Publications

genetic analysis of two bacterial rna polymerase mutants that inhibit the growth of bacteriophage t7.	the escherichia coli mutants 7009 and br3 are defective in the growth of bacteriophage t7. we have previously shown that both of these mutant hosts produce an altered rna polymerase which is resistant to inhibition by the t7 gene 2 protein (de wyngaert and hinkle 1979). in both strains, the mutation which prevents t7 growth is closely linked to rifa (rpob). both mutants are complemented by transformation with a multicopy plasmid carrying rpob and rpoc but not by a plasmid carrying only rpob. thi ...	1982	6759870
isolation and characterization of an operator-constitutive mutation in the reca gene of e. coli k-12.	the reca gene of e. coli is regulated by a specific repressor, the lexa protein, which binds to an operator in the reca regulatory region. we describe in this paper the isolation and characterization of a mutant thought to carry an operator-constitutive mutation in the reca gene. this mutation has the following properties: 1) it partially suppresses the uv sensitivity of lexa- strains. 2) it maps near the reca gene. 3) it allows constitutive high-level synthesis of reca protein in both lexa- and ...	1982	6761542
cloning and expression in escherichia coli k-12 of the genes for major outer membrane protein ompa from shigella dysenteriae, enterobacter aerogenes, and serratia marcescens.	the outer membranes of many gram-negative bacteria contain a major heat-modifiable protein which shows serological cross-reactivity with the ompa protein of escherichia coli k-12. using the cloned gene for the e. coli k12 protein as a dna-dna hybridization probe, we were able to identify the corresponding genes from shigella dysenteriae. enterobacter aerogenes, and serratia marcescens. these were cloned in a phage lambda vector, and their expression in e. coli k-12 was studied. all three ompa pr ...	1982	7033204
structure of the dna-binding region of lac repressor inferred from its homology with cro repressor.	it is shown that the amino acid sequence and the dna gene sequence of the 25 amino-terminal residues of the lac repressor protein of escherichia coli are homologous with the sequences of five dna-binding proteins: the cro repressor proteins from phage lambda and phage 434, the ci and cii proteins from phage lambda, and the repressor protein from salmonella phage p22. the region of homology between lac repressor and the other proteins coincides with the principal dna-binding region of cro repress ...	1982	6951187
the genome of frog virus 3, an animal dna virus, is circularly permuted and terminally redundant.	we examined the structure of the frog virus 3 (fv 3) genome by using electron microscopic and biochemical techniques. the linear fv 3 dna molecules (mr approximately 100 x 10(6) formed circles when partially degraded with bacteriophage lambda 5'-exonuclease and annealed, but not when the annealing was done without prior exonuclease digestion. the results suggest that the dna molecules contain direct terminal repeats. the repeated region composed about 4% of the genome. complete denaturation of n ...	1982	6952182
p1 site-specific recombination: nucleotide sequence of the recombining sites.	site-specific recombination between molecules of bacteriophage p1 dna occurs at sites called loxp and requires the action of a protein that is the product of the p1 cre gene. although recombination between two loxp sites is very efficient, recombination between loxp and a unique site in the bacterial chromosome (loxb) is inefficient and generates two hybrid lox sites called loxr and loxl. we present here the nucleotide sequences of all four lox sites. analysis of these sequences indicates that ( ...	1982	6954485
isolation of a human repetitive sequence and its application to regional chromosome mapping.	recombinant lambda phage charon 4a with repetitive human dna inserts have been constructed by using cellular dna from a human-chinese hamster ovary cell hybrid retaining the complete hamster genome and a single human chromosome 12. one recombinant phage, 12-11, contains several repetitive sequences, each with a different repetition pattern in the human genome. a 2.2-kilobase (kb) ecori fragment of this phage was subcloned in pbr325. this sequence has fewer than 5,000 copies in the human genome a ...	1982	6961418
short direct repeats flank the t-dna on a nopaline ti plasmid.	crown gall disease results from the insertion of a segment of the agrobacterium ti plasmid, called t-dna, into host plant nuclear dna. we have subjected to sequence analysis the border regions of pti t37 (ends of t-dna) and one left t-dna/plant dna border fragment isolated from bt37 tobacco teratoma by molecular cloning. these sequence studies, taken together with published sequence of a right t-dna/plant dna border fragment, allowed us to identify the positions of left and right borders at the ...	1982	16593241
functional expression of individual plasmid-coded rna bacteriophage ms2 genes.	the genes of the rna-containing bacteriophage ms2 were individually inserted into thermoinducible expression plasmids under control of the phage lambda p(l) promoter. three phage-coded proteins (a-protein, coat protein, and replicase) were expressed at high efficiency. induced cultures specifically complemented superinfecting amber mutants of phage ms2. regulatory mechanisms operative during the natural infection cycle of the phage were reproduced by the plasmid expression system.	1982	16453413
p lambda cm system: observations on the roles of transposable elements in formation and breakdown of plasmids derived from bacteriophage lambda replicons.	transduction with phage derived from a 2-year-old lysate of lambda cam105 (lambda::tn9) gave rise to chloramphenicol-resistant (cm(r)) transductants harboring a plasmid (plambdacm1) formed from lambda cam105 by a tn9-mediated adjacent deletion to position 36.07 kilobases in the n cistron of lambda. the plambdacm element can replicate as a plasmid, insert into the bacterial genome, or reproduce lytically as a phage on cells that provide n function. the feasibility of obtaining high titers in enca ...	1983	6296061
cloning and characterization of the rat nadph-cytochrome p-450 oxidoreductase gene.	a rat liver dna genomic library was prepared using the lambda phage cloning vector charon 28. recombinant phage were screened with a cdna clone (por-7) containing sequences complementary to mrna coding for nadph-cytochrome p-450 oxidoreductase. this cdna clone contains the poly(a) addition site and 60% of the mrna sequence (gonzalez, f. j., and kasper, c. b. (1982) j. biol. chem. 257, 5962-5968). four positive phage were identifed and plaque-purified, and their dna was isolated and subjected to ...	1983	6296077
purification and properties of t4 phage thymidylate synthetase produced by the cloned gene in an amplification vector.	we have introduced the t4 thymidylate synthetase gene, resident in a 2.7-kilobase ecori restriction fragment, into an amplification plasmid, pkc30. by regulating expression of this gene from the phage lambda pl promoter within pkc30 in a thya host containing a temperature-sensitive lambda repressor, the t4 synthetase could be amplified about 200-fold over that after t4 infection. at this stage, a 20-fold purification was required to obtain homogeneous enzyme, mainly by an affinity column procedu ...	1983	6296121
overexpression and purification of the sigma subunit of escherichia coli rna polymerase.	we have constructed a plasmid that overexpresses 100-fold the sigma subunit of escherichia coli rna polymerase. the plasmid was constructed by placing the plol promoter-operator of bacteriophage lambda upstream from rpod, the gene encoding the sigma subunit. a simple procedure for purification of the overexpressed protein has been developed based on guanidine hydrochloride denaturation/renaturation, deae cellulose chromatography, and sephacryl s-200 chromatography. the purified product has been ...	1983	6231214
mapping of the q-utilization site (qut) required for antitermination of late transcription in bacteriophage lambda.	to locate the site required for transcription antitermination by the gene q product, we constructed a plasmid containing the p'r promoter, the t'r1 terminator, and gene galk. we measured the galk expression in response to the lambda q product supplied in trans, while deleting various portions of lambda dna adjacent to p'r. the presence of the lambda p'r promoter together with the downstream dna coding for only a 34-bp segment of 5'-proximal 6s rna permits antitermination to occur, whereas deleti ...	1983	6231216
[vitamin para-aminobenzoic acid inhibits development of sos function in tif-1 mutants of escherichia coli at nonpermissive temperatures].	the development of "sos" inducible functions in lysogenic and non-lysogenic strains of escherichia coli tif-1 sfia11 (lambda) at nonpermissive temperature of 42 degrees c was strongly suppressed by para-aminobenzoic acid (paba). the rate of prophage lambda induction decreased 400 times, as compared to the control level; the efficiency of w-reactivation of uv-irradiated phage lambda decreased 37.5 to 16%. paba also inhibited to some extent (1.5 times) the process of inducible recombination on the ...	1983	6229450
infectious poxvirus vectors have capacity for at least 25 000 base pairs of foreign dna.	to test the capacity of poxviruses for added foreign dna, a recombinant was constructed that contains 24 700 bp of bacteriophage lambda dna inserted within the vaccinia virus thymidine kinase (tk) gene. the recombinant is stable, infectious and replicates in tissue culture at the same rate and to the same titer as standard vaccinia virus. this size flexibility of the poxvirus genome and the lack of stringent packaging requirements are useful features for an infectious eukaryotic cloning vector.	1983	6229451
escherichia coli plasmid vectors for high-level regulated expression of the bacteriophage lambda xis gene product.	the bacteriophage lambda xis protein is one of the proteins required for site-specific excisive recombination by which the lambda prophage is excised from the escherichia coli bacterial chromosome. we cloned the lambda xis gene under the control of several prokaryotic promoters to obtain a sufficient source of the protein for biochemical studies. our results demonstrate that e. coli lac promoter and lambda pl promoter fusions to the xis gene produce high levels of xis protein. induction of the e ...	1983	6229452
cloning of herpesvirus saimiri dna fragments representing the entire l-region of the genome.	purified particles of herpesvirus saimiri, a potent tumor-eliciting virus of primates, contain genomic dna molecules (145-170 kb) consisting of a unique l-dna region (112 kb) which is flanked by variable stretches of repetitive sequences (h-dna). restriction fragments representing the entire l-dna of h. saimiri strain no. 11 were cloned in plasmid and bacteriophage vectors. the internal fragments of l-dna generated by the enzymes ecori and kpni were inserted into plasmid pacyc184, cosmid pjc81, ...	1983	6229454
vectors for high conditional expression of cloned genes.	several multicopy plasmids carrying the control region of bacteriophage lambda lysogeny, including the gene of a thermosensitive repressor ci857 have been constructed. the phages allow high expression of proteins under the transcription control of lambda promoter pr and translation control of cro. the method has been assayed by measuring expression of either intact beta-galactosidase, truncated beta-galactosidase or beta-galactosidase fused to a mitochondrial gene product. it is shown that use o ...	1983	6225468
interactions of the 26-39 fragment of the cro protein from lambda bacteriophage with nucleic acids.	a tetradecapeptide with a sequence identical to residues 26-39 of the cro protein from bacteriophage lambda has been synthesized. this peptide has no secondary structure in an aqueous buffer but adopts an alpha-helical conformation in the presence of 20% hexafluoroisopropanol. the fluorescence of the single tyrosyl residue of the cro protein fragment is quenched upon binding to nucleic acids. proton magnetic resonance has been used to investigate complex formation of the cro protein fragment wit ...	1983	6225680
the interaction of cos with chi is separable from dna packaging in reca-recbc-mediated recombination of bacteriophage lambda.	chi (5'-gctggtgg) is a recombinator in reca-recbc-mediated recombination in escherichia coli. in bacteriophage lambda vegetative recombination, chi is fully active only when it is correctly oriented with respect to cos, the site that defines the ends of the packaged chromosome. here we demonstrate that packaging from cos is not necessary for this cos-chi interaction. our evidence suggests that correctly oriented cos is an activator of chi. cos, as an activator, is (1) dominant over cos-, (2) act ...	1983	6225696
effects of high levels of dna adenine methylation on methyl-directed mismatch repair in escherichia coli.	two methods were used in an attempt to increase the efficiency and strand selectivity of methyl-directed mismatch repair of bacteriophage lambda heteroduplexes in e. coli. previous studies of such repair used lambda dna that was only partially methylated as the source of methylated chains. also, transfection was carried out in methylating strains. either of these factors might have been responsible for the incompleteness of the strand selectivity observed previously. in the first approach to inc ...	1983	6225697
differential binding of rna polymerase to the prm and pr promoters of bacteriophage lambda.	escherichia coli rna polymerase binding to the promoters pr and prm of bacteriophage lambda was visualized and quantitated by electron microscopy. although the two promoters are located close together in the phage genome, their proximity to the end of an 889-bp haeiii dna fragment made it possible to position binary complexes within 18 bp (2%) intervals. thus, polymerase binding to pr and prm could be distinguished by comparing the locations of binary complexes formed with wild-type and mutant ( ...	1983	6225700
purification and properties of the bacteriophage lambda int protein.		1983	6225930
double holliday structure: a possible in vivo intermediate form of general recombination in escherichia coli.	from escherichia coli cells we purified '8'-shaped dimeric molecules in which two circular dna molecules of bacteriophage lambda were joined at a homologous site. some of them had a complex junction which we interpreted as being two closely spaced holliday structures because of (i) superhelicity of the molecule, (ii) the sedimentation rate of the molecule in sucrose gradients, and (iii) the appearance in the electron microscope. other 'figure-eights's' had two separate homologous junctions, pres ...	1983	6225938
the head genes of bacteriophage 21.	physical and genetic maps of the head genes of lambdoid phage 21 have been made and compared with the head gene map of lambda. because 21 and lambda have partial sequence homology throughout the head genes it was expected that the head genes of 21 would be analogous to those of lambda. eight head genes of 21 have been identified and it was found that each of the genes is analogous in position, structure, and/or function to a lambda head gene. phage 21 genes analogous to the lambda d and fi genes ...	1983	6226144
unexpected relationships between bacteriophage lambda hypothetical proteins and bacteriophage t4 tail-fiber proteins.	hypothetical lambda protein orf314 shows significant homology with the carboxyl end of phage t4 tail-fiber protein gp37. homology can also be demonstrated between hypothetical lambda protein orf194 and a fragment of bacteriophage t4 protein gp38. this sequence homology is also reflected in the genomic sequences of these two phages.	1983	6226290
imino proton assignments in the proton nuclear magnetic resonance spectrum of the lambda phage or3 deoxyribonucleic acid fragment.	the 17 base pair duplex d(tatcaccgcaagggatap) . d(tatcccttgcggtgatap) corresponding to the or3 operator site of lambda phage has been synthesized and studied by 1h nuclear magnetic resonance spectroscopy at 470 mhz. the 13 imino proton resonances observed at 20 degrees c have been assigned to specific base pairs at positions 3-15 on the basis of nuclear overhauser effect measurements and studies of the temperature dependence of peak intensities. resonances from the a-t base pairs at positions 1, ...	1983	6226312
expression of the phage lambda recombination genes exo and bet under lacpo control on a multi-copy plasmid.	the bacteriophage lambda genes exo and bet, whose products (lambda exonuclease and beta protein, respectively; red phenotype) mediate homologous recombination of lambda phages, have been cloned under lacpo laciq control on multi-copy plasmids. induction of reca3 cells harboring these plasmids with isopropylthiogalactoside (iptg) resulted in lambda exonuclease levels (assayed in vitro) that were proportional to the time of induction (for at least 4 h); recombination of lambda red- phages in vivo ...	1983	6226560
instability of bacteriophage lambda initiator o and p proteins in dna replication.	lambda dv plasmids having an amber mutation in an initiator gene, o or p, were constructed from mutant lambda phages by recombinant dna techniques and several properties of such derivatives were investigated. these plasmids are perpetuated in suppressor-plus (amber-permissive) cells, but not in non-suppressor cells. the plasmid copy number in the suppressor-plus cells was low as compared to that of the plasmid without the amber mutation. in cells carrying a thermosensitive suppressor 2, raising ...	1983	6226650
comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda.	the three-dimensional structures of cro repressor protein and of the amino-terminal domain of lambda repressor protein, both from bacteriophage lambda, are compared. the second and third alpha-helices, alpha 2 and alpha 3, are shown to have essentially identical conformations in the two proteins, confirming the significance of the amino acid sequence homology previously noted between these and other dna binding proteins in the region corresponding to these helices. the correspondence between the ...	1983	6226802
knotting of dna caused by a genetic rearrangement. evidence for a nucleosome-like structure in site-specific recombination of bacteriophage lambda.	intramolecular recombination between two attachment sites on a circular substrate can invert one segment of the circle with respect to the other. we have studied the topological form of the products of such site-specific inversion as a function of two parameters of the substrate circle: the degree of supercoiling and the distance between the recombining sites. for both integrative and excisive recombination, supercoiled substrates produced knotted recombinants; the complexity of the knots reflec ...	1983	6226803
role for dna homology in site-specific recombination. the isolation and characterization of a site affinity mutant of coliphage lambda.	site-affinity (or saf) mutations change the specificity of prophage insertion. we have isolated a saf mutation of the bacteriophage lambda attachment site by inserting the phage chromosome into and then excising it from a secondary host attachment site. this causes reciprocal exchange of two seven base-pair segments (the overlap regions) that lie within the cores of the two sites. since the two overlap regions differ from each other in nucleotide sequence, the recombinant sites are mutants. we h ...	1983	6226804
gene transfer into animal cells after fusion with bacteriophage lambda-infected e coli protoplasts.		1983	6227013
lambda phage dna sequences affecting the packaging process.	our previous work identified a minimal region of bacteriophage lambda dna that is necessary for packaging into phage particles. it consists of 40 bp of the right arm and 45 bp of the left arm [miwa and matsubara, gene 20 (1982)267-279]. a part of this region, 22 bp of the right arm and 38 bp of the left arm, is sufficient for cutting at cos lambda (the minimal sequence for cos lambda cutting). an 84-bp region to its right contains a binding site for lambda terminase, a complex of nu1 and a gene ...	1983	6227527
use of lambda unc transducing bacteriophages in genetic and biochemical characterization of h+-atpase mutants of escherichia coli.	the eight subunits of the h+-atpase of escherichia coli are coded by the genes of the unc operon, which maps between bglb and asna. a collection of unc mutations were transferred via p1 transduction into a strain in which lambda ci857 s7 was inserted into bglb. the lambda phage was induced, and asna+ transducing phage that carried unc were selected. transducing phage carrying mutations in the unca, b, d, e, and f genes were used for complementation analysis with a collection of unc mutants, incl ...	1983	6227607
genetic characterization of a gene for prolipoprotein signal peptidase in escherichia coli.	a mutation (lspa, prolipoprotein signal peptidase) rendering the prolipoprotein signal peptidase temperature-sensitive in escherichia coli has been analyzed. the mutation was mapped in the dnaj-rpst-iles-dapb region by interrupted mating with various hfr strains and p1 phage transduction. lambda transducing phage lambda ddapb2 that carries the rpst-iles-dapb region was shown to complement the lspa mutation. plasmid plc3-13 which had been isolated from clarke and carbon's collection as a plasmid ...	1983	6227793
pausing and termination of human rna polymerase ii transcription at a procaryotic terminator.	kinetic analyses of runoff transcription in a cell-free eucaryotic transcription system revealed that the bacteriophage lambda 4s rna terminator caused human rna polymerase ii to pause on the template and partially terminate transcription of transcripts initiated by the adenovirus 2 major late promoter. analogous to the procaryotic rna polymerase, the eucaryotic enzyme terminated just beyond the guanine-plus-cytosine-rich region of dyad symmetry in the terminator sequence. these results suggest ...	1983	6227805
genetic recombination of bacteriophage lambda dnas in xenopus oocytes.	pairs of genetically marked bacteriophage lambda dnas have been injected into xenopus laevis oocyte nuclei. after suitable incubation, dna was recovered and packaged into phage particles in vitro. when these were plated onto a selective host, phage recombinant for parental markers were observed. recombination was dependent on both parents being present in the same oocyte nucleus and was roughly proportional to the physical separation of the markers. thus, the oocytes appear to contain the machin ...	1983	6227916
early intermediates in bacteriophage lambda prohead assembly. ii. identification of biologically active intermediates.	the morphogenesis of bacteriophage lambda proheads is under the control of the four phage genes b, c, nu3, and e, as well as the e. coli genes groel and groes. it has been previously shown that extracts prepared from cells infected with a lambda c-e- mutant accumulate biologically active gpb and gpnu3 (murialdo, h., and becker, a., j. mol. biol. 125, 57-74 (1978) ). to characterize the nature of these intermediates in prohead assembly, extracts prepared from these cells were fractionated by deae ...	1983	6228056
enzyme immunoassay for igg and igm antibodies against dsdna and ssdna.	two enzyme-linked immunosorbent assays (elisas) for the detection of dna antibodies are presented, one using lambda-phage dna for the detection of dsdna antibodies, the other using denatured calf thymus dna for ssdna antibodies. it was shown that only dsdna antibodies of the igg class were specific for sle. igm-dsdna antibodies or ssdna antibodies were not sle-specific. of 62 sle patients 58% were positive for igg-dsdna antibodies. when only those patients with active disease were considered, 88 ...	1983	6228081
[para-aminobenzoic acid inhibits the manifestation of inducible sos functions in escherichia coli k-12].	in experiments with chemical mutagens (alkylating agents mnu, enu, mms and ems), para-aminobenzoic acid (paba) sharply inhibited the inducible processes in escherichia coli, namely, mutagenesis, induction of lambda prophage and w-reactivation of uv-irradiated phage lambda. based on experimental studies of e. coli strains deficient in different steps of dna repair, the conclusion was made that paba participates in regulation of the branch of dna repair that is controlled by reca+ recf+ alleles.	1983	6228486
lambda phage cro repressor interaction with dna.	we present here the complete identification of the resonances from the aromatic region of the 1h nmr spectrum of the cro repressor of the escherichia coli lysogenic phage lambda. this was accomplished by the use of two-dimensional nmr analysis as well as specifically deuterated tyrosines. not surprisingly, it shows that the published resonance assignment approached by more conventional methods by others includes substantial errors. the effect of complex formation with dna was examined in the 1h ...	1983	6220002
high-level expression of oncogenes in escherichia coli.	a plasmid, pjl6, was constructed that contains a unique cla i site 12 codons beyond the bacteriophage lambda cii gene initiation codon, as well as an adjacent unique hind iii site. these sites allowed us to fuse the sequences from the avian myelocytomatosis virus (mc29) v-myc gene, the avian myeloblastosis virus (amv) v-myb gene, and the harvey murine sarcoma virus (ha-musv) v-ras gene to the amino-terminal portion of the cii gene. transcription of the hybrid genes is controlled from the lambda ...	1983	6101025
structure and inherent properties of the bacteriophage lambda head shell. iv. small-head mutants.	missense mutants of bacteriophage lambda that produce small proheads were found among prophage mutants defective in the major head protein gpe. measurements of the sedimentation coefficient and molecular weight of the small proheads showed that they have the t = 4 structure composed of 240 molecules of gpe instead of the wild-type t = 7 structure composed of 420 molecules of gpe. when the phage mutants were grown in groe mutants of escherichia coli, they produced small unprocessed proheads, whic ...	1983	6228668
phage lambda receptor (lamb protein) in escherichia coli.	the main properties of the lambda receptor are summarized in the table. because these can be studied by a combination of genetic, biophysical, and biochemical techniques, the lambda receptor now appears to represent one of the best systems for study of structure-function relationships in a membrane protein. in addition, as explained in this volume, it also constitutes a good system for study of the export of proteins to extracytoplasmic locations.	1983	6228707
histones h3 and h2a are homologous to the lambda repressor and cro proteins in 22 residue segments implicated in dna binding.	the histones h3 and h2a from calf thymus are homologous to the repressor and cro repressor proteins of bacteriophage lambda in a 22-residue segment that has been implicated by mutational and model-building studies in dna binding. in the lambda proteins this segment is folded into a helix-turn-helix unit of supersecondary structure, and we propose that the homologous regions in the histones possess the same fold. homology was quantified with a unified procedure based on criteria of identity of ke ...	1983	6237652
[structure of a recombination site in the transducing bacteriophage lambda plac5 dna].	a recombination site in the transducing bacteriophage lambda plac5 dna has been structurally elucidated. comparison of primary structures of e. coli lac-operon (distal end of lacz gene, z-y spacer, and proximal end of lacy gene) described earlier with corresponding segments of bacteriophages lambda ci857 and lambda plac 5-2 dnas sequenced in this paper showed that the bacterial dna insert ends immediately after z-y spacer, just before the initiating triplet atg of lacy gene. it thus follows that ...	1983	6237658
a vector that uses phage signals for efficient synthesis of proteins in escherichia coli.	i have developed a plasmid vector pcqv2 for high-level expression of proteins in e. coli. the plasmid contains a very strong promoter and translation start point from bacteriophage lambda, and a restriction endonuclease site in which a gene may be placed under control of these initiation signals. the plasmid also contains the gene for a temperature-sensitive repressor of the lambda promoter, allowing 100-fold induction of protein expression. the vector pcqv2 has been used to synthesize sv40 smal ...	1983	6302192
separate sites for binding and nicking of bacteriophage lambda dna by terminase.	the cohesive end site (cos) is the site of action of bacteriophage lambda terminase, the enzyme that introduces staggered nicks to generate the 12-base cohesive ends of mature lambda dna. deletion mutations that remove the lambda cohesive end sequence have been isolated after in vitro mutagenesis. the deletions were obtained by digesting the dna of a cos duplication phage with s1 nuclease to remove the cohesive ends and adjacent base pairs, followed by blunt end ligation and dna packaging into p ...	1983	6302676
role of short regions of homology in intermolecular illegitimate recombination events.	the structures of three recombinants between bacteriophage lambda dna and plasmid pbr322 that were generated in a reca derivative of escherichia coli are described. each resulted from two illegitimate recombination events that resulted in the substitution of part of the lambda genome by part of the plasmid genome. the nucleotide sequences at the six lambda-plasmid junctions were determined and compared with the sequences of the lambda and plasmid genomes before recombination. each recombination ...	1983	6302684
an assay for the rates of cleavage of specific sites in dna by restriction endonucleases: its use to study the cleavage of phage lambda dna by ecori and phage p22 dna containing thymine or 5-bromouracil by hindiii.	a method to measure the rates of cleavage of specific sites in dnas by restriction endonucleases is described. partial digests are prepared by incubating dnas with limiting amounts of endonuclease. the termini generated by cleavage are labeled with 32p by the polynucleotide kinase-exchange reaction. the labeled termini are then identified by completing the digestion with the same endonuclease and separating the products by gel electrophoresis. as the products of complete digestion of dna are oft ...	1983	6303160
molecular cloning and characterization of endogenous feline leukemia virus sequences from a cat genomic library.	recombinant bacteriophage lambda clones from a cat genomic library derived from placental dna of a specific pathogen-free cat were screened to identify endogenous feline leukemia virus (felv) sequences. restriction endonuclease mapping of four different clones indicates that there are a number of similarities among them, notably the presence of a 6.0- to 6.4-kilobase pair (kbp) ecori hybridizing fragment containing portions of sequences homologous to the gag, pol, env, and long terminal repeat-l ...	1983	6304345
detection of chemicals that stimulate tn9 transposition in escherichia coli k12.	a spot test has been developed for detecting substances that enhance the transposition of tn9 in escherichia coli. phage lambda::tn9-infected cells were plated on chloramphenicol media and a drop of the test substance was placed at the center of the plate. following incubation, chloramphenicol-resistant colonies appeared due to the transposition of tn9 to the bacterial chromosome. by comparing the test plate and a control plate with respect to the number and distribution of colonies, the effect ...	1983	6304465
organization of gene and non-gene sequences in micronuclear dna of oxytricha nova.	in order to study the derivation of the macronuclear genome from the micronuclear genome in oxytricha nova micronuclear dna was partially digested with ecori, size fractionated, and then cloned in the lambda phage charon 8. clones were selected a) at random b) by hybridization with macronuclear dna or c) by hybridization with clones of macronuclear dna. one group of these clones contains only unique sequence dna, and all of these had sequences that were homologous to macronuclear sequences. the ...	1983	6304639
isolation and characterization of the gene coding for cytosolic phosphoenolpyruvate carboxykinase (gtp) from the rat.	the gene for cytosolic phosphoenolpyruvate carboxykinase (gtp) [gtp:oxaloacetate carboxy-lyase (transphosphorylating), ec 4.1.1.32] from the rat was isolated from a recombinant library containing the rat genome in phage lambda charon 4a. the isolated clone, lambda pck1, contains the complete gene for phosphoenolpyruvate carboxykinase and approximately equal to 7 kilobases (kb) of flanking sequence at the 5' end and 1 kb at the 3' terminus. restriction endonuclease mapping, r-loop mapping, and pa ...	1983	6304730
expression of plasmodium falciparum blood-stage antigens in escherichia coli: detection with antibodies from immune humans.	many proteins produced by blood stages of the malaria parasite plasmodium falciparum are natural immunogens in man. as an approach to determining which of these are relevant to protective immunity we have constructed an expression library of p. falciparum cdna sequences, cloned in escherichia coli. the cdna sequences were inserted into the beta-galactosidase gene of an ampicillin-resistant derivative of the temperature-sensitive lysogenic bacteriophage lambda gt11. about 5% of the resulting clon ...	1983	6304737
a papillomavirus dna from a cervical carcinoma and its prevalence in cancer biopsy samples from different geographic regions.	dna from one biopsy sample of invasive cancer of the cervix contained sequences hybridizing with human papillomavirus (hpv) type 11 dna only under nonstringent conditions. this dna was molecularly cloned in lambda phage. under stringent conditions of hybridization it cross-hybridized to a minor extent (less than 0.1%) with hpv types 10, 14, and 15 and showed no homology with dna of other human hpv types. we therefore propose to designate it tentatively as hpv 16. hpv 16 dna was used as a probe t ...	1983	6304740
site-specific recombination by gin of bacteriophage mu: inversions and deletions.	a 3000-bp invertible segment in the dna of bacteriophage mu determines the host range of the phage. the inversion is catalyzed by the phage-coded protein gin; the recombination sites are short inverted repeats. gin protein is only made in low amounts by mu. to further investigate the gin-mediated recombination reaction a gin overproducing strain was constructed. the gin gene was cloned on a plasmid behind the pl-promotor of phage lambda. this results in a 100-fold higher inversion frequency of a ...	1983	6305017
structure of the operator-binding domain of bacteriophage lambda repressor: implications for dna recognition and gene regulation.		1983	6305562
replication of bacteriophage lambda dna.		1983	6305582
[effect of plasmid pkm101 on the k-specific restriction-modification of bacteriophage lambda dna].		1983	6305613
improved plasmid vectors with a thermoinducible expression and temperature-regulated runaway replication.	improved expression vectors have been constructed which are derived from runaway-replication mutants of plasmid r1 and carry the strong leftward promoter (pl) of bacteriophage lambda. the activity of this promoter is controlled by a temperature-sensitive repressor, product of the phage gene ci cloned on a compatible plasmid. heat induction leads to amplification of the plasmid copy number and at the same time turns on the promoter. at a short distance downstream from the promoter, unique ecori, ...	1983	6305768
use of lambda phasmids for deletion mapping of non-selectable markers cloned in plasmids.	a nonselectable gene carried on a poorly selectable recombinant plasmid has been physically mapped by deletion analysis. our method involved cloning the plasmid into a coliphage lambda vector and treating the recombinant phage with a chelator. virtually all particles surviving this treatment carried large deletions within the plasmid insert. further deletion analysis was done by inserting a selectable lambda sequence into one such deletion derivative and repeating the chelator selection. chelato ...	1983	6305773
purification and characterization of escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda pl promoter and ci857 temperature-sensitive repressor.	the gene for escherichia coli guanine-xanthine phosphoribosyltransferase was placed after the high efficiency lambda phage leftward promoter in plasmid phegpt also containing the lambda ci857 temperature-sensitive repressor. guanine-xanthine phosphoribosyltransferase increases 780-fold when cells containing phegpt are shifted from 30 to 42 degrees c. guanine-xanthine phosphoribosyltransferase represents approximately 5% of the protein in a crude extract of induced cells. guanine-xanthine phospho ...	1983	6305942
blocked 5'-termini in the fragments of chromosomal dna produced in cells exposed to the antitumor drug 4'-[(9-acridinyl)-amino]methanesulphon-m-anisidide (mamsa).	comparison of the sensitivity of dna isolated from untreated and mamsa-treated py815 mouse mastocytoma cells to hydrolysis by e.coli 3'-exonuclease iii and phage lambda or phage t7 5'-exonucleases show that the fragments of chromosomal dna produced by mamsa treatment have free 3'-oh termini and blocked 5'-termini.	1983	6306581
molecular cloning of human interleukin 2 cdna and its expression in e. coli.	a recombinant plasmid containing human interleukin 2 (il2) cdna was identified in a cdna library constructed from mrna derived from pha-tpa induced splenocytes. using this cdna as a hybridization probe, a dna fragment containing the il2 gene was isolated from a collection of hybrid phages derived from human genomic dna. a unique reading frame was identified from the nucleotide sequence derived from these plasmids coding for a polypeptide of 153 amino acids and containing a putative signal sequen ...	1983	6306584
comparison of the sequence organization of related retrovirus-like multigene families in three evolutionarily distant rodent genomes.	sequences related to mouse intracisternal a-particle (iap) genes have been isolated from rat and syrian hamster gene libraries as recombinants in lambda phage. the sequences are moderately reiterated in both these genomes but their sequence organization in the hamster genome is different from that in the rat genome. restriction analysis and electron microscopy indicate that the syrian hamster iap sequences represent a family of relatively homogeneous well-conserved units; in this, they resemble ...	1983	6306589
a new restriction endonuclease from acetobacter pasteurianus.	a restriction endonuclease, apai, has been partially purified from acetobacter pasteurianus. this enzyme cleaves bacteriophage lambda dna and simian virus 40 dna at one site, adenovirus-2 dna at more than nine sites, but it does not cleave phi x174 dna nor plasmid pbr322 dna. this enzyme recognizes the sequence (formula; see text) and cuts at the sites indicated by the arrows.	1983	6306590
[nature of the plasmids determining the unstable inheritance of transposon tn9 in escherichia coli k-12].	unstable inheritance of transposon tn9 in the escherichia coli strain ks7201 had been connected with its integration into a certain bacterial chromosome site (atttn9a). however, the present work shows that the transposon is situated within an unstable plasmid in this strain. a possibility of such plasmid's formation, as a result of a deletion of a part of bacteriophage lambda dna, is shown.	1983	6307814
cloning and expression of a mouse adenine phosphoribosyltransferase gene.	a functional mouse adenine phosphoribosyltransferase (aprt) gene was identified and cloned by screening a mouse sperm genomic dna library in lambda charon 4a. the probe utilized for screening was a restriction fragment encoding much of the hamster aprt gene. six recombinants that hybridized with the probe were identified, and after digestion with restriction enzymes ecori and pvuii revealed three different patterns of digestion for each enzyme. of the six recombinants, five representing two of t ...	1983	6307822
the mouse genome contains two nonallelic pro-opiomelanocortin genes.	in the anterior pituitary pro-opiomelanocortin (pomc) is the protein precursor to both adrenocorticotropin and beta-lipotropin but in the intermediate pituitary pomc serves as the precursor to alpha-melanocyte-stimulating hormone and beta-endorphin. in addition, pomc expression in the anterior pituitary is inhibited by glucocorticoids but stimulated by corticotropin-releasing factor while pomc expression in the intermediate lobe is not responsive to glucocorticoids but is inhibited by dopamine. ...	1983	6308009
hybrid plasmids containing the pyruvate dehydrogenase complex genes and gene-dna relationships in the 2 to 3 minute region of the escherichia coli chromosome.	a sample of colonies from the clarke-carbon cole1-escherichia coli dna plasmid gene bank was screened by conjugation for complementation of the lipoamide dehydrogenase lesion of a deletion strain lacking all components of the pyruvate dehydrogenase complex, delta (arop acee acef lpd). two cole1-lpd+ hybrid plasmids were identified: pgs2 (cole1-ace lpd+; 24 kb) and pgs5 (cole1-lpd+; 14 kb). enzymological studies confirmed that pgs2 expressed all the activities of the pyruvate dehydrogenase comple ...	1983	6308128
isolation and characterisation of genomic and cdna clones for an androgen-regulated secretory protein of rat seminal vesicles.	testosterone controls the synthesis of seminal vesicle protein f in male rats by regulating the cellular concentration of its mrna (mrnaf). phage lambda recombinants have been isolated containing the complete f gene. in addition plasmids have been constructed containing cdnaf sequences some of which are probably full-length (approximately 700 bp). detailed restriction mapping shows that the f gene is 1.7 kbp long and contains approximately 1.0 kbp of intervening sequence arranged in at least two ...	1983	6308568
characterization and nucleotide sequence of a chicken gene encoding an opal suppressor trna and its flanking dna segments.	a naturally occurring opal suppressor serine trna has been purified from chicken liver and used as a probe to isolate the corresponding gene from a library of chicken dna in bacteriophage lambda. this minor trna is encoded by a single-copy gene that is not part of a trna gene cluster. dna sequence analysis of the gene and its flanking dna segments shows that the gene is encoded in an 87-base-pair segment without intervening sequences and specifies a trna that reads the termination codon uga. thi ...	1983	6308662
high-level expression in escherichia coli of enzymatically active harvey murine sarcoma virus p21ras protein.	the gene for the harvey murine sarcoma virus (ha-musv) p21ras protein was fused to the amino-terminal portion of the bacteriophage lambda cii gene on the expression vector pjl6. the fusion was such that transcription was controlled by the well-regulated phage lambda pl promoter, and translation initiated in the cii gene continued in frame into the ras gene sequences that code for p21. when the pl promoter was derepressed, the escherichia coli cells harboring the fusion plasmid synthesized 23,000 ...	1983	6308763
[construction of a genome library from a beta-0-thalassemic individual from ferrara: characterization of clones containing beta globin genes].	a library of genomic dna was prepared from a patient with beta o ferrara thalassaemia: random human dna fragments (15 - 20 kb) have been joined to phage lambda vectors and cloned has viable phage particles (4). 4x10(5) phages have been screened for their content in beta globin gene sequences, using a human beta cdna plasmid (5) as hybridization probe. five positive clones have been isolated and characterized by restriction endonuclease cleavage analysis and by the hybridization experiments. the ...	1983	6309196
sequence-specific recognition of deoxyribonucleic acid. chemical synthesis and nuclear magnetic resonance assignment of the imino protons of lambda or3 operator deoxyribonucleic acid.	using solid-phase phosphite triester methods, we have synthesized both strands of the phage lambda or3 dna sequence, reannealed them, and studied the native operator duplex by high-resolution nmr at 500 mhz. at 7 degrees c the imino protons of the two terminal base pairs at each end have disappeared from the spectrum by exchange broadening. the 13 detectable imino resonances have been assigned to their respective base pairs in the duplex by using sequential nearest-neighbor noe connectivity meth ...	1983	6309214
evidence that a nucleotide sequence, "boxa," is involved in the action of the nusa protein.	we report the isolation of a mutation, boxa1, in the nutr region of the phage lambda genome. the nutr region, located downstream of the pr promoter, includes the site nutr where the lambda n protein is thought to act to render subsequent transcription termination-resistant. we have previously suggested that the boxa sequence, 5'cgctctta3' (or its rna analog), located 8 bp promoter-proximal to nutr, might be the recognition site for the e. coli host factor, nusa, which has been shown to be necess ...	1983	6309406
cloning and mapping of the manganese superoxide dismutase gene (soda) of escherichia coli k-12.	an escherichia coli gene bank composed of large dna fragments (about 40 kilobases) was constructed by using the small cosmid phc79. from it, a clone was isolated for its ability to overproduce superoxide dismutase. the enzyme overproduced was manganese superoxide dismutase, as determined by electrophoresis and antibody precipitation. maxicell analysis and two-dimensional o'farrell polyacrylamide gel electrophoresis demonstrated that the structural gene, soda, of manganese superoxide dismutase wa ...	1983	6309739
analysis of the 3' end of the human pro-alpha 2(i) collagen gene. utilization of multiple polyadenylation sites in cultured fibroblasts.	three overlapping genomic clones covering 28 kilobases of the human pro-alpha 2(i) collagen gene have been isolated from a lambda phage library. the analysis of 12 introns and 12 exons in the 3' end region has shown that the human gene has a structure remarkably similar to that reported for the homologous chicken gene. one large intron, in the alpha-chain domain, contains an alui sequence flanked by short direct repeats; a second alui sequence is present 4 kilobases downstream from the terminati ...	1983	6309769
the rabbit uteroglobin gene. structure and interaction with the progesterone receptor.	the study of the regulation of uteroglobin gene in the rabbit endometrium constitutes a model for analyzing the mechanism of action of progesterone in mammals. the gene has been cloned into lambda phage and sequenced. comparison of the sequence of the gene with the amino acid sequence of preuteroglobin and the three-dimensional structure of uteroglobin established by crystal x-ray diffraction showed that the 3 exons correspond to different functional domains of the protein and that at least one ...	1983	6309802
new bacteriophage lambda vectors with positive selection for cloned inserts.		1983	6310332
detection and mapping of homologous, repeated and amplified dna sequences by dna renaturation in agarose gels.	a new molecular hybridization approach to the analysis of complex genomes has been developed. tracer and driver dnas were digested with the same restriction enzyme(s), and tracer dna was labeled with 32p using t4 dna polymerase. tracer dna was mixed with an excess amount of driver, and the mixture was electrophoresed in an agarose gel. following electrophoresis, dna was alkali-denatured in situ and allowed to reanneal in the gel, so that tracer dna fragments could hybridize to the driver only wh ...	1983	6310499
efficient expression of influenza virus ns1 nonstructural proteins in escherichia coli.	rna segment 8 of the influenza a virus genome codes for two nonstructural proteins, ns1 and ns2, for which the functions are unknown. cloned cdna copies of this gene from three different influenza a virus strains were inserted into an escherichia coli plasmid expression vector, pas1, carrying the strong regulatable lambda phage promoter, pl. after induction, the ns1 proteins were overproduced to levels of 20-25% of total cellular protein. this was surprising in that the codon composition for the ...	1983	6310615
detection of a + t-rich dna in gels by differential fluorescence.	the fluorochrome hoechst 33258 preferentially forms complexes with a + t-rich duplex dna, whereas ethidium bromide binds nucleic acids independent of base composition. both compounds can be conveniently used to visualize dna fractionated by gel electrophoresis. determination of fluorescence emission from hoechst 33258-stained restriction fragments normalized to fluorescence derived from the same sample after ethidium bromide staining provides a measure of emission due to a + t content, and allow ...	1983	6311048
high-level expression in escherichia coli of the carboxy-terminal sequences of the avian myelocytomatosis virus (mc29) v-myc protein.	a plasmid, pjl6, was constructed that contains a unique clai site twelve codons beyond the bacteriophage lambda cii gene initiation codon. this site allowed us to fuse the carboxy-terminal sequences of the avian myelocytomatosis virus (mc29) v-myc gene to the amino-terminal portion of the cii gene. transcription of the hybrid gene is controlled from the phage lambda pl promoter. when this promoter is derepressed, escherichia coli cells harboring the chimeric plasmid produce a level of cii-myc fu ...	1983	6311677
molecular cloning and expression of a bacillus subtilis beta-glucanase gene in escherichia coli.	a bacillus subtilis gene coding for an endo-beta-1,3-1,4-glucanase has been transferred to escherichia coli by molecular cloning using bacteriophage lambda and plasmid vectors. the gene is contained within a 1.6-kb ecori-pvui dna fragment and directs the synthesis in e. coli of a beta-glucanase which specifically degrades barley glucan and lichenan. a novel dye-staining method has been developed to detect beta-glucanase activity in colonies on agar plates.	1983	6311687
purification and characterization of herpes simplex virus (type 1) thymidine kinase produced in escherichia coli by a high efficiency expression plasmid utilizing a lambda pl promoter and ci857 temperature-sensitive repressor.	the structural gene for herpes simplex virus (type 1) thymidine kinase was cloned downstream from the lambda phage high efficiency leftward promotor in a plasmid (phetk2) also containing the gene for the lambda ci857 temperature-sensitive repressor. thymidine kinase is synthesized as a run-on product containing the nh2 terminus of the lambda n protein. heat inactivation of the lambda repressor by growth at 42 degrees c results in the accumulation of thymidine kinase as approximately 4% of the to ...	1983	6311815
characterization of human papillomavirus type 13 from focal epithelial hyperplasia heck lesions.	focal epithelial hyperplasia heck lesions of a turkish patient were shown to contain papillomavirus-specific dna, which was molecularly cloned into bacteriophage lambda. it proved to be related to human papillomavirus (hpv) type 6 dna and hpv type 11 dna. reassociation kinetics revealed a cross-hybridization of 4 and 3%, respectively. there was no cross-reactivity with hpv type 1, 2, 3, 4, 5, 8, or 10. this papillomavirus type will be referred to as hpv type 13. the dna was characterized by clea ...	1983	6312071
molecular cloning of integrated gardner-rasheed feline sarcoma virus: genetic structure of its cell-derived sequence differs from that of other tyrosine kinase-coding onc genes.	gardner-rasheed feline sarcoma virus (gr-fesv) is an acute transforming retrovirus which encodes a gag-onc polyprotein possessing an associated tyrosine kinase activity. the integrated form of this virus, isolated in the charon 21a strain of bacteriophage lambda, demonstrated an ability to transform nih/3t3 cells at high efficiency upon transfection. foci induced by gr-fesv dna contained rescuable sarcoma virus and expressed gr-p70, the major gr-fesv translational product. the localization of lo ...	1983	6312085
the bacteriophage lambda terminase enzyme.		1983	6312259
viability of lambda phages carrying a perfect palindrome in the absence of recombination nucleases.	in escherichia coli in vitro constructions of perfect palindromes larger than 30 base pairs (bp) long have in general been unstable. a perfect palindrome has the unique possibility of forming a cruciform structure, and it is this feature which probably results in its instability. negative supercoiling favours the formation of the cruciform conformation, which in turn causes the molecule to relax. this relaxation may render replicons containing large perfect palindromes inviable. an alternative h ...	1983	6312322
molecular identification and isolation of the waxy locus in maize.	the waxy (wx) locus in maize determines the amylose content of pollen and endosperm tissue. there are several mutant alleles of the locus caused by insertion of transposable controlling elements. in the present study, we have used the properties of controlling element alleles to identify the wx locus and its gene product, with the subsequent objective of isolating the elements causing the mutations. we present evidence that the wx locus encodes a starch granule-bound 58 kd polypeptide that is sy ...	1983	6313224
transformation of l cells with virus thymidine kinase genes introduced by red cell-mediated microinjection.	fusion of red cell ghosts containing foreign materials with cells results in the introduction of the materials into the cells (red cell-mediated microinjection). until now, 'two-step dialysis' has mainly been used for trapping proteins in the ghosts. large-sized materials such as dna, however, are rarely trapped in the ghosts, since the holes in the red cell membrane caused by osmotic shock are too small for such materials to pass through. in this study, we improved the trapping technique. some ...	1983	6313414
yeast h3 and h4 histone messenger rnas are transcribed from two non-allelic gene sets.	the genes coding for the h3 and h4 histones of saccharomyces cerevisiae have been isolated by recombinant dna cloning. the genes were detected in a bacteriophage lambda library of the yeast genome by hybridization with plasmids containing the cloned psammechinus miliaris sea urchin histone genes (pch7) and the cloned drosophila histone genes (cdm500). two non-allelic sets of the h3 and h4 genes have been isolated. each set consists of one h3 gene and one h4 gene arranged as a divergently transcr ...	1983	6313932
site-specific recombination of bacteriophage lambda. the change in topological linking number associated with exchange of dna strands.	the changes in supercoiling that accompany site-specific recombination have been measured. in each experiment, the substrate was a circle that contained two attachment sites oriented as an inverted repeat; recombination between the sites inverts one segment of the circle with respect to the other. using conditions developed in the accompanying work, a measurable amount of the recombinant is in the form of unknotted, simple circles. the difference between the topological linking number of this pr ...	1983	6313937
the dnak protein of escherichia coli possesses an atpase and autophosphorylating activity and is essential in an in vitro dna replication system.	the escherichia coli dnak gene product, originally defined by mutations that blocked lambda phage dna replication, is known to be necessary for e. coli viability. we have purified dnak protein to homogeneity and have demonstrated that it possesses a weak dna-independent atpase activity, which results in the production of adp and pi. the proof that this atpase activity is encoded by the dnak+ gene relies primarily on the fact that the dnak756 mutation results in the production of an atpase activi ...	1983	6314326
structural organization of the rat gene for the arginine vasopressin-neurophysin precursor.	the rat arginine vasopressin-neurophysin precursor gene has been isolated from a genomic library cloned in lambda phage charon 4a. restriction mapping and nucleotide sequence analysis demonstrated that the gene is 1.85 kilobase pairs long and contains two intervening sequences located in the protein coding region. exon a encodes a putative signal peptide, the hormone arginine vasopressin and the variable n terminus of the carrier protein neurophysin, exon b encodes the highly conserved middle pa ...	1983	6315416
structure of the bacteriophage lambda cohesive end site: location of the sites of terminase binding (cosb) and nicking (cosn).	the extents of the sites for nicking (cosn) and binding (cosb) of bacteriophage lambda dna by terminase have been determined by studying cos cleavage and terminase binding in vitro. the cosn site is located in the segment from -22 to +24 bp (numbered from the center of the cohesive end sequence in the circular lambda genome). the cosb site is located in the segment from +51 to +120 (the +120 boundary determined by miwa and matsubara, 1983). additional sequences are necessary for packaging into i ...	1983	6315537