Publications

molecular characterization by pcr-fingerprinting of candida dubliniensis strains isolated from two hiv-positive patients in spain.	six candida dubliniensis isolates were recovered from two hiv-infected individuals in the course of a prospective study of recurrent oral candidosis among hiv-positive patients in spain. candida albicans strains as well as non-albicans strains were also obtained from these two patients. c. dubliniensis strains were germ-tube-positive and produced abundant chlamydospores. fingerprinting the genomic dnas of these six c. dubliniensis with the c. albicans-specific probe 27a as well as karyotyping wa ...	1999	10579091
genotypic relatedness of yeast isolates from women infected with human immunodeficiency virus and their children.	the objective of this study was to compare polymerase chain reaction (pcr) fingerprinting with other molecular typing methods as an epidemiologic tool to investigate the transmission of candida strains between hiv-positive mothers and their children. forty-nine yeast strains (including candida albicans, candida glabrata, rhodotorula rubra, candida tropicalis, candida famata, candida dubliniensis, saccharomyces cerevisiae) from 30 individuals (15 children and 15 hiv-infected mothers or accompanyi ...	1999	10536430
c8-guanine adduct-induced stabilization of a -1 frame shift intermediate in a nonrepetitive dna sequence.	the mechanism of frame shift mutagenesis induced by n-(deoxyguanosin-8-yl)-1-aminopyrene, the major dna adduct formed by the carcinogen 1-nitropyrene, was investigated by thermal melting studies of a 13-mer in which the adduct was flanked by a 5' and a 3' c. compared to the unmodified 13-mer, the adduct destabilized the duplex by 4-5 kcal/mol, and the deltadeltag value remained approximately the same regardless of which base was placed opposite the adduct. in contrast, deletion of the base oppos ...	1999	10529252
[genetic distances and taxonomic analysis of human populations of the volga-ural region based on data on dna polymorphism].	dna polymorphism was studied in the human diallelic loci met and d7s23 linked to the cystic fibrosis gene, diallelic locus pah (the phenylketonuria gene), polyallelic locus apob, and hypervariable dna sequences identified by means of dna fingerprinting with phage m13 dna as a probe. the obtained data were used to calculate genetic distances and perform taxonomic analysis of populations of the volga-ural region (turkic and finno-ugric ethnic groups). the dna polymorphic systems studied were demon ...	1999	10519075
[identification and characterization of strains of bacillus thuringiensis by genomic fingerprinting using biotinylated phage m13 dna].	genomic dna of the entomopathogenic bacterium bacillus thuringiensis was analyzed by the genomic fingerprinting technique. the biotin-labeled single-stranded dna of the phage m13 was used as a marker of hypervariable sequences. a procedure for analyzing the differentiation among various bacillus thuringiensis strains was developed. characteristic patterns of fingerprints were obtained for several strains, the main representatives of subspecies that are most frequently used in the manufacture of ...	1999	10505264
escherichia coli cells bearing muta, a mutant glyv trna gene, express a reca-dependent error-prone dna replication activity.	a base substitution mutation (muta) in the escherichia coli glyv trna gene potentiates asp --> gly mistranslation and confers a strong mutator phenotype that is sos independent, but requires reca, recb and recc genes. here, we demonstrate that muta cells express an error-prone dna polymerase by using an in vitro experimental system based on the conversion of phage m13 single-stranded viral dna bearing a model mutagenic lesion to the double-stranded replicative form. amplification of the newly sy ...	1999	10447883
isolation of fibroblast growth factor receptor binding sequences using evolved phage display libraries.	a fusion protein construct consisting of the short form of human fibroblast growth factor (fgfr) fused to the heavy chain of mouse igg1 was used to screen four phage display libraries displaying 8, 13, 38 and 43 amino acids at the amino terminus of the bacteriophage m13 gene iii minor coat protein. phage with specific fgfr binding activity were isolated from the 13, 38 and 43 mer libraries. one of the highest affinity phage clones from the 13mer library was chosen to be further evolved by oligon ...	1999	10420969
[analysis of dna polymorphism in populations of the volga-ural region using genome fingerprinting with phage m13 dna].	the hyperpolymorphism of minisatellite dna hybridizing with dna of bacteriophage m13 was analyzed in seven turkic and finno-ugric populations from the volga-urals region. in total, hybridization revealed 80 bspri genomic dna fragments ranging in size from 1.7 to 10 kb; the average frequency of an individual fragment was 0.299 +/- 0.020. the average number of hybridization fragments per pattern (varying from 14 to 20 in different populations) and frequencies of individual fragments showed signifi ...	1999	10420275
synthesis of a eukaryotic virus protein in a prokaryotic viral-cell system: production of the adenovirus type 2 fiber shaft fragment by a tightly regulated t7pol-m13 expression system.	the use of recombinant technology for the production of proteins of interest in biotechnology and medicine has grown immensely during the last decade. a major problem often encountered is the degradation of the recombinant product by host cell proteases. we developed a novel system based on the cloning and expression of an inducible phage t7 rna polymerase into the main intergenic region of the phage m13-ko7. after infection of permissive bacterial strains with the engineered phage, the polymera ...	1999	10381082
determination of phage antibody affinities to antigen by a microbalance sensor system.	over the past decade, phage display has maturated to be a frequently used method for the generation of monoclonal antibodies of human origin. the essential step of this method is the "biopanning" of phage carrying functional antibody fragments on their surface on an immobilized antigen. the screening of large combinatorial gene libraries with this method usually leads to a set of diverse clones specifically binding to the antigen that need to be characterized further. beside its specificity, the ...	1999	10337489
[dna-fingerprinting of representatives of bovinae subfamilies using the telomere markers (ttaggg)4].	the (ttaggg)4 oligonucleotide homologous to telomeric tandem repeats of human chromosomes was used for the first time as a multilocus hybridization probe for the analysis of genome variability in the two genera (bos and bison) of the bovinae subfamily. dna profiles for cattle, banteng, aurochs, and bison were obtained. hybridization spectra were represented by the discrete individual- and species-specific bands characterized by codominant inheritance. for comparison, dna profiles of the same sam ...	1999	10330618
crystal structure of the two n-terminal domains of g3p from filamentous phage fd at 1.9 a: evidence for conformational lability.	infection of escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein g3p and involves two distinct cellular receptors, the f' pilus and the periplasmic protein tola. recently we have shown that the two receptors are contacted in a sequential manner, such that binding of tola by the n-terminal domain g3p-d1 is conditional on a primary interaction of the second g3p domain d2 with the f' pilus. in order to better understand this process, we have solved the crystal ...	1999	10329170
characterization of cerebrospinal fluid antibody specificities in neurocysticercosis using phage display peptide library.	to identify epitopes for antibodies present in cerebrospinal fluid (csf) samples from two patients with confirmed neurocysticercosis, we used a phage peptide library that displayed random dodecapeptides as a fusion to the minor coat protein (piii) of phage m13. to increase the specificity of selection, plates coated with anti-human fc antibody were used in five rounds of biopanning. the dna inserts of 30 selected clones were determined and the deduced amino acid sequences were analyzed. sequence ...	1999	10219262
conformational and aggregational properties of the gene 9 minor coat protein of bacteriophage m13 in membrane-mimicking systems.	the membrane-bound state of the gene 9 minor coat protein of bacteriophage m13 was studied in various membrane-mimicking systems, including organic solvents, detergent micelles, and phospholipid bilayers. for this purpose we determined the conformational and aggregational properties of the chemically synthesized protein by cd, ftir, and hpsec. the protein appears to be in a monomeric or small oligomeric alpha-helical state in tfe but adopts a mixture of alpha-helical and random structure after s ...	1999	9894010
a phage single-stranded dna (ssdna) binding protein complements ssdna accumulation of a geminivirus and interferes with viral movement.	geminiviruses are plant viruses with circular single-stranded dna (ssdna) genomes encapsidated in double icosahedral particles. tomato leaf curl geminivirus (tolcv) requires coat protein (cp) for the accumulation of ssdna in protoplasts and in plants but not for systemic infection and symptom development in plants. in the absence of cp, infected protoplasts accumulate reduced levels of ssdna and increased amounts of double-stranded dna (dsdna), compared to accumulation in the presence of wild-ty ...	1999	9882367
evolution of peptides that modulate the spectral qualities of bound, small-molecule fluorophores.	fluorophore dyes are used extensively in biomedical research to sensitively assay cellular constituents and physiology. we have created, as proof of principle, fluorophore dye binding peptides that could have applications in fluorescent dye-based approaches in vitro and in vivo.	1998	9862799
abnormal, error-prone bypass of photoproducts by xeroderma pigmentosum variant cell extracts results in extreme strand bias for the kinds of mutations induced by uv light.	xeroderma pigmentosum (xp) is a rare genetic disease characterized by a greatly increased susceptibility to sunlight-induced skin cancer. cells from the majority of patients are defective in nucleotide excision repair. however, cells from one set of patients, xp variants, exhibit normal repair but are abnormally slow in replicating dna containing uv photoproducts. the frequency of uv radiation-induced mutations in the xp variant cells is significantly higher than that in normal human cells. furt ...	1999	9858539
differential use of the signal recognition particle translocase targeting pathway for inner membrane protein assembly in escherichia coli.	assembly of several inner membrane proteins-leader peptidase (lep), a lep derivative (lep-inv) that inserts with an inverted topology compared with the wild-type protein, the phage m13 procoat protein, and a procoat derivative (h1-procoat) with the hydrophobic core of the signal peptide replaced by a stretch from the first transmembrane segment in lep-has been studied in vitro and in escherichia coli strains that are conditional for the expression of either the 54 homologue (ffh) or 4.5s rna, wh ...	1998	9843943
human platelet antigen genotyping using a fluorescent sscp technique with an automatic sequencer.	the typing of human platelet antigens (hpa) can be useful in many clinical situations such as neonatal alloimmune thrombocytopenia, post-transfusion purpura, and platelet transfusion refractoriness. the fluorescent-based single-strand conformation polymorphism (f-sscp) technique is a fast and convenient way to perform hpa genotyping. universal sequences from phage m13 were introduced at both ends of specific pcr-products by using 5'-tailed primers. a short second round of pcr with universal prim ...	1998	9827917
characterization of a new intrabody directed against the n-terminal region of human p53.	genes encoding the rearranged immunoglobulin heavy and light chain variable regions of do-1, a monoclonal antibody directed against human p53, have been used to construct a single-chain antibody. do-1 recognizes an n-terminal epitope in the region involved in the transactivation function of p53 and the binding of mdm2. the do-1 single chain scfv expressed in the periplasm of e. coli or at the surface of the filamentous phage m13 retained the immunological specificity and affinity of the full len ...	1998	9824155
on the fate of orally ingested foreign dna in mice: chromosomal association and placental transmission to the fetus.	we have previously shown that, when administered orally to mice, bacteriophage m13 dna, as a paradigm foreign dna without homology to the mouse genome, can persist in fragmented form in the gastrointestinal tract, penetrate the intestinal wall, and reach the nuclei of leukocytes, spleen and liver cells. similar results were obtained when a plasmid containing the gene for the green fluorescent protein (pegfp-c1) was fed to mice. in spleen, the foreign dna was detected in covalent linkage to dna w ...	1998	9819049
solution structure of the m13 major coat protein in detergent micelles: a basis for a model of phage assembly involving specific residues.	the three-dimensional structure of the major coat protein of bacteriophage m13, solubilized in detergent micelles, has been determined using heteronuclear multidimensional nmr and restrained molecular dynamics. the protein consists of two alpha-helices, running from residues 8 to 16 and 25 to 45, respectively. these two helices are connected by a flexible and distorted helical hinge region. the structural properties of the coat protein make it resemble a flail, in which the hydrophobic helix (re ...	1998	9735296
efficient display of an hcv cdna expression library as c-terminal fusion to the capsid protein d of bacteriophage lambda.	we describe the construction and characterization of a hepatitis c virus (hcv) cdna expression library displayed as a fusion to the carboxy terminus of the capsid protein d of bacteriophage lambda. cdna inserts were obtained by tagged random-priming of the hcv genome and cloned into a lambda vector from which chimeric phage bearing both wild-type d protein and d fusion products on the capsid surface were produced. the resulting library was affinity-selected with anti-hcv human monoclonal antibod ...	1998	9733645
cyclic peptides as non-carboxyl-terminal ligands of syntrophin pdz domains.	syntrophins, a family of intracellular peripheral membrane proteins of the dystrophin-associated protein complex (dapc), each contain a single pdz domain. syntrophin pdz domains bind c-terminal peptide sequences with the consensus r/k-e-s/t-x-v-cooh, an interaction that mediates association of skeletal muscle sodium channels with the dapc. here, we have isolated cyclic peptide ligands for syntrophin pdz domains from a library of combinatorial peptides displayed at the n terminus of protein iii o ...	1998	9705339
multifunctional g3p-peptide tag for current phage display systems.	we have previously described a monoclonal antibody (mab), 10c3, directed against the gene-3 protein (g3p) of filamentous phage m13, which was produced to study g3p fusion protein expression in escherichia coli and its incorporation in the phage capsid [tesar, m., beckmann, c., röttgen, p., haase, b., faude, u., timmis, k., 1995. monoclonal antibody against piii of filamentous phage: an immunological tool to study piii fusion protein expression in phage display systems. immunology 1, 53-54]. in t ...	1998	9672201
mimicking initial interactions of bacteriophage m13 coat protein disassembly in model membrane systems.	the structure and changes in environment of the m13 major coat protein were studied in model systems, mimicking the initial molecular process of the phage disassembly. for this purpose we have systematically studied protein associations with various detergents and lipids in two different coat protein assemblies: phage particles and s-forms. it is remarkable that the major coat protein can change its conformation to accommodate three distinctly different environments: phage filament, s-form, and ...	1998	9665724
virus inactivation in superoxide dismutase preparations by ultraviolet light irradiation.	viral inactivation in superoxide dismutase (sod) derived from human red cells was carried out by ultraviolet light c (uvc) irradiation. with 400 j/m2 uvc irradiation, the titer of canine parvovirus (cpv, a nonenveloped virus), m13 bacteriophage (m13, a nonenveloped phage) and vesicular stomatitis virus (vsv, an enveloped virus), which were spiked into sod solution, were reduced by > 4.6 log10 (detection limit), 7.0 log10 and 6.2 log10, respectively. the sod activity was maintained and the band p ...	1998	9657049
increased misincorporation fidelity observed for nucleoside analog resistance mutations m184v and e89g in human immunodeficiency virus type 1 reverse transcriptase does not correlate with the overall error rate measured in vitro.	nucleoside analog-resistant variants of human immunodeficiency virus type 1 (hiv-1) reverse transcriptase (rt) that displayed higher in vitro polymerase fidelity were previously identified via nucleotide insertion and mispair extension assays. to evaluate the contribution of increased nucleotide insertion and primer extension fidelities on the overall error rate of hiv-1 rt, we have measured the impact of two such mutations, e89g and m184v, on dna copying fidelity in an m13 phage-based forward m ...	1998	9557711
sec/srp-independent insertion of two thylakoid membrane proteins bearing cleavable signal peptides.	two imported thylakoid membrane proteins, psii-x and psii-w, are synthesised with cleavable n-terminal signal peptides that closely resemble those of sec-dependent lumenal proteins. in this report we have reconstituted the insertion of pre-psii-x and pre-psii-w into isolated thylakoids. we show that insertion does not require either nucleoside triphosphates or stromal extracts, both of which are required for sec- and signal recognition particle (srp)-dependent targeting mechanisms. insertion is ...	1998	9537524
uptake of foreign dna from the environment: the gastrointestinal tract and the placenta as portals of entry.	foreign dna (deoxyribonucleic acid) is part of our environment. considerable amounts of foreign dna of very different origin are ingested daily with food. in a series of experiments we fed the dna of bacteriophage m13 as test dna to mice and showed that fragments of this dna survive the passage through the gastrointestinal (gi) tract in small amounts (1-2%). food-ingested m13 dna reaches peripheral white blood cells, the spleen and liver via the intestinal epithelia and cells in the peyer's patc ...	1998	9531678
recombinant aspergillus fumigatus allergens: from the nucleotide sequences to clinical applications.	members of the genus aspergillus are opportunistic pathogens for cold- and warm-blooded animals. they are associated with an impressive spectrum of diseases in humans, ranging from benign colonization of the lung to life-threatening diseases such as invasive aspergillosis or allergic bronchopulmonary aspergillosis (abpa). aspergillus fumigatus is the etiological agent identified in most of the aspergillus-related human diseases and is therefore of particular clinical relevance. a major problem i ...	1998	9482698
the major mitomycin c-dna monoadduct is cytotoxic but not mutagenic in escherichia coli.	to determine the mutagenic and genotoxic properties of the major guanine n2-adduct formed by the antitumor drug mitomycin c, we have synthesized a decanucleotide, d(ttacg[mc]tatct), containing the adduct, which was inserted into a gapped bacteriophage m13 genome. analysis of the constructed genome indicated that 41% ligation of the adducted 10-mer occurred on both sides of the gap, whereas the control 10-mer ligated with 34% efficiency. after transfection of the adducted single-stranded m13 dna ...	1998	9477227
a novel soluble tissue factor variant with an altered factor viia binding interface.	tissue factor (tf) residues lys20 and asp58 form part of a binding epitope previously shown by alanine scanning to be critical for high affinity interactions with factor viia (fviia). to explore the possibility of enhancing the affinity of a tf-based antagonist for fviia, we created libraries in which residues at 20, 58, and adjacent positions were varied in constructs containing the soluble extracellular domain of tf (stf) fused to the bacteriophage m13 tail coat protein. tf variants monovalent ...	1998	9461610
[the genetic typing of strains in the genus francisella using universal probes].	the determination of the genetic relationship of bacteria of the genus francisella and their differentiation is one of the topical tasks of the epidemiology and infectology of f. tularensis, the causative agent of tularemia, belonging to this genus. to solve this task, investigation was carried out with a view to the determine the possibility of the genomic typing of francisella. genomic typing was based on the use of the hybridization of fragments of francisella chromosomal dna, split by restri ...	1997	9460874
specificity of mutagenesis by 4-aminobiphenyl: mutations at g residues in bacteriophage m13 dna and g-->c transversions at a unique dg(8-abp) lesion in single-stranded dna.	mutagenesis by the human bladder carcinogen 4-aminobiphenyl (abp) was studied in single-stranded dna from a bacteriophage m13 cloning vector. in comparison to abp lesions in double-stranded dna, lesions in single-stranded dna were approximately 70-fold more mutagenic and 50-fold more genotoxic. sequencing analysis of abp-induced mutations in the lacz gene revealed exclusively base-pair substitutions, with over 80% of the mutations occurring at g sites; the g at position 6310 accounted for 25% of ...	1997	9450488
purification and properties of a dna primase from nicotiana tabacum.	a dna primase was isolated from a nuclear fraction from leaves of tobacco (nicotiana tabacum l. cv. samsun) and from purified nuclei prepared from tobacco suspension culture cells. the dna primase was purified to homogeneity (i) for preparations from leaves, by ammonium sulphate fractionation, followed by chromatography on columns of phosphocellulose, q-sepharose, heparin-sepharose and single-stranded dna cellulose, and sedimentation in a glycerol gradient, or (ii) for preparations from cells, b ...	1998	9443386
display of functional thrombin inhibitor hirudin on the surface of phage m13.	a synthetic gene for hirudin was ligated into phagemid pcantab5e. this construct allows production of either soluble hirudin or phage having hirudin displayed on the surface. similarly, hirudin variants with extensions either at their n- or c-terminus were generated. the genes were expressed in their soluble form in a non-suppressor strain of e. coli. periplasmatic fractions were evaluated in standard thrombin inhibition assays. extending hirudin by a single gln residue at the n-terminus reduces ...	1997	9434182
molecular tracking of candida albicans in a neonatal intensive care unit: long-term colonizations versus catheter-related infections.	nosocomial neonatal candidiasis is a major problem in infants requiring intensive therapy. the subjects of this retrospective study were nine preterm infants admitted to the neonatal intensive care unit of the hospital central de asturias between march 1993 and august 1994. the infants were infected with or colonized by candida albicans. five patients developed c. albicans bloodstream infections. a total of 36 isolates (including isolates from catheters and parenteral nutrition) were examined fo ...	1997	9399489
identification of pathogenic yeasts of the imperfect genus candida by polymerase chain reaction fingerprinting.	with the increase in the number of immunocompromised hosts, the number of fungal pathogens has increased markedly. identification and classification, especially of yeast species and strains, is often difficult when based solely on phenotypic characteristics. since it became clear that different fungal pathogens require specific treatment strategies, there is a need for simple, rapid and reliable methods to identify fungal isolates. polymerase chain reaction (pcr) fingerprinting was successfully ...	1997	9378120
[characterization of plasmids which mediate resistance to multiple antibiotics in gram-negative bacteria of nosocomial origin].	the genetic and molecular mechanisms involved in antimicrobial resistance of 10 strains of gramnegative bacilli (1 serratia marcescens; 2 escherichia coli; 1 proteus mirabilis; 4 klebsiella pneumoniae; 1 enterobacter cloacae y 1 alcaligenes faecalis), isolated from adult patients with nosocomial pulmonary infection at the in-patient facilities of the university hospital of los andes, mérida, venezuela, have been studied.	1997	9376400
monoclonal antibody against piii of filamentous phage: an immunological tool to study piii fusion protein expression in phage display systems.	a monoclonal antibody directed against the gene 3 product (piii) of filamentous phage m13 was produced to study piii-fusion protein expression in e. coli and its incorporation in the phage capsid. the protein was gel-purified from e. coli expression cultures harboring the genetic information of piii under the control of an inducible lac promoter. to study piii-fusion protein expression, phage display systems were applied in which either the whole piii or the c-terminal half was used (mccafferty ...	1995	9373333
improving the copy numbers of antibody fragments expressed on the major coat protein of bacteriophage m13.	antibody fragments have been expressed on the major coat protein of filamentous phage using a gene viii expression system, but with low copy numbers (averaging 0.2 fab/phage).	1996	9373312
in situ aggregational state of m13 bacteriophage major coat protein in sodium cholate and lipid bilayers.	the in situ aggregational behavior of the bacteriophage m13 major coat protein was determined for the protein isolated in sodium cholate and reconstituted into dopc lipid bilayers. for this purpose, the cysteine mutants a49c and t36c of the major coat protein were labeled with either a maleimido spin-label or a fluorescence label (iaedans). the steric restrictions sensed by the spin-label were used to evaluate the local protein conformation and the extent of protein-protein interactions at the p ...	1997	9315865
potential involvement of both type i and type ii mechanisms in m13 virus inactivation by methylene blue photosensitization.	we have investigated the mechanism of virus photoinactivation with methylene blue (mb) by conducting deuterium oxide (d2o), azide ion (n3-) and oxygen-dependent studies. inactivation of m13 bacteriophage and singlet oxygen (1o2) generation by mb photosensitization were irradiation dose dependent. inactivation of m13 was enhanced by d2o and inhibited by n3-, suggesting that 1o2 participates in m13 inactivation by mb photosensitization. however, n3- did not inhibit m13 inactivation completely. on ...	1997	9277138
replication of m13 single-stranded dna bearing a site-specific ethenocytosine lesion by escherichia coil cell extracts.	previous investigation on the mutagenic effects of 3, n4-ethenocytosine (epsilon c), a nonpairing dna lesion, revealed the existence of a novel sos-independent inducible mutagenic mechanism in e. coli termed uvm for uv modulation of mutagenesis. to investigate whether uvm is mediated by an alteration of dna replication, we have set up an in vitro replication system in which phage m13 viral single-stranded dna bearing a single site-specific (epsilon c) residue is replicated by soluble protein ext ...	1997	9261557
mutations that render the promoter of the histidine operon of salmonella typhimurium insensitive to nutrient-rich medium repression and amino acid downshift.	the effects of mutations in the promoter of the histidine operon of salmonella typhimurium were examined in vivo. the wild-type chromosomal copy of the his promoter was replaced with mutations in the -10 hexamer sequence and in the region between the -10 hexamer and the transcriptional start point-termed the discriminator sequence. the substitutions were performed with a phage m13 allele replacement system. expression of the his operon is known to correlate with levels of guanosine 5',3'-bispyro ...	1997	9260966
conventional and saturation-transfer epr of spin-labeled mutant bacteriophage m13 coat protein in phospholipid bilayers.	a mutant of bacteriophage m13 was prepared in which a cysteine residue was introduced at position 25 of the major coat protein. the mutant coat protein was spin-labeled with a nitroxide derivative of maleimide and incorporated at different lipid-to-protein (l/p) ratios in dopc or dopg. the rotational dynamics of the reconstituted mutant coat protein was studied using epr and saturation transfer (st) epr techniques. the spectra are indicative for an anisotropic motion of the maleimide spin label ...	1997	9247162
obtaining a family of high-affinity, high-specificity protein inhibitors of plasmin and plasma kallikrein.	human lipoprotein-associated coagulation inhibitor (laci) is a serum protein containing three kunitz domains. we displayed the first domain (laci-d1) on the iii protein of phage m13 and made libraries of this domain. we iteratively varied 13 residues in the region corresponding to the bpti-trypsin interface and selected for binding to human plasmin (pla) and human plasma kallikrein (pkal). for pla, our first-round best binder, epi-p211, had kd = 2 nm. using information from the first selection, ...	1996	9238642
a combinatorial method for constructing libraries of long peptides displayed by filamentous phage.	we describe the construction and screening of a random peptide library displayed by filamentous phage. the peptides are expressed in multiple copies on the filamentous phage m13 as amino-terminal fusions with the major coat protein, the product of gene viii. these libraries are efficiently screened for reactive peptides, using a combination of panning in solution followed by a plaque lift assay. advantages of this system are that both high- and low-affinity phage clones are simultaneously identi ...	1995	9237193
use of random amplification of polymorphic dna (rapd) and pcr-fingerprinting for genotyping a scedosporium prolificans (inflatum) outbreak in four leukemic patients.	four isolates of the pathogenic fungus scedosporium prolificans (inflatum), causing a previously reported nosocomial outbreak in four leukemic patients, were typed by random amplification of polymorphic dna (rapd) with two different 10-mer primers and pcr-fingerprinting with the core sequence of phage m13 as a single primer. both techniques allowed 10 additional clinical isolates of scedosporium prolificans from different areas of spain, including scedosporium prolificans ncpf 2884, to be classi ...	1997	9236303
mutations in the siv env and the m13 lacza gene generated in vitro by reverse transcriptases and dna polymerases.	to investigate the accuracy of retroviral in vitro dna replication we have examined with two fidelity assays the reverse transcriptases (rts) from sivagm, hiv-1, momlv as well for comparison the klenow fragment from e. coli and dna polymerase a from calf-thymus. these forward mutation assays measured the loss of bacteriophage m13 lacza gene function by mutations. in the envlacza assay frameshift mutations occurring during polymerisation of a 176 b long simian immunodeficiency virus (siv) envelop ...	1997	9229004
a selection system to study protein-rna interactions: functional display of hiv-1 tat protein on filamentous bacteriophage m13.	the transactivator protein (tat) of the human immunodeficiency virus (hiv) is a key regulatory protein in the viral replication cycle and belongs to the rna binding proteins of the arginine-rich motif (arm) family. very little is known about their mechanism of rna recognition. to study the principles of rna-protein recognition we constructed a system to display hiv-1 tat on the surface of the filamentous bacteriophage m13. hiv-1 tat (1-72) and a mutant tat lacking five cysteine residues were clo ...	1997	9207243
screening panels of monoclonal antibodies using phage-displayed antigen.	a procedure is described to screen panels of hybridomas or purified monoclonal antibodies using antigen displayed on the surface of filamentous bacteriophage. in this system, samples containing murine monoclonal antibodies are incubated with phage-displayed antigen in microtiter plates coated with rabbit anti-mouse igg, and bound antibody-phage complex is detected with horseradish peroxidase-sheep anti-phage m13 conjugate. the assay has been validated with a panel of 16 monoclonal antibodies dir ...	1997	9177746
comparison of four molecular typing methods for evaluating genetic diversity among candida albicans isolates from human immunodeficiency virus-positive patients with oral candidiasis.	candida albicans strain delineation by karyotyping. noti restriction pattern analysis, hybridization with specific probe 27a, and pcr fingerprinting with the phage m13 core sequence were performed with 30 isolates from the oral cavities of 30 human immunodeficiency virus (hiv)-infected patients and 8 reference strains. within the panel of clinical isolates, 20 were geographically related, although 10 isolates were susceptible to fluconazole and 10 isolates were resistant to fluconazole. the rema ...	1997	9157142
development of hiv-1 protease expression methods using the t7 phage promoter system.	new and simple human immunodeficiency virus type 1 (hiv-1) protease expression methods in escherichia coli were developed using the t7 phage promoter system. in order to suppress leaky hiv-1 protease expression under the control of the t7 polymerase, two new methods were tested. one involved the introduction of supplementary t7 promoter regions into host cells [e. coli bl-21 (de3)] containing the hiv-1 protease gene under the control of the t7 promoter. it was expected that the supplementary t7 ...	1997	9114515
distribution of sequence-dependent curvature in genomic dna sequences.	the distribution of inherent, sequence-dependent curvature was calculated for a number of prokaryotic (m. genitalium, h. influenzae, m. jannaschii), viral (adenovirus 2, equine herpes virus 1), phage (m13, lambda), eukaryotic (s. cerevisiae) and mitochondrial genomes as well as e. coli and human genomic fragments. the genomic averages are in the range of 6-8 degrees/helical turn and only about 20% of dna is curved less than 3 degrees/helical turn. the prokaryotes and phages appear to have a cons ...	1997	9109388
backbone dynamics of the major coat protein of bacteriophage m13 in detergent micelles by 15n nuclear magnetic resonance relaxation measurements using the model-free approach and reduced spectral density mapping.	the backbone dynamics of the major coat protein (gviiip) of the filamentous bacteriophage m13, solubilized in detergent micelles, have been studied using 15n nuclear magnetic resonance spectroscopy at three frequencies. motional parameters and overall and internal correlation times were derived with the model-free approach. it was also checked whether these parameters had to be modified due to anisotropic motion of the protein/micelle complex. reduced spectral density mapping was used to calcula ...	1997	9092832
production of a single-chain fragment of the murine anti-idiotypic antibody aca125 as phage-displayed and soluble antibody by recombinant phage antibody technique.	the f(ab')2 fragment of the murine monoclonal anti-idiotypic antibody aca125 mimicking the tumor-associated antigen ca125 is used as a vaccine for the induction of an anti-tumoral immunity in patients with ovarian carcinoma. we tried to generate a single-chain fragment (scfv) composed of aca125 heavy- and light-chain variable domains connected by a polypeptide linker as an alternative to the corresponding f(ab')2 fragment. heavy- and light-chain genes of antibody-producing mouse hybridoma cell l ...	1997	9085128
destabilizing interactions between the partners of a bifunctional fusion protein.	hybrid male-gvp is a bifunctional protein in vitro since it binds maltose as protein male of escherichia coli and since it is dimeric and specifically binds single-stranded dna as protein gvp of phage m13. the oxidation rate of a unique cysteine residue was used to compare the stabilities of gvp in its free and hybrid forms, under conditions where male was either folded or unfolded by a denaturing agent. the results showed that both the covalent link and tertiary non-covalent interactions betwee ...	1996	9005445
molecular cloning, expression, and characterization of a functional single-chain fv antibody to the mycotoxin zearalenone.	the heavy-chain and kappa light-chain variable region genes of an antizearalenone hybridoma cell line (2g3-6e3-2e2) were isolated by pcr and joined by a dna linker encoding peptide (gly4ser)3 as a single-chain fv (scfv) dna fragment. the scfv dna fragment was cloned into a phagemid (pcantab5e) and expressed as a fusion protein with e tag and phage m13 p3 in escherichia coli tg1. in the presence of helper phage m13k07, the scfv fusion protein was displayed on the surfaces of recombinant phages. h ...	1997	8979354
organization of the bacillus subtilis 168 chromosome between kdg and the attachment site of the sp beta prophage: use of long accurate pcr and yeast artificial chromosomes for sequencing.	within the bacillus subtilis genome sequencing project, the region between lysa and ilva was assigned to our laboratory. in this report we present the sequence of the last 36 kb of this region, between the kdg operon and the attachment site of the sp beta prophage. a two-step strategy was used for the sequencing. in the first step, total chromosomal dna was cloned in phage m13-based vectors and the clones carrying inserts from the target region were identified by hybridization with a cognate yea ...	1996	8969496
[identification and classification of strains of microorganisms using genomic fingerprinting with biotinylated phage m13 dna].	to analyze dna polymorphisms of various bacterial strains, a nonradioactive variant of the genomic fingerprinting method was developed. the method was based on the application of biotin-labeled single-stranded phage m13 dna as a probe. characteristic patterns of fingerprints obtained by mvai, haeiii, and hinfi restriction enzymes are presented for several species of bacilli and other bacteria. the advantages of this method in microbiology for the identification and characterization of different ...	1996	8964460
stable high-copy-number bacteriophage lambda promoter vectors for overproduction of proteins in escherichia coli.	the construction of new high-copy-number (hcn) lambda-promoter expression vectors is described. all these vectors (1) contain tandem lambda pr and pl promoters upstream of an extensive multiple cloning site (mcs) for insertion of genes, (2) direct expression of the lambda cits857 gene, enabling their use in any escherichia coli host strain for thermal induction of gene overexpression, and (3) bear the par locus of plasmid psc101, ensuring their stable maintenance at hcn in the absence of continu ...	1996	8918231
an improved method for the synthesis of mercurated dutp. enzymic synthesis of hg-labelled dna of high molecular weight suitable for use in an image based dna sequencing strategy.	the development of high-resolution scanning-probe microscopes has reawakened interest in the possibility of sequencing large nucleic acid molecules by direct imaging. such an approach would be facilitated by the availability of effective methods for increasing contrast by labelling specific nucleotides, and the utility of introducing mercury atoms into complete dna molecules through the enzymic polymerisation of mercurated pyrimidine deoxynucleoside triphosphates has been re-investigated. a simp ...	1996	8912922
analyzing sequencing reactions from bacteriophage m13 by matrix-assisted laser desorption/ionization mass spectrometry.	the current demand for improved dna sequencing methodologies posed by the human genome project has spurred the investigation of alternatives to gel electrophoresis. matrix-assisted laser desorption/ionization (maldi) mass spectrometry has great potential for the rapid analysis of dna fragments. mock sanger sequencing mixtures have been successfully analyzed by maldi by pooling synthesized oligonucleotides corresponding to the m13 bacteriophage sequence. more recently, analyses of sanger sequenci ...	1996	8885418
analysis of peptide-binding motifs for two disease associated hla-dr13 alleles using an m13 phage display library.	major histocompatibility complex (mhc) molecules bind peptides bearing an appropriate 'sequence motif' for mhc binding. the use of phage display libraries exploits the ability of mhc class ii molecules to exchange peptides in solution and thus select out peptide sequences with high-affinity binding from a large array of random peptides. we have analysed the peptide binding motifs of hla-drb11301 and 1302 using affinity purified hla-dr13 molecules to purify sequentially hla-dr13-binding peptide ...	1996	8881746
a new concept in (adenoviral) oncogenesis: integration of foreign dna and its consequences.	a new concept for viral oncogenesis is presented which is based on experimental work on the chromosomal integration of adenovirus dna into mammalian genomes. the mechanism of adenovirus dna integration is akin to non-sequence-specific insertional recombination in which patch homologies between the recombination partners are frequently observed. this reaction has been imitated in a cell-free system by using nuclear extracts from hamster cells and partly purified fractions derived from them. as a ...	1996	8876634
partial cviji digestion as an alternative approach to generate cosmid sublibraries for large-scale sequencing projects.	we demonstrate an alternative method for the generation of random subclones for large-scale shotgun human dna sequencing projects. miniprep dna from a human cosmid clone was partially digested with cviji, size-fractionated by agarose gel electrophoresis and cloned into bacteriophage m13. a library consisting of 10(5) subclones of 1.1 kb average size was recovered from one gel fraction containing approximately 300 ng of partially digested dna. dna sequences from an initial 103 subclones demonstra ...	1996	8816243
anti-vaccinia virus effect of m13 bacteriophage dna.	single-stranded dna derived from m13 phage was evaluated for antiviral activity in mice infected with vaccinia virus. m13 dna at a dose as low as 16.7 mg/kg was effective in reducing the number of tail lesions caused by vaccinia virus by more than 90%. a single administration of m13 dna 1 day before infection was sufficient to reduce significantly the number of tail lesions caused by vaccinia virus. denatured eukaryotic nucleic acids such as calf thymus dna and human placenta dna were not effect ...	1996	8793011
[genomic polymorphism in mycobacterium tuberculosis strains].	different genomic fingerprinting techniques (universal probes, such as rrna genes, phage m13 dna, is 6110 probe) have been used to investigate the genomic polymorphism of mycobacterium tuberculosis strains isolated in different geographical regions of russia and in some cis countries. as shown with the use of these techniques and a specially developed pcr-mediated system for genetic typing, m.tuberculosis strains are genotypically heterogeneous in regions with a sporadic level of tuberculosis mo ...	1996	8771734
accessibility and environment probing using cysteine residues introduced along the putative transmembrane domain of the major coat protein of bacteriophage m13.	the major coat protein of the filamentous bacteriophage m13 is located in the inner membrane of host cell escherichia coli prior to assembly into virions. to identify the transmembrane domain of the coat protein, we have introduced unique cysteine residues along the putative transmembrane domain at position 25, 31, 33, 36, 38, 46, 47, 49, or 50. the mutant major coat protein was solubilized by membrane-mimicking detergents or reconstituted into mixed bilayers of phospholipids. information about ...	1996	8756694
molecular typing by random amplification of polymorphic dna and m13 southern hybridization of related paired isolates of aspergillus fumigatus.	three forms of dna-based typing procedures for aspergillus fumigatus isolates have been developed over the last five years. the procedures are random amplification of polymorphic dna (rapd), restriction fragment length polymorphism (rflp) detection, and southern hybridizations with various repetitive sequence-based probes. using two of these procedures, we compared 16 selected isolates, grouped into eight pairs on the basis of epidemiology or previously assigned rflp types. rapd with four primer ...	1996	8748280
genetic dissimilarity of two fluconazole-resistant candida albicans strains causing meningitis and oral candidiasis in the same aids patient.	we describe a patient with aids who simultaneously developed candida meningitis with three positive cerebrospinal fluid cultures and oral candidiasis. this patient also had a history or recurrent episodes of oral candidiasis treated with fluconazole. the patient did not respond to this therapy but was cured with amphotericin b and flucytosine. in vitro susceptibility tests revealed that each infection was caused by fluconazole-resistant candida albicans isolates. strain delineation by karyotypin ...	1996	8735114
concordance of clinical and environmental isolates of cryptococcus neoformans var. gattii by random amplification of polymorphic dna analysis and pcr fingerprinting.	sixty-one clinical and forty-nine environmental isolates of cryptococcus neoformans var. gattii from australia and the united states were analyzed by random amplification of polymorphic dna (rapd), using 12- to 22-mer primers in pairs, and/or pcr fingerprinting with a single primer derived from the microsatellite core sequence of the wild-type phage m13 (5' gagggtggcggttct 3'). three major genetic profiles were identified by both typing techniques. a single rapd profile (vgi) predominated among ...	1996	8727912
design of immunogens as components of a new generation of molecular vaccines.	three new approaches to design effective immunogens are considered. at first, we derived an expression vector from bacteriophage m13 allowing the exposure of short peptides on the virion surface. eia demonstrates that antibodies against a recombinant phage carrying the antigenic determinant of the hiv-1 gag protein reacted with the 17-kda core protein of the virus and also with its polyprotein precursor p55 in immunoblotting. in another approach, we chose the hepatitis b core antigen (hbcag) par ...	1996	8717396
the solution structure of the synthetic circular peptide cgvsrqgkpyc. nmr studies of the folding of a synthetic model for the dna-binding loop of the ssdna-binding protein encoded by gene v of phage m13.	the cyclic disulfide peptide cgvsrqgkpyc was prepared to obtain a constrained analogue of residues 17-27 of the dna-binding loop of the gene-v-encoded sdna-binding protein of filamentous bacteriophage m13. amino acid sequences very similar to that of the beta-loop have been found in various phage-encoded ssdna-binding proteins, and it has been proposed that such a loop may occur as a common motif in this class of proteins. the conformation, in aqueous solution, of the synthetic gene-v-protein bi ...	1996	8706671
[detection of bovine infectious rhinotracheitis virus by hybridization using nonradioactive dna-probes].	biotin-labeled dna probes for infectious bovine rhinotracheitis virus also known as bovine herpesvirus-1 (bhv-1) have been developed. the procedure is based on dot-blot hybridization using biotin-labeled bacteriophage m13 and plasmid probes containing cloned psti and ecori-psti restriction fragments of viral genome. the probes obtained were used to detect viral nucleic acids in specimens of bovine spermatic fluid or nasal swabs of calves. the method is simple and rapid, taking less than 24 h, an ...	1995	8686268
iterative optimization of high-affinity proteases inhibitors using phage display. 1. plasmin.	we generated a series of libraries having variants of the first kunitz domain of human lipoprotein-associated coagulation inhibitor (laci-d1, also known as tissue-factor pathway inhibitor-i) displayed on bacteriophage m13 as piii-fusions. we varied laci-di iteratively in two regions: the p1 region (positions 10-21) and the "second loop", (positions 31-39), which together form one end of the domain. display-phage library lib#1 allows 31 200 amino-acid sequences in p1 region (residues 13, 16-19). ...	1996	8672509
reactions of mitochondrial cruciform cutting endonuclease 1 (cce1) of yeast saccharomyces cerevisiae with branched dnas in vitro.	cruciform-cutting endonuclease 1 (cce1) is an x-solvase from yeast saccharomyces cerevisiae [kleff, s., kemper, b. & sternglanz, r. (1992) embo j. 11, 699-704]. we report here the purification of the cloned enzyme cce1 to near homogeneity from over-expressing escherichia coli cells. the purified protein has a globular shape and an apparent molecular mass of 38 kda. cce1 reacts specifically with branched dnas, preferably with four-armed cruciforms. the enzyme linearizes native supercoiled dna by ...	1996	8665955
lysogenic conversion by a filamentous phage encoding cholera toxin.	vibrio cholerae, the causative agent of cholera, requires two coordinately regulated factors for full virulence: cholera toxin (ct), a potent enterotoxin, and toxin-coregulated pili (tcp), surface organelles required for intestinal colonization. the structural genes for ct are shown here to be encoded by a filamentous bacteriophage (designated ctxphi), which is related to coliphage m13. the ctxphi genome chromosomally integrated or replicated as a plasmid. ctxphi used tcp as its receptor and inf ...	1996	8658163
cloning aspergillus fumigatus allergens by the pjufo filamentous phage display system.	a cdna library from aspergillus fumigatus has been displayed on the surface of filamentous phage m13 and screened for gene products binding to human serum ige. the physical linkage of cdna gene products to the genetic information required for their production, achieved by exploiting the high-affinity interaction of the jun and fos leucine zippers, allows rapid and easier screening of large libraries in semifluid systems. the pjufo cloning vector is designed to display proteins on the surface of ...	1996	8645976
mutational properties of the primary aflatoxin b1-dna adduct.	the mutagenic activity of the major dna adduct formed by the liver carcinogen aflatoxin b1 (afb1) was investigated in vivo. an oligonucleotide containing a single 8,9-dihydro-8-(n7-guanyl)-9-hydroxyaflatoxin b1 (afb1-n7-gua) adduct was inserted into the single-stranded genome of bacteriophage m13. replication in sos-induced escherichia coli yielded a mutation frequency for afb1-n7-gua of 4%. the predominant mutation was g --> t, identical to the principal mutation in human liver tumors believed ...	1996	8643667
protein-protein interactions between the escherichia coli single-stranded dna-binding protein and exonuclease i.	it was demonstrated previously that a deoxyribophosphodiesterase (drpase) activity is associated with the dna repair enzyme exonuclease i, and that this activity is stimulated by the addition of the e. coli single-stranded dna-binding protein (ssb). this activity catalyzes the release of deoxyribose-phosphate groups at apurinic/apyrimidinic (ap) sites in the dna that have been cleared by the action of an ap endonuclease. we have now used the yeast two-hybrid system to demonstrate that a protein- ...	1996	8619028
polymerase chain reaction fingerprinting in fungi using single primers specific to minisatellites and simple repetitive dna sequences: strain variation in cryptococcus neoformans.	minisatellites and simple repetitive dna sequence motifs are used as conventional oligonucleotide probes in dna-hybridization-based fingerprinting. the same oligonucleotides can be used as single primers in the polymerase chain reaction (pcr) to generate individual pcr fingerprints. in this study, the simple repetitive sequences, (ca)8, (ct)8, (cac)5, (gtg)5, (gaca)4 and (gata)4, and a minisatellite core sequence derived from the wild-type phage m13 (5' gagggtggcggttct 3') were used as specific, ...	1995	8582350
molecular characterization and cytogenetic analysis of highly repeated dnas of lake trout, salvelinus namaycush.	the chromosomes of lake trout (salvelinus namaycush) contain a considerable amount of heterochromatin located at the centromeres and/or telomeres of several chromosomes, including a sex-specific block located distally on the x chromosome. in order to investigate further the repetitive dnas of lake trout, genomic dna from a female was size fractionated (<600 bp) with the restriction endonuclease alui and fragments were cloned into the bacteriophage m13. a total of 42 clones were isolated. relativ ...	1995	8565700
pcr-fingerprinting used for comparison of ex type strains of trichoderma species deposited in different culture collections.	pcr-fingerprinting with primers (gaca)4, (gtg)5, m13 (core sequence of phage m13), and opb-05 was used to compare ex type strains of various species of trichoderma. the ex type strain of each species was obtained from different culture collections. pcr-fingerprints of each ex type culture, despite of separate cultivation over a long period of time (sometimes decades) by different culture collections, were identical. ex type strains could be discriminated from a number of other strains belonging ...	1995	8564364
[dna fingerprinting in horses].	using a multilocus dna probe, individual - specific hybridization patterns, the so-called dna fingerprints (tab) were determined in six horse families by the dna fingerprinting method. the probe with evolutionally preserved nucleotide sequence from bacteriophage m13 determines hypervariable regions placed in genomic minisatellite dna. the use of this probe permits an identification of an individual and execution of paternity relationships with a probability over 99.99 per cent.	1993	8511839
trypsin display on the surface of bacteriophage.	the gene iii and viii-encoded coat proteins (piii and pviii) from bacteriophage m13 have been fused to the c terminus of the serine protease, trypsin (tsn). the genes encoding the fusions were then inserted directly into m13mp18 to create vectors which expressed both the tsn-coat protein hybrids and the wild-type (wt) coat proteins. immunoblot analysis confirmed that the bacteriophage express tsn on their surface. isolated fusion phage possess kinetic parameters which approximate those of the wt ...	1993	8508953
phage display as a rapid gene expression system: production of bioactive cytokine-phage and generation of neutralizing monoclonal antibodies.	proteins, such as hormones, enzymes, or antibody binding sites, can be expressed in an active conformation on the surface of filamentous bacteriophage. although the phage display technology was originally developed for binding studies, we demonstrate here that this technique can rapidly provide cytokines for studies of biological activity and for raising neutralizing monoclonal antibodies. a phage m13-based cloning vector was constructed that facilitated the expression of human interleukin 3 (hi ...	1993	8505547
cloning, expression and in vitro characterisation of the m13 gene 5 protein.	the gene 5 protein encoded in the genome of bacteriophage m13 is a single stranded dna binding protein essential for phage replication. we have cloned a fragment of the m13 genome containing gene 5, and investigated the effect of upstream elements on expression of the gene by means of bal 31 deletion analysis. the gene was also expressed from the lac promoter of the phagemid vector puc119, and the recombinant protein purified and characterised for dna binding. the affinity of the recombinant pro ...	1993	8504168
conformational states of mutant m13 coat proteins are regulated by transmembrane residues.	mutational and structural analysis of the 28 viable bacteriophage m13 mutants obtained by randomized mutagenesis of the effective transmembrane (tm) segment of the 50-residue major coat (gene viii) protein (residues 21-39) demonstrated that m13 coat protein functionality, as reflected by phage viability, is incompatible with an increase in gly + beta-branched residue content in its tm core. sds-polyacrylamide gel electrophoresis and circular dichroism spectroscopy performed in membrane environme ...	1993	8444834
mutagenicity and genotoxicity of the major dna adduct of the antitumor drug cis-diamminedichloroplatinum(ii).	the mutagenicity and genotoxicity of cis-[pt(nh3)2[d(gpg)-n7(1),-n7(2)]] (gg), the major dna adduct of the antitumor drug cisplatin, has been investigated in escherichia coli. a duplex bacteriophage m13 genome was constructed to contain the gg adduct at a specific site in the (-) strand. the singly platinated duplex genome exhibited a survival of 22% relative to that of the unplatinated control genomes, and this value rose to 38% in cells treated with ultraviolet light to induce the sos resp ...	1993	8422401
hybridization probes for conventional dna fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of cryptococcus neoformans.	in conventional dna fingerprinting, hypervariable and repetitive sequences (minisatellite or microsatellite dna) are detected with hybridization probes. as demonstrated here, these probes can be used as single primers in the polymerase chain reaction (pcr) to generate individual fingerprints. several conventional dna fingerprinting probes were used to prime the pcr, yielding distinctive, hypervariable multifragment profiles for different strains of cryptococcus neoformans. pcr fingerprinting wit ...	1993	8408543
dna- and pcr-fingerprinting in fungi.	dna-fingerprinting has been successfully used to detect hypervariable, repetitive dna sequences (minisatellites and microsatellites) in fungi. combined with methods used to identify random amplified polymorphic dna (rapd), conventional dna-fingerprinting hybridization probes can also be used as single primers to detect dna polymorphisms among fungal species and strains. the oligonucleotides (ca)8, (ct)8, (cac)5, (gtg)5, (gaca)4 and (gata)4, as well as the phage m13 and its core sequence, have be ...	1993	8400701
the macroscopic organization of reconstituted m13 coat protein-phospholipid systems. an epr spectroscopy and polarizing microscope study.	the coat protein of the bacteriophage m13 in the alpha-helical state is reconstituted in macroscopically oriented systems of dioleoylphosphatidylcholine that are prepared by squeezing the reconstituted material between glass plates. the coat protein dramatically influences the macroscopic orientation of the multibilayers, as is investigated by polarizing microscopy and epr spectroscopy of the cholestane spin label embedded in the bilayers. it is found that with increasing amounts of protein the ...	1993	8399296
exploring the dna binding domain of gene v protein encoded by bacteriophage m13 with the aid of spin-labeled oligonucleotides in combination with 1h-nmr.	the dna binding domain of the single-stranded dna binding protein gene v protein encoded by the bacteriophage m13 was studied by means of 1h nuclear magnetic resonance, through use of a spin-labeled deoxytrinucleotide. the paramagnetic relaxation effects observed in the 1h-nmr spectrum of m13 gvp upon binding of the spin-labeled ligand were made manifest by means of 2d difference spectroscopy. in this way, a vast data reduction was accomplished which enabled us to check and extend the analysis o ...	1993	8396429
m13 and puc vectors with new unique restriction sites for cloning.	several vectors based on the widely used phage m13 and plasmid puc were constructed. the vectors contain polylinkers (mcs) for dna insertions with several new restriction sites (e.g., apai, noti, stui, sacii). moreover, the nari site in the nonessential part of the vector molecule was changed into a bsshii site, so that the nari site in the mcs became unique.	1993	8393824
exploration of the single-stranded dna-binding domains of the gene v proteins encoded by the filamentous bacteriophages ike and m13 by means of spin-labeled oligonucleotide and lanthanide-chelate complexes.	scrutiny of noe data available for the protein encoded by gene v of the filamentous phage ike (ike gvp), resulted in the elucidation of a beta-sheet structure which is partly five stranded. the dna-binding domain of ike gvp was investigated using a spin-labeled deoxytrinucleotide. the paramagnetic-relaxation effects observed in the 1h-nmr spectrum of ike gvp, upon binding of this dna fragment, could be visualized using two-dimensional difference spectroscopy. in this way, the residues present in ...	1993	8375389
analysis of 31p nuclear magnetic resonance lineshapes and transversal relaxation of bacteriophage m13 and tobacco mosaic virus.	the experimentally observed 31p lineshapes and transversal relaxation of 15% (wt/wt) m13, 30% m13, and 30% tobacco mosaic virus (tmv) are compared with lineshapes and relaxation curves that are simulated for various types of rotational diffusion using the models discussed previously (magusin, p. c. m. m., and m. a. hemminga. 1993. biophys. j. 64:1851-1860). it is found that isotropic diffusion cannot explain the observed lineshape effects. a rigid rod diffusion model is only successful in descri ...	1993	8369412
a theoretical study of rotational diffusion models for rod-shaped viruses. the influence of motion on 31p nuclear magnetic resonance lineshapes and transversal relaxation.	information about the interaction between nucleic acids and coat proteins in intact virus particles may be obtained by studying the restricted backbone dynamics of the incapsulated nucleic acids using 31p nuclear magnetic resonance (nmr) spectroscopy. in this article, simulations are carried out to investigate how reorientation of a rod-shaped virus particle as a whole and isolated nucleic acid motions within the virion influence the 31p nmr lineshape and transversal relaxation dominated by the ...	1993	8369411