembly was greatly reduced. prohead assembly was also blocked in cells ...	1983	6602416
relationship between promoter structure and template specificities exhibited by the bacteriophage t3 and t7 rna polymerases.	to explore the basis for the template specificities of the bacteriophage t3 and t7 rna polymerases (ec 2.7.7.6), we determined the nucleotide sequences of six promoters recognized by the t3 rna polymerase and compared them with the previously determined promoter sequences recognized by the bacteriophage t7 rna polymerase. recombinant plasmids containing random hpa ii and taq i fragments of t3 dna were screened for t3 promoter activity in vitro in a transcription assay using purified t3 rna polym ...	1983	6574450
[effect of low temperatures of the survival and intracellular multiplication of escherichia coli bacteriophages].	the purpose of this work was to investigate the survival and intracellular growth of escherichia coli bacteriophages phi x174, t3 and t4 subjected to freezing down to -196 degrees c. the survival was 98.4% for phage t3, 80.55% for phage phi x174, and 65.13% for phage t4. single growth cycles, dna and protein biosynthesis did not change in phages phi x174 and t3 after freezing. if bacteria were infected with phage t4 subjected to freezing, the rates of phage dna and protein synthesis decreased, t ...	1981	6454057
abortive infection of f-plasmid-containing escherichia coli cells by bacterial virus t7 is determined by the right end of t7 gene 1.	phage t7 infects male (f-plasmid-carrying) escherichia coli cells abortively, whereas the closely related phage t3 grows normally. the inability or ability of phage to replicate in male host cells depends on whether the right end of gene 1 (coding for the phage-specific rna polymerase) consists of t7 or t3 dna base sequences.	1983	6338244
virus-plasmid interactions: mutants of bacteriophage t3 that abortively infect plasmid f-containing (f+) strains of escherichia coli.	bacteriophage t7 and many closely related phages abortively infect plasmid f-containing (f+) strains of escherichia coli. however phage t3, which is also closely related to t7, grows normally in f+ hosts. mutants of phage t3 that, like t7, are subject to f-mediated restriction have been isolated. these t3 mutants lack or are defective in one or both of two genes that are nonessential for phage growth in f-, wild-type strains. our results show that the products of phage t3 gene 1.1 or 1.2, or bot ...	1984	6324192
locations and nucleotide sequences of three major class iii promoters for bacteriophage t3 rna polymerase on t3 dna.	the dna sequences of three major class iii t3 rna polymerase promoters located at 45.0, 55.0, and 64.8% on the standard t3 genetic map have been determined. the precise rna initiation sites were also determined by 5'-terminal rna sequence analysis of the transcripts synthesized from the promoter-containing dna fragments. alignment of these three class iii promoters and a previously determined t3 rna polymerase promoter at 1.05% on t3 genetic map, with start points of transcription (+1) in regist ...	1984	6319418
restriction of bacteriophage t3 and t7 ocr+ strains by the type ii restriction endonuclease ecorv.	when e. coli cells carrying the plasmid plg13 (coding for the newly discovered type ii restriction endonuclease ecorv) are infected with phage t3 or t7, only t7 is able to replicate normally. t3 wild-type as well as its ocr- mutants are subject to dna restriction in vivo and in vitro. the ecorv enzyme cuts t3 dna at 5 sites. t7 and its ocr- mutants have no ecorv sites in their dna. in contrast to the anti-restriction activity of the t3 and t7 ocr+ gene function against type i and iii restriction ...	1983	6308393
on the terminally redundant sequences of bacteriophage t3 dna.	the nucleotide sequences of the termini of mature dna from t3 phage were determined. a directly repeated sequence of 230 base pairs, corresponding to the terminal redundancy of t3 dna, was found in the left and right end of the genome. the sequence of the terminal regions of t3 dna was compared with that of t7 dna. there are discrete sequences with significant homology, specifically in the regions around the two ends of the terminally redundant sequences. 5'-cctaaag and its variants appear frequ ...	1983	6297159
isolation and characterization of bacteriophage t3 mutants sensitive to restriction by ecori.		1982	6291231
influence of phage t3 and t7 gene functions on a type iii(ecop1) dna restriction-modification system in vivo.	the ocr+ gene function (gp 0.3) of bacteriophages t3 and t7 not only counteracts type i (ecob, ecok) but also type iii restriction endonucleases (ecop1). despite the presence of recognition sites, phage dna as well as simultaneously introduced plasmid dna are protected by ocr+ expression against both the endonucleolytic and the methylating activities of the ecop1 enzyme. nevertheless, the ecop1 protein causes the exclusion of t3 and t7 in p1-lysogenic cells, apparently by exerting a repressor-li ...	1982	6285143
location, function, and nucleotide sequence of a promoter for bacteriophage t3 rna polymerase.	the major promoters for bacteriophage t3 rna polymerase on the t3 genome have been mapped by dna.rna filter hybridization. one promoter is located in a 300-base-pair hpa i restriction fragment near the genetic "left" end of t3 dna. the sequence in the vicinity of the major initiation site of transcription in this region has been determined. a part of the (-)strand sequence is 5' t-a-t-t-t-a-c-c-c-t-c-a-c-t-a-a-a-g-+1 g-g-a-a-u 3'. comparison of this sequence with the prototype 23-base-pair promo ...	1981	6264429
bacteriophage t3 and bacteriophage t7 virus-host cell interactions.		1981	6261110
construction of a restriction map of bacteriophage t3 dna.	a restriction endonuclease cleavage map of bacteriophage t3 dna has been constructed. the enzymes used and, within parentheses, the number of their cleavage sites on t3 dna are: hindiii (1), xbai (1), bglii (1), kpni (2), mboi (9), and hpai (17). the size and the relative location of each fragment have been established, defining an accurate physical map of t3 dna.	1980	6260585
derivation of a restriction map of bacteriophage t3 dna and comparison with the map of bacteriophage t7 dna.	the dna of bacteriophage t3 was characterized by cleavage with seven restriction endonucleases. avai, xbai, bglii, and hindiii each cut t3 dna at 1 site, kpni cleaved it at 2 sites, mboi cleaved it at 9 sites, and hpai cleaved it at 17 sites. the sizes of the fragments produced by digestion with these enzymes were determined by using restriction fragments of t7 dna as molecular weight standards. as a result of this analysis, the size of t3 dna was estimated to be 38.74 kilobases. the fragments w ...	1980	6251266
purification and properties of gene 18 product of bacteriophage t3.	two noncapsid proteins of t3 and t7 phage, the products of gene 18(gp18) and gp19, are required for dna packaging. by using in vitro complementation for dna packaging as an assay system, t3 gp18 was purified to near homogeneity from an extract prepared cells infected with a mutant of gene 19(19- extract). the purified gp18 consisted of a single polypeptide having a molecular weight of 10,000, and was eluted as dimers and higher multimers from sephadex g-75 columns. t7 gp18 was purified by the sa ...	1984	6240154
role of differential air pressure zones in the control of aerosols in a large animal isolation facility.	the uncontrolled transmission of hog cholera in a large animal isolation facility, designed to control the movement of aerosols within and between individual wings of a multiunit building, indicated the need for a critical study of aerosol behavior under existing conditions of operation. studies with aerosols of escherichia coli b t3 bacteriophage (t3 coliphage) conclusively demonstrated the impossibility of obtaining the desired control by means of a "static" air balance relationship between ad ...	1966	5951332
the enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. x. bacteriophage t3-induced s-adenosylmethionine cleavage.		1966	5946625
methylation of dna.	the methylated bases of dna are formed by the transfer of the methyl group from s-adenosylmethionine to a polynucleotide acceptor. this transfer is catalyzed by highly specific enzymes which recognize a limited number of available sites in the dna. the mechanism for the recognition is presently unknown. in some instances, there is evidence that other cellular components, such as lipopolysaccharides, can influence the methylation reaction. certain bacteriophages induce new methylases upon infecti ...	1966	5338563
the photodynamic action of acridine orange and proflavine on the survival of escherichia coli b and its capacity for phage t3.		1966	5330573
complementary fractions of denatured dna of coliphage t3 as templates for transcription.	this paper discusses the evidence that two fractions obtained by the chromatography of denatured dna of phage t3 on columns of methylated albumin-kieselguhr represent the complementary strands. this evidence derives from a variety of temperature-absorbance measurements and from the base composition of the rna products synthesized by rna polymerase under the direction of the two single-stranded dna templates.	1969	5263007
liquid-holding effects in u.v.-irradiated phage t3.		1972	5037229
native and denatured dna of phage t3 and of e. coli b as templates for rna polymerase.		1969	4975275
studies on the nucleotide arrangement in deoxyribonucleic acids. x. frequency and composition of pyrimidine isostichs in microbial deoxyribonucleic acids and in the dna of e. coli phage t3.		1966	4961463
induction of a new rna polymerase in escherichia coli infected with bacteriophage t3.		1971	4930861
photodynamic action of proflavine on coliphage t3. ii. protection by l-cysteine.	three kinetically different reactions (rx1, rx2, and rx3) have been distinguished in the photoinactivation of phage t3 in the presence of the dye proflavine. the response of these reactions to the presence of the radical trap l-cysteine has been examined. at dye concentrations equal to or less than 2.2 mug/ml, rx1 was composed of at least two parallel first-order reactions, one cysteine-insensitive (rx1a) and one cysteine-inhibited (rx1b). rx2 was completely cysteine-insensitive (rx2a). the cyst ...	1971	4927524