Publications

soluble precursor of an integral membrane protein: synthesis of procoat protein in escherichia coli infected with bacteriophage m13.	prior to virus assembly, the major coat protein of coliphage m13 is an integral protein of the host cytoplasmic membrane. coat protein synthesized in vitro is initially made with an nh2-terminal "leader peptide" of 23 amino acids and is termed "procoat." we now report that procoat is a biosynthetic precursor of coat protein in vivo. conversion of procoat to coat occurs within 30 sec in cells infected with wild-type virus. this proteolytic processing is delayed in cells infected by m13 mutants (i ...	1979	375229
construction of an m13 histidine-transducing phage: a single-stranded cloning vehicle with one ecori site.	in order to create a ready source of single-stranded dna for dna sequence determination by the dideoxy chain-termination method, the promoter-proximal part of the histidine operon, the hisogd region of salmonella typhimurium, was cloned onto the single-stranded phage m13. both orientations of the his dna were cloned to supply dna template for sequencing of each strand. insertion was achieved at an haeiii site in the intergenic region (ir) of m13, and a single ecori site was purposely regenerated ...	1979	376403
nucleotide sequence of the genes iii, vi and i of bacteriophage m13.	a dna region of 2750 base pairs encompassing the genes iii, vi and i of bacteriophage m13 has been sequenced by the maxam-gilbert procedure. by establishing the nucleotide changes introduced by several amber mutations, the coding region and the regulatory signals of each gene have been deduced. the genes appear to span 1275 base pairs (gene iii; mol.wt. 44,748) 339 base pairs (gene vi; mol.wt. 12,264) and 1047 base pairs (gene i; mol.wt. 39,500). their separating non-codogenic regions are extrem ...	1979	379830
identification of two new capsid proteins in bacteriophage m13.		1979	387445
a fast and simple method for sequencing dna cloned in the single-stranded bacteriophage m13.		1979	448736
molecular basis of the am8h1 lesion in bacteriophage m13.		1979	462808
cloning of a functional replication origin of phage g4 into the genome of phage m13.		1979	231682
replication of bacteriophage m13. xv. location of the specific nick in m13 replicative form ii accumulated in escherichia coli polaex1.	m13 replicative form ii (rfii) dna was prepared from escherichia coli rs5052 (polaex1) cells in the late stage of infection, and the dna sequence at the discontinuity was examined. the data presented here suggest that the single discontinuity in the late stage of infection rfii maps at the same position as the gene ii protein nicking site on fd rfi which was determined in vitro (meyer et al., nature (london) 278:365-367, 1979) and has a 5' terminal nucleotide sequence identical to that at the ni ...	1980	6246252
template function of restriction enzyme fragments of phage m13 replicative form dna.		1980	6246375
nucleotide sequence of the filamentous bacteriophage m13 dna genome: comparison with phage fd.	the 6407 nucleotide-long sequence of bacteriophage m13 dna has been determined using both the chemical degradation and chain-termination methods of dna sequencing. this sequence has been compared with that of the closely related bacteriophage fd (beck et al., 1978). m13 dna appears to be only a single nucleotide shorter than fd dna. there is an average of 3.0% of nucleotide-sequence differences between the two genomes, but the distribution of these changes is not random; the sequence of some gen ...	1980	6254849
construction and characterization of new coliphage m13 cloning vectors.	new single-stranded dna cloning vectors have been constructed by the insertion of additional dna fragments into a haeii restriction site in the bacteriophage m13 duplex replicative form (rf). these inserts into the m13 genome bring a single restriction sites useful for cloning, including psti, xorii, ecori, ssti, xhoi, kpni, and pvuii. drug-resistance genes cloned into m13 include the beta-lactamase (bla) gene and the chloramphenicol acetyl transferase (cat) gene. these vectors provide a conveni ...	1980	6260570
synthesis, assembly into the cytoplasmic membrane, and proteolytic processing of the precursor of coliphage m13 coat protein.		1980	6986388
purification and characterization of leader (signal) peptidase from escherichia coli.	many membrane proteins and secreted proteins are synthesized in precursor form with 15 to 30 additional nh2-terminal residues. these "leader peptides" (pre-pieces, signal peptides) are removed as these proteins cross or insert into cellular membranes. "leader peptidase" activities which catalyze this cleavage have been detected in crude extracts and found to be dependent on membrane fractions. we now describe a 6,000-fold purification of a leader peptidase from the membranes of uninfected escher ...	1980	6995457
procoat, the precursor of m13 coat protein, requires an electrochemical potential for membrane insertion.	the coat protein of coliphage m13 spans the host cell cytoplasmic membrane prior to its assembly into extruding virus. it is made as a soluble cytoplasmic precursor, termed "procoat," with 23 extra amino acid residues at the nh2 terminus. procoat binds to the cell membrane and is converted proteolytically to coat protein. when the electrochemical gradient of an infected cell is rapidly dissipated by uncouplers, procoat still binds to the plasma membrane but is not converted to coat. we report he ...	1980	7001463
expression of a dna strand initiation sequence of cole1 plasmid in a single-stranded dna phage.	in order to investigate initiation of h-strand (lagging strand) replication of the plasmid cole1, the origin region fragment (hae ii-e) of cole1 was inserted into the intergenic region of filamentous dna phage m13 and cloned. a site capable of promoting dna strand initiation on a single-stranded dna template has been detected on the l-strand (leading strand) of the cloned fragment. the site, named rri-1 rifampicin-resistant initiation), directs conversion of chimeric phage single-stranded dna to ...	1980	7005899
expression of bacteriophage m13 dna in vivo. isolation, identification and characterization of phage-specific mrna species.		1980	7007041
mechanisms of membrane assembly: effects of energy poisons on the conversion of soluble m13 coliphage procoat to membrane-bound coat protein.	the coat protein (gene 8 product) of coliphage m13 spans the host cell plasma membrane prior to its assembly into extruding virions. it is made as a soluble precursor, termed procoat, with an extra 23 nh2-terminal amino acid residues. we have examined the effect of metabolic poisons on the assembly of procoat into the plasma membrane and its proteolytic conversion to coat protein. protein synthesis and proline uptake were measured to assess the effect of each poison on cellular high-energy phosp ...	1980	6928682
replication of the plasmid pbr322 under the control of a cloned replication origin from the single-stranded dna phage m13.	the replication origins of viral and complementary strands of bacteriophage m13 dna are contained within a 507-nucleotide intergenic region of the viral genome. chimeric plasmids have been constructed by inserting restriction endonuclease fragments of the m13 intergenic region into the plasmid pbr322. replication of these hybrid plasmids, under conditions not permissive for the plasmid replicon, depends on specific segments of the m13 origin region and on the presence of m13 helper virus. thus m ...	1980	6933512
a clear-plaque mutation of bacteriophage m13 affects the regulation of viral dna synthesis.	a clear-plaque mutation (c2) of bacteriophage m13 has been shown to affect the regulation of viral dna synthesis. this mutation increases the amount of the duplex replicative form dna per cell while decreasing the synthesis of viral single strands. the relative synthesis of the m13 gene 5 protein is approximately half that observed in wild-type infections, suggesting that the effect of the c2 mutation on the regulation of viral dna synthesis is a result of reduced expression of gene 5.	1980	7365875
nucleotide sequences in bacteriophage f1 dna: nucleotide sequence of genes v, vii, and viii.	the sequence of nucleotides comprising genes v, vii, and viii of bacteriophage f1 was determined. the sequence was found to differ from that of the corresponding region of the related fd genome by eight base substitutions in gene v and one in gene viii. the structure of gene vii was completely conserved between these two viruses and was identical to that of bacteriophage m13. both transitions and transversions were found in cases where bases were substituted, but all substitutions were in the th ...	1980	7373712
nmr studies of the interaction of gene-v protein of bacteriophage m13 with oligonucleotides.	this paper describes the preparation of deuterated phenylalanine ([2h7]-phenylalanine) and the isolation of phage m13 encoded gene-v protein in which this deuterated amino acid was incorporated. using this protein spectral assignments of resonances in the aromatic region of the 1h-nmr spectrum of the gene-v protein have been made. furthermore the interaction of the gene-v protein with the tetranucleotide d(pc-g-c-g) and the hexanucleotide d(pc-g-c-g-c-g) was investigated. from the changes in the ...	1980	6966158
double-resonance experiments at 500 mhz on gene-5 protein and its complex with octadeoxyriboadenylic acid.	in this paper, a detailed description is presented of the aromatic part of the 500-mhz 1h nuclear magnetic resonance (nmr) spectrum of the helix-destabilizing gene-5 protein (gvp) encoded by the coliphage m13. as a result of the resolution obtained at 500 mhz, it was possible to perform selective decoupling and time-resolved selective overhauser experiments. the magnitudes of the observed overhauser effects compare favorably with magnitudes expected on the basis of theoretical calculations. thes ...	1981	6974567
genes vi, vii, and ix of phage m13 code for minor capsid proteins of the virion.	the minor capsid proteins c and d from phage m13 have been characterized by differential amino acid labeling and amino-terminal sequence analysis. we demonstrate that d protein (mr 12,260) is the product of gene vi, whereas the c component is composed of the products of both gene vii (mr 3580) and gene ix (mr 3650). our data further show that the proteins of genes vi, vii, and ix are not subject to proteolytic processing but are packaged into mature virions as their primary translational product ...	1981	6945579
filamentous bacteriophage contract into hollow spherical particles upon exposure to a chloroform-water interface.	the bacteriophage m13 is a 1 micrometer long filament consisting of a circular single-stranded dna loop firmly held within a tubular protein and capsid. we report here that exposure to a chloroform-water interface initiates a 20 fold contraction of each filament into a hollow protein sphere. in these 0.04 micrometer diameter particles, termed m13 "spheroids," two thirds of the dna is apparently extruded through a hole in the wall of the spheroid; the portion of dna remaining inside the shell cen ...	1981	7226228
membrane assembly: posttranslational insertion of m13 procoat protein into e. coli membranes and its proteolytic conversion to coat protein in vitro.	the major coat protein (gene 8 product) of bacteriophage m13 is an integral membrane protein during infection of host cells. it is synthesized as a larger precursor (procoat) with a leader sequence of 23 amino acids at its amino terminus. in vivo studies have shown that procoat only inserts into the host-cell plasma membrane after its synthesis is completed. we now demonstrate that procoat can post-translationally insert into inverted cytoplasmic membrane vesicles from e. coli and can be process ...	1981	7237555
deletion analysis of the cloned replication origin region from bacteriophage m13.	a cloned 270-nucleotide fragment from the origin region of the m13 duplex replicative form dna confers an m13-dependent replication mechanism upon the plasmid vector pbr322. this m13 insert permits m13 helper-dependent replication of the hybrid plasmid in pola cells which are unable to replicate the pbr322 replicon alone. using in vitro techniques, we have constructed several plasmids containing deletions in the m13 dna insert. the endpoints of these deletions have been determined by dna sequenc ...	1981	7288922
mechanism of coliphage m13 contraction: intermediate structures trapped at low temperatures.	the filamentous coliphage m13 can be transformed into a spherical particle (termed spheroid) by exposure to an interface of water and slightly polar but hydrophobic solvent such as chloroform-water at 24 degrees c. we report here that exposure of m13 filaments to a chloroform-water interface at 2 degrees c trapped the phage particles in forms morphologically intermediate to filaments and spheroids. these structures were rods 250 nm long and 15 nm wide, and each had a closed, slightly pointed end ...	1981	7321105
genes vi, vii and ix of bacteriophage m13: identification of their products as minor capsid proteins.	in earlier work, two new minor capsid proteins of molecular weight 3500 (c-protein) and 11,500 (d-protein) were detected in m13 virions. to determine their genetic origin, differential amino acid labeling, amino acid analysis and edman degradation analysis were performed on these proteins. the data demonstrate that d-protein is the product of gene vi whereas c-protein is composed of both the proteins specified by gene vii and the recently discovered gene ix. by selective labeling with arginine, ...	1981	7330055
leader peptidase is found in both the inner and outer membranes of escherichia coli.	many membrane proteins are synthesized as transient precursors with an nh2-terminal leader (or signal) peptide. during insertion of these proteins into the membrane, leader peptides are removed by leader peptidase. one such enzyme has been detected in detergent extracts of escherichia coli membranes and extensively purified using as an assay the removal of the leader sequence of procoat, the precursor of the major coat protein of bacteriophage m13. we now report that this leader peptidase is fou ...	1981	7009614
structure of the neuraminidase gene in human influenza virus a/pr/8/34.	the complete structure of the neuraminidase gene in influenza a/pr/8/34 has been determined by cloning into the bacteriophage m13 and sequencing with dideoxynucleotide chain terminators. the gene is 1,413 nucleotides long, codes for a protein of 454 amino acids and has five potential glycosylation sites. we suggest that the neuraminidase, unlike the influenza haemagglutinin, is oriented with its n-terminus buried in the viral membrane.	1981	7010182
procoat, the precursor of m13 coat protein, inserts post-translationally into the membrane of cells infected by wild-type virus.	in growing cells infected by wild-type coliphage m13, the synthesis of procoat protein is completed before it inserts into the plasma membrane ane is converted to coat protein.	1981	7014926
membrane assembly from purified components. i. isolated m13 procoat does not require ribosomes or soluble proteins for processing by membranes.	the coat protein of coliphage m13 is an integral protein of the host-cell cytoplasmic membrane prior to its assembly into virions. it is initially synthesized as procoat, a soluble precursor with a 23 amino acid leader sequence at its amino terminus. 35s-labeled procoat accumulates during an in vitro translation reaction that contains 35s-methionine and rna from m13-infected cells. radiochemically pure procoat has been isolated from in vitro translation reactions by extraction into an organic so ...	1981	7026042
membrane assembly from purified components. ii. assembly of m13 procoat into liposomes reconstituted with purified leader peptidase.	the major coat protein of coliphage m13 is an integral protein of the e. coli plasma membrane prior to its assembly into new virus particles. it is generated from its precursor, procoat, by a membrane-bound leader peptidase. we now describe the reconstitution of a highly purified preparation of this enzyme into vesicles of e. coli phospholipids. these vesicles bind procoat made in vitro and procoat isolated from in vitro synthesis. both the crude and the purified substrates were converted post-t ...	1981	7026043
radiation-induced base substitution mutagenesis in single-stranded dna phage m13.		1981	7029307
nucleotide-sequence heterogeneity and sequence rearrangements in influenza virus cdna.	double-stranded cdna has been synthesized from influenza virus rna and cloned into derivatives of the bacteriophage m13 for sequence analysis. the characterization of over 200 clones has permitted an analysis both of nucleotide sequence heterogeneity and of clones containing unusual rearrangements of sequence. heterogeneity, due to genetic variability in the rna population and to in vitro synthetic errors, was detected at the low level of one nucleotide difference per 3 700 nucleotides. by contr ...	1981	6895362
the dna sequences of cloned complex satellite dnas from hawaiian drosophila and their bearing on satellite dna sequence conservation.	a class of restriction endonuclease fragments near 185 bp in length and comprising approximately 20% of the genomes of 3 species of hawaiian drosophila has been cloned using bacteriophage m13. the nucleotide sequences of 14 clones have been determined and the variation between clones has been found to be due to deletions and base changes. analyses of uncloned material show that the cloning system itself does not introduce the variation. the variation of the basic repeat within and between specie ...	1981	6262029
[substrate specificity of ca2+,mg2+-dependent dnaase from sea urchin (strongylocentrotus intermedius) embryos].	ca2+,mg2+-dependent dnase from sea urchin embryos is specific to the secondary structure of substrates irrespective of the nature of activating cations. the enzyme does not split synthetic single-stranded oligo and polynucleotides, such as d(ptptptpcpc), d(pgpgptptpt). d(papaptptpc), d(pgpapaptptpc), d(pa)5-poly(dt), d(papaptptpc)-poly(dt), poly(da) and poly (dt) and hydrolyses the double-stranded substrates poly d(at), poly (da) . poly (dt) and highly polymerized dna. native double-stranded dna ...	1981	6271260
the atp operon: nucleotide sequence of the region encoding the alpha-subunit of escherichia coli atp-synthase.	part of the atp (or unc) operon encoding the alpha, beta, gamma, delta, and epsilon subunits of escherichia coli atp-synthase has been cloned into the plasmid pacyc 184. the dna coding for the largest of these proteins, the alphas subunit, has been sequenced by cloning into the bacteriophage m13 and sequencing with dideoxy nucleotide chain terminators. it comprises 1539 nucleotides corresponding to a protein of 513 amino acids.	1981	6272228
viable deletions of the m13 complementary strand origin.	the single-stranded dna of bacteriophage m13 is converted to a duplex replicative form by a mechanism involving rna-primed initiation at a single unique site on the viral dna. the dna sequence that specifies the rna primer is contained largely within one of two adjacent hairpin structures protected from dnase degradation by rna polymerase. we have used in vitro techniques to construct a series of m13 mutants having deletions in the region of the complementary strand origin. deletions of the dupl ...	1981	6273888
sequencing long dna fragments cloned in bacteriophage m13 by using internal primers. the sequence analysis of a yeast dna fragment containing a replication origin.	in the ;shotgun' procedure for sequencing dna, dna fragments are cloned into a phage m13 vector and sequenced by using a flanking primer. in a variation of this procedure a longer dna sequence is cloned into m13, the two single-stranded recombinants identified and sequenced by using a set of internal primers prepared by exonuclease iii digestion of restriction fragments.	1981	6280678
construction of gapped circular dna from phage m13 by in vitro hybridization.		1982	6282331
cloning and transcriptional control of a eucaryotic permease gene.	the uracil permease gene of the yeast saccharomyces cerevisiae was cloned on a hybrid plasmid which replicates autonomously in both yeast and escherichia coli. cloning was carried out by complementation in yeast. the smallest dna fragment found to complement the uracil permease deficiency in recipient yeast cells measured approximately 2.3 kilobases. in strains transformed by the plasmid with the uracil permease gene inserted, initial rates of uracil uptake increased up to 25 times more than the ...	1982	6290876
nucleotide sequence of bacteriophage f1 dna.	the nucleotide sequence of the dna of the filamentous coliphage f1 has been determined. in agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. phage f1 dna differs from that of phage m13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd dna by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid ...	1982	6292494
oligonucleotide-directed mutagenesis of gene ix of bacteriophage m13.	the synthetic oligodeoxyribonucleotide pcgaaagactacac has been applied as a site-specific mutagen to introduce a t leads to g transversion mutation at nucleotide position 1223 of the m13 dna sequence. the in vitro-induced conversion of a tat codon into a tag at this position resulted in gene ix mutants with an amber mutant character thereby confirming that this reading frame defines a gene of an essential phage protein. the gene ix amber mutants obtained grew well on sui (ser) and suiii (tyr) su ...	1982	6278437
carboxy terminus of polyoma middle-sized tumor antigen is required for attachment to membranes, associated protein kinase activities, and cell transformation.	we have constructed a transformation-defective polyoma virus mutant (py 1387-t) that directs the synthesis of a normal small tumor antigen, a functional large tumor antigen, and a truncated (51,000-dalton) middle-sized tumor (mt) antigen that lacks 37 amino acids at its cooh terminus. the shortened mt polypeptide is missing the hydrophobic "tail" thought to be responsible for the anchorage of this protein into the plasma membrane and is in fact in cytosol fractions. this truncated mt polypeptide ...	1982	6179082
use of a rapid dna sequencing system to demonstrate the induction of frameshift mutations by bleomycin.	the rapid dna sequencing system based on the single-stranded bacteriophage m13 and the chain-terminator method has been used to look directly for mutational alterations. a small dna fragment that primes dna synthesis through the n-terminal 200 base pairs of the beta-galactosidase gene was prepared, and used to detect changes in base sequence among phages that give white plaques after treatment of the host cells with bleomycin. bleomycin treatment of e. coli in which m13 mp2 was growing gave an i ...	1982	6183148
rapid purification of bacterial plasmids and coliphage m13 rf without cscl centrifugation.		1982	6187239
an efficient synthetic primer for the m13 cloning dideoxy sequencing system.	the deoxytetradecamer d(aaaacgacggccag) has been shown to be an excellent universal primer for sequence determination of dna cloned into the bacteriophage m13 mp7, mp8, and mp9 series. this new primer offers several advantages over others currently available and it has been used to define the cloning of hinf i fragments of bacteriophage s13 dna into the eco ri site of m13 mp7, utilizing the homologous complementary base pairing of the two restriction sites. of the four possible sequence derivati ...	1982	6753962
the yeast his3 promoter contains at least two distinct elements.	phenotypic analysis of 65 mutations indicates that the yeast his3 promoter is composed of at least two separate regions of dna. each is necessary, but neither is sufficient for wild-type levels of his3 expression. deletion mutations that destroy either promoter element express his3 poorly or not at all. the upstream element is located between 112 and 155 base pairs before the site of transcriptional initiation (nucleotides -112 to -155). a comparison of derivatives strongly suggests that the dow ...	1982	6760196
effects of dna base analogs on transcription termination at the tryptophan operon attenuator of escherichia coli.	we have devised a method to specifically incorporate deoxyribonucleotide base analogs in vitro into either strand of the tryptophan (trp) operon attenuator region, using primed synthesis on bacteriophage m13 derivatives carrying cloned trp attenuator dna. we have employed these techniques to extend previous studies implicating both rna-rna and rna-dna interactions in transcription termination in an attempt to determine the nature of the contribution from the template dna molecule in termination ...	1982	7041118
the biosynthesis of membrane-bound m13 coat protein. energetics and assembly intermediates.	the major coat protein of bacteriophage m13 spans the plasma membrane of infected cells prior to its assembly into extruding virus. it is initially made as a precursor, termed procoat, with a 23-residue leader sequence at its nh2 terminus. procoat is found bound to the inner surface of the plasma membrane. the electrical potential of the cell membrane is required for procoat insertion and conversion to coat protein, although the order of these events has been unknown. we now report studies of th ...	1982	7042715
evidence for two genetically distinct dna primase activities specified by plasmids of the b and i incompatibility groups.	plasmid colib-p9 of the i alpha incompatibility group is known to encode a dna primase that acts in the conjugal transfer of the plasmid and can substitute for mutant dnag gene product in vegetative replication of the escherichia coli chromosome. the relevant genetic determinant (sog) has previously been cloned into a small multicopy vector plasmid. prototype incb plasmid r16 also suppresses host dnag mutations. the equivalent gene(s) (pri) of r16 was cloned into plasmid pbr325 and shown by filt ...	1982	7045070
mutability of bacteriophage m13 by ultraviolet light: role of pyrimidine dimers.	the role of pyrimidine dimers in mutagenesis by ultraviolet light was examined by measuring the uv-induced reversion of six different bacteriophage m13 amber mutants for which the neighboring dna sequences are known. the mutational response at amber (tag) codons preceded by a guanine or adenine (where no pyrimidine dimer can be formed) were compared with those preceded by thymine or cytosine (where dimer formation is possible). equivalent levels of uv-induced mutagenesis were observed at both ki ...	1982	7048024
[transfection of bacterial cells by dna of phage m13 entrapped in phospholipid vesicles].	the possibility of transfection of bacterial cells by phage m13 dna entrapped into phospholipid vesicles (liposomes) has been studied. two types of liposomes differing in size were used. entrapped dna was transferred by liposomes into ca2+-treated e. coli cells. efficiency of the transfection in the case of small (ca. 400 a) liposomes was 2--3 orders of magnitude higher than that of free dna extracted from such liposomes.	1982	7048068
19f nuclear magnetic resonance studies of the coat protein of bacteriophage m13 in synthetic phospholipid vesicles and deoxycholate micelles.	the nonlytic, filamentous coliphage m13 offers an excellent model system for the study of membrane-protein interactions. we prepare derivatives of the protein containing fluorine-labeled amino acids and use 19f nuclear magnetic resonance (nmr) to study the protein in both deoxycholate micelles and phospholipid vesicles. we have previously described the in vivo preparation of an m-fluorotyrosyl derivative of m13 coat protein and also a method for incorporation of high levels of this protein into ...	1982	7055622
bilayer acyl chain dynamics and lipid-protein interaction: the effect of the m13 bacteriophage coat protein on the decay of the fluorescence anisotropy of parinaric acid.	nanosecond fluorescence polarization anisotropy decay is used to determine the effect of the bacteriophage m13 coat protein on lipid bilayer acyl chain dynamics and order. the fluorescent acyl chain analogues cis- and trans-parinaric acid were used to determine the rate and extent of the angular motion of acyl chains in liquid crystalline (39 degrees c) dimyristoylphosphatidylcholine bilayers free of coat protein or containing the coat protein at a protein:lipid ratio of 1:30. subnanosecond time ...	1982	7055623
beta-thalassemia in a kurdish jew. single base changes in the t-a-t-a box.	we recently described a "non-random" sequencing procedure for dna inserts in bacteriophage m13 using bal 3 nuclease and the dideoxy chain termination method (poncz, m., solowiejczyk, d., ballantine, m., schwartz, e., and surrey, s. (1982) proc. natl. acad. sci. u. s. a., in press). using this procedure, we have determined the nucleotide sequence of a cloned human beta-globin gene from a kurdish jew with beta +-thalassemia major. comparison with the previously reported human beta-globin gene sequ ...	1982	7076659
circular single stranded phage m13-dna as a template for dna synthesis in protein extracts from xenopus laevis eggs: evidence for a eukaryotic dna priming activity.	unfractionated protein extracts from activated xenopus laevis eggs contain all functions required for the chain elongation reactions in replicative dna synthesis (a.richter, b. otto and r.knippers, 1981, nucl.ac.res. 9, 3793-3807). in order to further explore the dna synthesizing capacity of this in vitro system and to obtain information on the dna priming activity in these extracts single stranded phage m13-dna was used as template for in vitro dna synthesis. the main results of this investigat ...	1982	7145711
"nonrandom" dna sequence analysis in bacteriophage m13 by the dideoxy chain-termination method.	we describe a rapid "nonrandom" dna sequence analysis procedure that facilitates the nucleotide sequence determination of large contiguous regions of dna. the method consists of cloning a restriction endonuclease fragment of interest into bacteriophage m13 followed by construction of a series of nuclease bal-31 deletion mutants originating from a single site in m13 that is close to the dna insert. determination of the size of the deletion mutant is accomplished by hybridization to a complementar ...	1982	6956859
rna processing errors in patients with beta-thalassemia.	we have developed a method that permits rapid identification of the consequences of mutations that alter beta-globin rna processing in erythroid cells. s1 nuclease mapping techniques were used to analyze total bone marrow rna obtained fron 15 patients who are clinically homozygous for beta-thalassemia and from 5 patients with erythroid hyperplasia from other causes. this analysis was facilitated by the use of single-stranded uniformly labeled dna probes of high specific activity that were prepar ...	1982	6956887
1h nmr studies of the binding of bacteriophage-m13-encoded gene-5 protein to oligo(deoxyadenylic acid)s of varying length.	the binding of gene-5 protein to oligo(deoxyadenylic acid)s varying in length from 2 to 16 nucleotides has been studied by titrating the protein with the oligonucleotides and recording the 1h nmr spectra at 360 mhz. to obtain information about the mode of binding of the protein the aromatic parts of the spectra have been analysed by performing spectral simulations, starting from the assignments obtained from nuclear overhausfer enhancements at 500 mhz [alma, n. c. m., harmsen, b. j. m., hull, w. ...	1982	6977447
insertion of bacteriophage m13 coat protein into membranes.		1982	19431483
analysis of sequences conferring autonomous replication in baker's yeast.	a method is presented for rapid sequencing and mapping of elements which support autonomous replication in yeast. the strategy relies on a novel phage m13 vector which allows detection of ars (autonomously replicating sequence) function in cloned fragments. deletion mapping of an ars element linked to the ho gene of saccharomyces cerevisiae has identified a 57-bp region 3' to the gene, which is essential for autonomous replication. this region shows sequence homology to other ars elements.	1983	11892814
coat protein conformation in m13 filaments, i-forms and spheroids.	circular dichroism studies of the filamentous coliphage m13 were carried out to determine conformational changes in the major capsid protein (the b protein) that occur during contraction of the filaments to i-forms and spheroids. the alpha-helicity of the b protein is somewhat lower in the i-forms than in filaments and much lower in spheroids. this conformational change may explain the increased detergent and lipid solubility of both i forms and spheroids relative to filaments.	1983	6847652
proteins encoded near the adenovirus late messenger rna leader segments.	small fragments of adenovirus 2 dna cloned into the single-strand phage m13 were used to select adenoviral messenger rnas transcribed from the r-strand between map positions 16 and 30. cell-free translation of these mrnas produced proteins of 13.5k, 13.6k, and 11.5k, respectively encoded between the first and second segments of the tripartite major late leader, within the "i"-leader segment, and immediately preceding the third leader segment. partial sequence analysis of the 13.6k protein is con ...	1983	6857999
characterization and properties of a modified human interferon-alpha containing an additional 18 amino acids at the n-terminus.	a modified human interferon-alpha 2 was produced in escherichia coli cells infected with phage m13 mp7 containing an interferon-alpha gene. after purification by immunochromatography with the monoclonal antibody nk2, the n-terminal amino acid sequence was determined. the n-terminal methionine was absent but an additional sequence of 18 amino acids at the n-terminus was retained. the modified interferon-alpha 2 was indistinguishable from authentic interferon-alpha 2 in its ability to activate nat ...	1983	6875519
on the processivity of dna replication.	in this paper we describe the nature and importance of processive enzymatic reactions in biological processes. a model is set up to describe the processive synthetic process in dna replication, and experiments are presented to define and test the model, using the components of the t4 phage-coded five-protein (in vitro) dna replication system of alberts. nossal and coworkers. these experiments are performed either with a homogeneous oligo dt-poly da primer-template system, or with a natural prime ...	1983	6400896
a detailed mutational analysis of the eucaryotic trnamet1 gene promoter.	we have isolated phage m13 clones containing the x. laevis trnamet1 gene, each having one or a few c leads to t transitions in the trna coding sequence. nearly every g-c and c-g base pair in the tdna has been mutagenized. the importance of these altered nucleotides in transcription by rna polymerase iii has been assessed by injecting the cloned dnas into frog oocyte nuclei together with alpha-32p-gtp and measuring the synthesis of labeled trnamet1. several g-c and c-g base pairs in the structura ...	1983	6552939
splicing of adenovirus rna in a cell-free transcription system.	a soluble whole-cell extract prepared accurately from hela cells splices 2-3% of the rna transcribed from a dna template containing the first and second leader exons of late adenovirus rna. the spliced rna was detected by a sensitive technique using hybridization to a single-stranded phage m13 cdna clone, followed by binding to nitrocellulose filters. the identity of the spliced rna was established by rnase t1 and pancreatic rnase two-dimensional peptide mapping. the bond formed during the in vi ...	1983	6577417
fluorescence studies of the complex formation between the gene 5 protein of bacteriophage m13 and polynucleotides.		1983	6601193
a 500-mhz proton nuclear magnetic resonance study of the structure and structural alterations of gene-5 protein-oligo(deoxyadenylic acid) complexes.	the complex of the gene-5 protein of bacteriophage m13 with octadeoxyadenylic acid [d(a)8] has been shown earlier to differ in various respects from the complex with polynucleotides [alma, n. c. m., harmsen, b. j. m., van boom, j. h., van der marel, g., & hilbers, c. w. (1982) eur. j. biochem. 122, 319-326]. in this paper the gene-5 protein-d(a)8 complex is compared with the complex formation between the gene-5 protein and a mixture of longer oligonucleotides, i.e., d(a)25-30. nuclear overhauser ...	1983	6602628
decay of mrna in escherichia coli: investigation of the fate of specific segments of transcripts.	an assay was developed to investigate the fate of specific segments of beta-lactamase (bla) and ompa gene transcripts in escherichia coli. dna probes cloned in bacteriophage m13 were treated with an endonuclease capable of cleaving single-stranded dna, the fragments produced were annealed with total cellular rna, and the resulting rna . dna hybrids were subjected to s1 nuclease treatment and gel fractionation. by using this assay, direct evidence was obtained for 3'-to-5' directionality in the d ...	1983	6187001
sandwich hybridization as a convenient method for the detection of nucleic acids in crude samples.	a method based on three-dna-component, sandwich hybridization has been designed for the detection and quantitation of nucleic acids in crude samples using adenovirus dna as a model. two non-overlapping restriction fragments of adenovirus type 2 (ad2) dna were cloned into two vectors, the pbr322 plasmid and m13 phage. the recombinant plasmid dna was immobilized onto nitrocellulose filters and the single-stranded recombinant phage dna was labeled with 125i and used as a probe. when these two reage ...	1983	6301952
construction of a cloned library of adenovirus dna fragments in bacteriophage m13.	the construction of recombinant m13 phages containing adenovirus dna inserts was undertaken to provide strand-specific hybridization probes for analyses of adenovirus type 2 rna transcripts. a library of molecular probes was constructed by cloning restriction endonuclease fragments of adenovirus types 2 and 5 dna in the duplex replicative form dna of the single-stranded bacteriophage vectors, m13mp7, m13mp8, and m13mp9 (messing, j., and vieira, j. (1982) gene 19,269-276). adenovirus dna segments ...	1983	6309766
microinjected simian virus 40 crna is spliced, as evidenced by electron microscopy.	simian virus 40 crna was transcribed in vitro from the early viral dna strand. the rna was injected through glass capillaries into the nuclei of monkey cells. after a 2-h incubation, the rnas were extracted and hybridized to single-stranded simian virus 40 dna sequences contained in a bacteriophage m13 vector. electron microscopy revealed processed crnas with splice loops in the region of the intron of large t antigen.	1983	6310149
kilo-sequencing: creation of an ordered nest of asymmetric deletions across a large target sequence carried on phage m13.		1983	6310345
expression of the human interferon-beta gene cloned in phage m13 mp7.	the single-stranded dna phage, m13 mp7 was used in the construction of an expression vector containing the coding sequence for mature interferon-beta (ifn-beta). two clones expressed a fused polypeptide showing the biological and physicochemical properties of ifn-beta, despite the fact that the n-terminal amino acid sequence had been changed; 10(6) i.u./l of culture were produced with a molecular weight of 20 000.	1983	6311267
characterization of the dna binding protein encoded by the n-specific filamentous escherichia coli phage ike. binding properties of the protein and nucleotide sequence of the gene.	a dna binding protein encoded by the filamentous single-stranded dna phage ike has been isolated from ike-infected escherichia coli cells. fluorescence and in vitro binding studies have shown that the protein binds co-operatively and with a high specificity to single-stranded but not to double-stranded dna. from titration of the protein to poly(da) it has been calculated that approximately four bases of the dna are covered by one monomer of protein. these binding characteristics closely resemble ...	1983	6312049
new versatile cloning and sequencing vectors based on bacteriophage m13.	a new pair of cloning and sequencing vectors based on bacteriophage m13mp7 has been developed. these vectors (m13tg130 and m13tg131) contain, in addition to the ecori, bamhi, hindiii, smai, sali and psti sites present in other vectors [cf., m13mp8 and m13mp9, messing and vieira, gene 19 (1982) 269-276], unique restriction recognition sequences for the enzymes ecorv, kpni, sphi, ssti and xbai. a restriction site for the enzyme bglii has been incorporated into the polylinker region of one of the v ...	1983	6323254
use of m13mp phages to study gene regulation, structure and function: cloning and recombinational analysis of genes of the salmonella typhimurium histidine operon.	a restriction map was determined for a phi 80 lambda dhis transducing phage dna carrying the salmonella typhimurium histidine operon. dna fragments containing the promoter/regulatory region and the first two structural genes of the histidine operon (hisogd) were identified by their ability to direct regulated synthesis of histidinol dehydrogenase (product of hisd) in a coupled in vitro protein synthesizing system. a 3.1-kb sali-ecori restriction fragment containing the hisogd region, was subclon ...	1983	6323256
m13 procoat and a pre-immunoglobulin share processing specificity but use different membrane receptor mechanisms.	bacteriophage m13 procoat is accurately processed to transmembrane coat protein by salt-washed or n-ethylmaleimide-treated rough microsomes from dog pancreas. these treatments inhibit the processing of eukaryotic secreted protein precursors. m13 procoat can assemble into dog pancreas microsomes post-translationally. thus, the microsomal proteins needed for assembly may be determined by the nature of the precursor protein itself. these results, and our finding that the mouse igg kappa chain fragm ...	1983	6344069
the use of bacteriophage m13 carrying defined fragments of the escherichia coli glta gene to determine the location and structure of the citrate synthase promoter region.	the glta gene from escherichia coli, which encodes citrate synthase, has been located on a 3.24 kb hindiii/ecorl restriction fragment. this region contains one restriction site for bamhl and two for bglii. defined restriction fragments from this region were cloned into suitably cleaved replicative form m13mp8 and m13mp9. the recombinants (m13gtla1 leads to 10) were isolated as single stranded dna and characterised on the basis of molecular weight and dna sequence. the single stranded dna was con ...	1983	6355771
in vitro deletional mutagenesis for bacterial production of the 20,000-dalton form of human pituitary growth hormone.	the 20,000-dalton (20k) variant form of human growth hormone (hgh) present in extracts from pituitary glands differs from the major form of hgh (22k, 191 amino acids) by the deletion of amino acid residues 32-46. using oligonucleotide-mediated mutagenesis, the dna coding for these amino acids was deleted from the gene previously constructed by us (goeddel et al., 1979) for microbial hgh production. the dna to be deleted was looped out by the annealing of a synthetic oligodeoxyribonucleotide to t ...	1983	6357679
transitory recombination between plasmid phv33 and phage m13.	plasmid phv33 and phage m13 which have no homology exceeding 13 bp, combine in escherichia coli cells. the chimeric genome is encapsidated in phage proteins and injected into a recipient cell, where it decombines to regenerate the two parental genomes. we call this combination-decombination process 'transitory recombination'.	1983	6365530
different base/base mismatches are corrected with different efficiencies by the methyl-directed dna mismatch-repair system of e. coli.	the efficiency of methyl-directed dna mismatch-repair of e. coli acting in vivo on heteroduplex genomes of phage m13 was found to be strongly dependent on the nature of the base/base mismatch to be corrected. three efficiency classes were characterized:high (t/g, c/a and g/g); intermediate (a/a); and low (g/a, a/g, t/t, c/c, c/t and t/c). methyl-directed dna mismatch repair was lost completely for any type of mismatch in strains carrying either mutl or muts mutations. data obtained with a muth m ...	1984	6386179
in vitro generation of specific deletions in dna cloned in m13 vectors using synthetic oligodeoxyribonucleotides: mutants in the 5'-flanking region of the yeast alcohol dehydrogenase ii gene.	deletion mutants are particularly useful in defining the boundaries of noncoding genetic functions. such mutants can be precisely generated using synthetic oligodeoxyribonucleotides as mutagens. in this paper we describe the application of this method to recombinant dna cloned in a phage m13-derived vector. the mutagenic oligodeoxyribonucleotides, 20 and 21 nucleotides in length, were used to delete a tract of 20 da-dt base-pairs and an adjacent 22 base-pair perfect dyad from the adr3 locus, the ...	1984	6324118
screening recombinant phage m13 plaques with rna probes; a one-step procedure which identifies clones containing either of the complementary dna strands.	we describe a method for detecting specific dna sequences cloned in m13 phage vectors, based on the procedure of woo (in wu, r., methods in enzymology, vol. 68, academic press, new york, 1979, pp. 389-395). m13 plaques are adsorbed to a nitrocellulose filter that has been pre-saturated with bacteria. the filter is incubated on an agar plate to amplify the phage; the dna is alkali-denatured and then hybridized with a radioactive rna probe. unlike standard procedures, this method detects and disti ...	1984	6325302
some extrachromosomal circular dnas containing the alu family of dispersed repetitive sequences may be reverse transcripts.	a 300 base-pair (bp) size class of small polydisperse circular dna (spcdna) isolated from the bsc-1 line of african green monkey kidney cells was cleaved with the restriction endonuclease sau3a, and the resulting fragments (100 to 200 bp) were cloned in bacteriophage m13 mp7. the nucleotide sequence of each of 24 clones containing dna sequences homologous to the alu family of mobile, dispersed, repetitive elements was then determined. analysis of these sequences revealed that many, and perhaps a ...	1984	6325707
initiation and termination signals for transcription in bacteriophage m13.	transcription of the infrequently expressed phage m13 genome domain, comprising genes iii, vi, i and iv, has been studied in detail by hybridization and s1-nuclease mapping studies. the contiguous genes iii and vi are transcribed via an 1800 nucleotide-long rna molecule that is initiated at a promoter which overlaps with the rho-independent termination signal between genes iii and viii. its synthesis is terminated at a rho-dependent terminator in the proximal part of gene i. transcription of gen ...	1984	6328409
interference between m13 and orim13 plasmids is mediated by a replication enhancer sequence near the viral strand origin.	the origin of replication for the viral strand of bacteriophage m13 dna is contained within a 507 base-pair intergenic region of the phage chromosome. the viral strand origin is defined as the specific site at which the m13 gene ii protein nicks the duplex replicative form of m13 dna to initiate rolling-circle synthesis of progeny viral dna. using in vitro techniques we have constructed deletion mutations in m13 dna at the unique avai site which is located 45 nucleotides away on the 3' side of t ...	1984	6332917
template requirements for the initiation of adenovirus dna replication.	the first step in the replication of the adenovirus genome is the covalent attachment of the 5'-terminal nucleotide, dcmp, to the virus-encoded terminal protein precursor (ptp). this reaction can be observed in vitro and has been previously shown to be dependent upon either viral dna or linearized plasmid dna containing viral terminal sequences. plasmids containing deletions or point mutations within the viral terminal sequence were constructed by site-directed mutagenesis. in the case of linear ...	1984	6320160
replication functions of pc194 are necessary for efficient plasmid transduction by m13 phage.	escherichia coli plasmids pbr313 and pbr322 were transduced by phage m13 with low efficiency (10(-8) transductants/phage). hybrid plasmids phv12 or phv33, composed of staphylococcus aureus plasmid pc194 and pbr313 or pbr322, respectively, were transduced much more efficiently (10(-4) transductants/phage). inactivation of either of the two zones necessary for pc194 replication, one coding for a protein, the other not, reduced the transforming efficiency of hybrids to the level of pbr322. activity ...	1984	6323171
genes involved in transitory recombination between phage m13 and plasmid phv33.	plasmid phv33 and phage m13 combine in escherichia coli cells to form a chimera, which decombines to regenerate two parental genomes. combination can occur via two genetic pathways, one defined by the recbc genes, the other by reca, recf and possibly recl genes. decombination can also occur via two pathways, one defined again by the recbc genes, the other by a gene not identified, but active only in the absence of the recl gene product.	1984	6323172
ribonucleoprotein organization of eukaryotic rna. xxxi. structure of the u1 small nuclear ribonucleoprotein.	a small nuclear ribonucleoprotein, u1 snrnp, has been implicated in mrna processing. in this investigation sites of protein binding on u1 rna were mapped by nuclease protection and rna sequencing. partially purified human u1 snrnp was sequentially digested with escherichia coli rnaase iii and s1 nuclease. the resistant ribonucleoprotein fragments were deproteinized, preparatively hybridized to the u1 rna--complementary dna strand of a human u1 gene cloned in bacteriophage m13, and displayed by e ...	1984	6084724
use of short dna oligonucleotides for determination of dna sequence modifications induced by benzo[a]pyrene diol epoxide.	various organic agents that alkylate dna are known to induce mutations in bacterial and animal cells. the precise nature and location of modified dna sequences in such mutants are often difficult to ascertain. in this report, a 10-base-pair oligomer (bamhi linker) is treated with (+/-)-trans-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide and inserted into replicative form dna of phage m13 by ligation at a specific restriction site. escherichia coli are transfected with the recombinant dna containin ...	1984	6091121
high-sensitivity s1 mapping with single-stranded [32p]dna probes synthesized from bacteriophage m13mp templates.	a method is described by which high-specific-activity single-stranded (ss) [alpha-32p]dna of a defined size complementary to sequences cloned into bacteriophage m13 is synthesized. the ss dna template is annealed with a universal sequencing primer, the primer extended with dna polymerase i klenow fragment and the dna duplex cut at a unique site 5' to the multiple cloning sites in the m13 phage. the reaction products are denatured and the ss alpha-32p probe fragment complementary to the cloned se ...	1984	6096224
integration of a temperate phage infecting spiroplasma citri.	a physical map of the genome of a temperate type 3 spiroplasma-virus, ai, has been constructed. host dna has been digested with restriction enzymes, and recombinant dna clones of ai fragments in coliphage m13 vectors have been used as probes to detect viral dna sequences integrated into spiroplasmas. all strains of spiroplasma citri examined contained a deleted form of ai integrated as a cryptic prophage which was unable to confer resistance to ai superinfection. stable ai lysogens also containe ...	1984	6096304
the gapped duplex dna approach to oligonucleotide-directed mutation construction.	a simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage m13. the method rests on gapped duplex dna (gddna) molecules of the phage m13 genome as the key intermediate. in this gddna, the (+) and the (shorter) (-) strand carry different genetic markers in such a way, that a rigorous selection can be applied for phage carrying the markers of the (-) strand. for introduction of the mutation, a synthetic oligonucleotid ...	1984	6096830
minimal size plasmids containing an m13 origin for production of single-strand transducing particles.	we have studied the requirements for efficient production of single-strand transducing particles from minimal size plasmids containing the phage m13 origin of replication. the most favorable origin fragment for production of transducing particles was found to extend from nucleotides 5372 to 5943 of the phage sequence, which includes a segment of the phage gene iv coding region and eliminates part of the gene ii promoter. minimizing vector size for m13 origin plasmids appears to be beneficial sin ...	1984	6099398
rapid mutational analysis of regulatory loci in escherichia coli k-12 using bacteriophage m13.	a derivative of bacteriophage m13mp8 , designated m13mp8 /p, was prepared in which the promoter and nh2-terminal codons of bacterial genes may be fused to a portion of beta-galactosidase, resulting in an easily scorable phenotype. because transcription from the inserted promoter remains responsive to the host regulatory system, it is simple to screen mutagenized phage for isolates with aberrant regulatory phenotypes and to determine the mutational changes by dideoxy sequence analysis. the feasib ...	1984	6427775