Publications

identification and mapping of self-assembling protein domains encoded by the escherichia coli k-12 genome by use of lambda repressor fusions.	self-assembling proteins and protein fragments encoded by the escherichia coli genome were identified from e. coli k-12 strain mg1655. libraries of random dna fragments cloned into a series of lambda repressor fusion vectors were subjected to selection for immunity to infection by phage lambda. survivors were identified by sequencing the ends of the inserts, and the fused protein sequence was inferred from the known genomic sequence. four hundred sixty-three nonredundant open reading frame-encod ...	2004	14973045
in vivo recombineering of bacteriophage lambda by pcr fragments and single-strand oligonucleotides.	we demonstrate that the bacteriophage lambda red functions efficiently recombine linear dna or single-strand oligonucleotides (ss-oligos) into bacteriophage lambda to create specific changes in the viral genome. point mutations, deletions, and gene replacements have been created. while recombineering with oligonucleotides, we encountered other mutations accompanying the desired point mutational change. dna sequence analysis suggests that these unwanted mutations are mainly frameshift deletions i ...	2004	14980479
bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda.	bistability and switching are two important aspects of the genetic regulatory network of lambda phage. positive and negative feedbacks are key regulatory mechanisms in this network. by the introduction of threshold values, the developmental pathway of lambda phage is divided into different stages. if the protein level reaches a threshold value, positive or negative feedback will be effective and regulate the process of development. using this regulatory mechanism, we present a quantitative model ...	2004	14990387
the pko2 linear plasmid prophage of klebsiella oxytoca.	temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only phages n15 and py54 are known to have a linear plasmid prophage with closed hairpin telomeres. we report here the complete nucleotide sequence of the 51,601-bp klebsiella oxytoca linear plasmid pko2, and we demonstrate experimentally that it is also a prophage. we call this bacteriophage phiko2. an analysis of the 64 predicted phiko2 genes indicate that it is a fairly close relative of phage n15; they share ...	2004	14996813
switching the polarity of a bacteriophage integration system.	during lysogenic growth many temperate bacteriophage genomes are integrated into the host's chromosome and efficient integration and excision are therefore an essential part of the phage life cycle. the streptomyces phage phic31 encodes an integrase related to the resolvase/invertases and is evolutionarily and mechanistically distinct from the integrase of phage lambda. we show that during phic31 integration the polarity of the recombination sites, attb and attp, is dependent on the sequences of ...	2004	15009897
distribution of minigenes in the bacteriophage lambda chromosome.	the bar loci in the chromosome of bacteriophage lambda inhibit phage vegetative growth in bacteria defective for peptidyl-trna hydrolase (pth). expression of the bar regions results in accumulation of peptidyl-trna, inhibition of protein synthesis, and arrest of mutant cell growth. these effects have been ascribed to the expression of two-codon orfs present in translatable sequences named 'minigenes' in the lambda bar regions. to investigate the nature, frequency, and distribution of minigenes i ...	2004	15033534
pressure inactivation kinetics of phage lambda ci 857.	inactivation curves of phage lambda ci 857 inactivated by high hydrostatic pressure were obtained at three pressure levels (300, 350, and 400 mpa) in buffered media and ultrahigh-temperature 2% reduced fat milk. pressurization of phage lambda in buffered media at 300 mpa for 300 min, 350 mpa for 36 min, and 400 mpa for 8 min reduced the titer of phage lambda by 7.5, 6.7, and 7.7 log, respectively. pressurization of phage lambda in milk at 300 mpa for 400 min, 350 mpa for 80 min, and 400 mpa for ...	2004	15035365
recruitment of host atp-dependent proteases by bacteriophage lambda.	upon infection of a bacterial cell, the temperate bacteriophage lambda executes a regulated temporal program with two possible outcomes: (1) cell lysis and virion production or (2) establishment of a dormant state, lysogeny, in which the phage genome (prophage) is integrated into the host chromosome. the prophage is replicated passively as part of the host chromosome until it is induced to resume the lytic cycle. in this review, we summarize the evidence that implicates every known atp-dependent ...	2004	15037238
data-based model and parameter evaluation in dynamic transcriptional regulatory networks.	finding the causality and strength of connectivity in transcriptional regulatory networks from time-series data will provide a powerful tool for the analysis of cellular states. presented here is the design of tools for the evaluation of the network's model structure and parameters. the most effective tools are found to be based on evolution strategies. we evaluate models of increasing complexity, from lumped, algebraic phenomenological models to hill functions and thermodynamically derived func ...	2004	15048826
transgenic expression of reca of the spirochetes borrelia burgdorferi and borrelia hermsii in escherichia coli revealed differences in dna repair and recombination phenotypes.	after unsuccessful attempts to recover a viable reca-deficient mutant of the lyme borreliosis agent borrelia burgdorferi, we characterized the functional activities of reca of b. burgdorferi, as well as reca of the relapsing fever spirochete borrelia hermsii and the free-living spirochete leptospira biflexa, in a reca mutant of escherichia coli. as a control, e. coli reca was expressed from the same plasmid vector. dna damage repair activity was assessed after exposure of the transgenic cells to ...	2004	15060027
functional properties of borrelia burgdorferi reca.	functions of the borrelia burgdorferi reca protein were investigated in escherichia coli reca null mutants. complementation with b. burgdorferi reca increased survival of e. coli reca mutants by 3 orders of magnitude at a uv dose of 2,000 microj/cm(2). the viability at this uv dose was about 10% that provided by the homologous reca gene. expression of b. burgdorferi reca resulted in survival of e. coli at levels of mitomycin c that were lethal to noncomplemented hosts. b. burgdorferi reca was as ...	2004	15060028
in vivo non-specific binding of lambda ci and cro repressors is significant.	we propose a thermodynamic model that includes the non-specific binding of the lambda phage regulatory proteins ci and cro. by fitting the model to experimental in vivo data on activities of the two promoters p(rm) and p(r) versus concentration, we estimate the free energy upon non-specific binding to be -4.1+/-0.9 kcal/mol for ci and -4.2+/-0.8 kcal/mol for cro. for concentrations >100 nm of ci or cro, we find that >50% of these proteins are non-specifically bound. in particular, in a lysogen ( ...	2004	15063724
unequal access of chromosomal regions to each other in salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements.	we have investigated the fluidity of the salmonella chromosome architecture using the phage lambda site-specific recombination system as a probe. we determined how chromosome position affects the extent of integrase-mediated recombination between pairs of inversely oriented att sites at various loci. we also investigated the accessibility of each chromosomal att site to an extrachromosomal partner carried on a low-copy plasmid. recombination events were assayed by semi-quantitative polymerase ch ...	2004	15066024
initial cos cleavage of bacteriophage lambda concatemers requires proheads and gpfi in vivo.	the development of bacteriophage lambda and double-stranded dna viruses in general involves the convergence of two separate pathways: dna replication and head assembly. clearly, packaging will proceed only if an empty capsid shell, the prohead, is present to receive the dna, but genetic evidence suggests that proheads play another role in the packaging process. for example, lambda phages with an amber mutation in any head gene or in fi, the gene encoding the accessory packaging protein gpfi, are ...	2004	15066036
crystal structure of the excisionase-dna complex from bacteriophage lambda.	the excisionase (xis) protein from bacteriophage lambda is the best characterized member of a large family of recombination directionality factors that control integrase-mediated dna rearrangements. it triggers phage excision by cooperatively binding to sites x1 and x2 within the phage, bending dna significantly and recruiting the phage-encoded integrase (int) protein to site p2. we have determined the co-crystal structure of xis with its x2 dna-binding site at 1.7a resolution. xis forms a uniqu ...	2004	15066428
genetic immunisation against hepatitis b using whole bacteriophage lambda particles.	mice and rabbits have been vaccinated with whole bacteriophage lambda particles containing a dna vaccine expression cassette under the control of the cmv promoter (enhanced green fluorescent protein [lambda-egfp] or hepatitis b surface antigen [lambda-hbsag]). mice were vaccinated twice intramuscularly (i.m.) with 5x10(9) of lambda-egfp phage (containing 250 ng dna) and exhibited specific anti-egfp responses 28 days post-vaccination. rabbits were vaccinated i.m. with 4x10(10) of lambda-hbsag pha ...	2004	15068849
a homolog of escherichia coli reca in mitochondria of the cellular slime mold dictyostelium discoideum.	the cellular slime mold dictyostelium discoideum expresses a gene encoding a 452-amino-acid polypeptide that is 47% identical to escherichia coli reca. a reca-deficient e. coli, je6651, was transformed by pysn1, which was designed to express the truncated form of the d. discoideum gene, and used in suppression assays. the viability of the transformant, je6651(pysn1), increased following uv irradiation or mitomycin c treatment. phage lambda (red(-) gam(-)), which required reca activity for dna pa ...	2004	15084313
modulation of dna repair and recombination by the bacteriophage lambda orf function in escherichia coli k-12.	the orf gene of bacteriophage lambda, fused to a promoter, was placed in the galk locus of escherichia coli k-12. orf was found to suppress the recombination deficiency and sensitivity to uv radiation of mutants, in a delta(recc ptr recb recd)::p(tac) gam bet exo pae ci deltarecg background, lacking recf, reco, recr, ruvab, and ruvc functions. it also suppressed defects of these mutants in establishing replication of a psc101-related plasmid. compared to orf, the reca803 allele had only small ef ...	2004	15090511
pap: detection of ultra rare mutations depends on p* oligonucleotides: "sleeping beauties" awakened by the kiss of pyrophosphorolysis.	pyrophosphorolysis-activated polymerization (pap) was initially developed to enhance the specificity of allele-specific pcr for detection of known mutations in the presence of a great excess of wild-type allele. the high specificity of pap derives from the serial coupling of activation of a 3' blocked pyrophosphorolysis-activable oligonucleotide (p()) with extension of the unblocked, activated p(). in theory, pap can detect a copy of a single base mutation present in 3x10(11) copies of the wil ...	2004	15108273
involvement of colicin in the limited protection of the colicin producing cells against bacteriophage.	the restriction/modification system is considered to be the most common machinery of microorganisms for protection against bacteriophage infection. however, we found that mitomycin c induced escherichia coli containing cole7-k317 can confer limited protection against bacteriophage m13k07 and lambda infection. our study showed that degree of protection is correlated with the expression level of the cole7 operon, indicating that colicin e7 alone or the colicin e7-immunity protein complex is direct ...	2004	15110756
the sigma 70 subunit of rna polymerase mediates a promoter-proximal pause at the lac promoter.	the sigma(70) subunit of rna polymerase plays an essential role in transcription initiation. in addition, sigma(70) has a critical regulatory role during transcription elongation at the bacteriophage lambda late promoter, lambda p(r'). at this promoter, sigma(70) mediates a pause in early elongation through contact with a dna sequence element in the initially transcribed region that resembles a promoter -10 element. here we provide evidence that sigma(70) also mediates a pause in early elongatio ...	2004	15122345
the emergence of catalytic and structural diversity within the beta-clip fold.	the beta-clip fold includes a diverse group of protein domains that are unified by the presence of two characteristic waist-like constrictions, which bound a central extended region. members of this fold include enzymes like deoxyuridine triphosphatase and the set methylase, carbohydrate-binding domains like the fish antifreeze proteins/sialate synthase c-terminal domains, and functionally enigmatic accessory subunits of urease and molybdopterin biosynthesis protein moea. in this study, we recon ...	2004	15146494
dna binding regions of q proteins of phages lambda and phi80.	bacteriophage lambda gene q protein and the related proteins of other lambdoid phages are transcription antiterminators that interact both with dna in the late gene promoter segment and with rna polymerase subunits. using hybrids between q of lambda and the related q of phage 80, we characterized elements of both q and dna that contribute to the dna binding function. in particular, we found a c-terminal segment of the protein that is responsible for binding specificity and an approximately 15 re ...	2004	15150248
mammalian cell transduction and internalization properties of lambda phages displaying the full-length adenoviral penton base or its central domain.	in recent years a strong effort has been devoted to the search for new, safe and efficient gene therapy vectors. phage lambda is a promising backbone for the development of new vectors: its genome can host large inserts, dna is protected from degradation by the capsid and the ligand-exposed d and v proteins can be extensively modified. current phage-based vectors are inefficient and/or receptor-independent transducers. to produce new, receptor-selective and transduction-efficient vectors for mam ...	2004	15150649
a novel cell-free protein synthesis system.	an efficient cell-free protein synthesis system has been developed using a novel energy-regenerating source. using the new energy source, 3-phosphoglycerate (3-pga), protein synthesis continues beyond 2 h. in contrast, the reaction rate slowed down considerably within 30-45 min using a conventional energy source, phosphoenol pyruvate (pep) under identical reaction conditions. this improvement results in the production of twice the amount of protein obtained with pep as an energy source. we have ...	2004	15163516
genomic characterization of thermophilic geobacillus species isolated from the deepest sea mud of the mariana trench.	the thermophilic strains hta426 and hta462 isolated from the mariana trench were identified as geobacillus kaustophilus and g. stearothermophilus, respectively, based on physiologic and phylogenetic analyses using 16s rdna sequences and dna-dna relatedness. the genome size of hta426 and hta462 was estimated at 3.23-3.49 mb and 3.7-4.49 mb, respectively. the nucleotide sequences of three independent lambda-phage inserts of g. stearothermophilus hta462 have been determined. the organization of pro ...	2004	15168170
dna mapping using microfluidic stretching and single-molecule detection of fluorescent site-specific tags.	we have developed a rapid molecular mapping technology--direct linear analysis (dla)--on the basis of the analysis of individual dna molecules bound with sequence-specific fluorescent tags. the apparatus includes a microfluidic device for stretching dna molecules in elongational flow that is coupled to a multicolor detection system capable of single-fluorophore sensitivity. double-stranded dna molecules were tagged at sequence-specific motif sites with fluorescent bispna (peptide nucleic acid) t ...	2004	15173119
dual role of boxb rna motif in the mechanisms of termination/antitermination at the lambda tr1 terminator revealed in vivo.	rho-dependent transcription termination at the phage lambda tr1 terminator is governed primarily by the upstream rut element that encodes two rna regions ruta and rutb. the two regions are separated by the boxb rna motif, which is believed to be dispensable for rho activity but serves as a binding site for lambda n protein in the antitermination process. by using a minimal in vivo termination system, we show that the intervening boxb rna motif has a double function in the mechanisms of terminati ...	2004	15178249
sequence-specific rho-rna interactions in transcription termination.	the bacteriophage lambda tr1 terminator encodes a region of the nascent cro transcript containing rna residues recognized by termination factor rho. to identify ribonucleotide-protein interactions contributing to termination, a library of reporter gene plasmids was constructed containing predominantly single-nucleotide substitutions in a 24 nt region previously shown to be critical for efficient termination. screening 16 822 bacterial transformants identified 110 terminator mutants, most of whic ...	2004	15181174
selection-subtraction approach (ssa): a universal genetic screening technique that enables negative selection.	screening of expression libraries for bioactive clones that modulate the growth of mammalian cells has been limited largely to positive selections incapable of revealing growth suppressive or lethal genetic elements. we have developed a technique, selection-subtraction approach (ssa), that allows growth-modulating clones to be isolated based on alterations in their relative abundance in growing cell populations that have been transduced with an expression library. ssa utilizes tagged retroviral ...	2004	15187233
identification and characterization of outer membrane proteins g1a and g1b of moraxella catarrhalis.	moraxella catarrhalis is an important cause of otitis media, sinusitis, and lower respiratory tract infections in patients with chronic obstructive pulmonary disease. the purified outer membrane of m. catarrhalis contains a 29 kda band, previously named outer membrane protein g1 (omp g1). polyclonal antiserum to the omp g1 band was used to screen a genomic lambda phage library and the gene for omp g1a was cloned and sequenced. analysis of outer membrane by isoelectric focusing and amino-terminal ...	2004	15193378
bacteriophage lambda is a highly stable dna vaccine delivery vehicle.	the stability of whole bacteriophage lambda particles, used as a dna vaccine delivery system has been examined. phage were found to be highly stable under normal storage conditions. in liquid suspension, no decrease in titre was observed over a 6-month period at 4 and -70 degrees c, and phage stability was unaffected by freeze/thawing. the measured half life of phage in suspension was 36 days at 20 degrees c, 3.4 days at 37 degrees c and 2.3 days at 42 degrees c. freeze drying of a phage suspens ...	2004	15193403
the recognition and modification sites for the bacterial type i restriction systems kpnai, styseai, styseni and stysgi.	using an in vivo plasmid transformation method, we have determined the dna sequences recognized by the kpnai, styseai, styseni and stysgi r-m systems from klebsiella oxytoca strain m5a1, salmonella eastbourne, salmonella enteritidis and salmonella gelsenkirchen, respectively. these type i restriction-modification systems were originally identified using traditional phage assay, and described here is the plasmid transformation test and computer program used to determine their dna recognition sequ ...	2004	15199175
solubilization and delivery by groel of megadalton complexes of the lambda holin.	groel can solubilize membrane proteins by binding them in its hydrophobic cavity when detergent is removed by dialysis. the best-studied example is bacteriorhodopsin, which can bind in the groel chaperonin at two molecules per tetradecamer. applying this approach to the holin and antiholin proteins of phage lambda, we find that both proteins are solubilized by groel, in an atp-sensitive mode, but to vastly different extents. the antiholin product, s107, saturates the chaperonin at six molecules ...	2004	15215521
holliday junction binding and resolution by the rap structure-specific endonuclease of phage lambda.	rap endonuclease targets recombinant joint molecules arising from phage lambda red-mediated genetic exchange. previous studies revealed that rap nicks dna at the branch point of synthetic holliday junctions and other dna structures with a branched component. however, on x junctions incorporating a three base-pair core of homology or with a fixed crossover, rap failed to make the bilateral strand cleavages characteristic of a holliday junction resolvase. here, we demonstrate that rap can mediate ...	2004	15223317
quantitative microfluidic separation of dna in self-assembled magnetic matrixes.	we present an experimental study of the microfluidic electrophoresis of long dna in self-assembling matrixes of magnetic bead columns. results are presented for the rapid separation of lambda-phage, 2lambda-dna, and bacteriophage t4 dna, where separation resolutions greater than 2 between lambda and t4 are achieved in times as short as 150 s. the use of a computer-piloted flow control system and injection results in high reproducibility between separations. we compare the experimentally measured ...	2004	15228353
p2 growth restriction on an rpoc mutant is suppressed by alleles of the rz1 homolog lysc.	escherichia coli strain 397c carries a temperature-sensitive mutation, rpoc397, that removes the last 50 amino acids of the rna polymerase beta' subunit and is nonpermissive for plating of bacteriophage p2. p2 gor mutants productively infect 397c and define a new gene, lysc, encoded by a reading frame that extensively overlaps the p2 lysis accessory gene, lysb. the unusual location of lysc with respect to lysb is reminiscent of the rz/rz1 lysis gene pair of phage lambda. indeed, coexpression of ...	2004	15231796
male mouse meiotic chromosome cores deficient in structural proteins sycp3 and sycp2 align by homology but fail to synapse and have possible impaired specificity of chromatin loop attachment.	the targeted deletion of the meiotic chromosome core component mmsycp3 results in chromosome synaptic failure at male meiotic prophase, extended meiotic chromosomes, male sterility, oocyte aneuploidy and absence of the mmsycp2 chromosome core component. to test the functions of sycp2 and sycp3 proteins in the cores, we determined the effect of their deletion on homology recognition by whole chromosome painting and the effect on chromatin loop attachment to the cores with endogenous and exogenous ...	2004	15237206
polymorphic cytochrome p450 2d6: humanized mouse model and endogenous substrates.	cytochrome p450 2d6 (cyp2d6) is the first well-characterized polymorphic phase i drug-metabolizing enzyme, and more than 80 allelic variants have been identified for the cyp2d6 gene, located on human chromosome 22q13.1. human debrisoquine and sparteine metabolism is subdivided into two principal phenotypes--extensive metabolizer and poor metabolizer--that arise from variant cyp2d6 genotypes. it has been estimated that cyp2d6 is involved in the metabolism and disposition of more than 20% of presc ...	2004	15237854
genotoxicity of acrylamide and glycidamide.	acrylamide, a known rodent carcinogen, is found in the human diet. however, the mechanism by which acrylamide exerts its carcinogenic effects remains unclear.	2004	15240786
translation repression by an rna polymerase elongation complex.	bacteriophage lambda n and bacterial nus proteins together with a unique site nut in the leader of the early viral n gene transcript bind rna polymerase (rnap) and form a highly processive antitermination complex; n bound at nut also represses n translation. in this study, we investigate whether n and nut cause n translation repression as part of the antitermination complex by testing conditions that inhibit the formation of the n-modified transcription complex for their effect on n-mediated tra ...	2004	15255895
a fragile lattice: replacing bacteriophage lambda's head stability gene d with the shp gene of phage 21 generates the mg2+-dependent virus, lambda shp.	phage lambda dna packaging is accompanied by prohead expansion, due to structural changes in gpe, the major capsid protein. rearrangement of the gpe lattice creates binding sites for trimers of gpd, the head stabilization protein. lambda-like phage 21's shp gene is homologous to lambda's d gene. gpd and gpshp share 49% amino acid identity. to ask whether gpshp could stabilize the lambda head shell, we replaced lambda's d gene with shp, creating lambda shp. unlike lambda or 21, lambda shp was str ...	2004	15262493
cloning and sequence analysis of the glyceraldehyde-3-phosphate dehydrogenase gene from the zygomycetes fungus rhizomucor miehei.	rhizomucor miehei is important from a biotechnological aspect in consequence of its content of aspartic proteinase, which has high milk-clotting activity. a genomic library of r. miehei nrrl 5901 has been constructed in a phage (lambda fix ii) vector. the glyceraldehyde-3-phosphate dehydrogenase (gpd) gene was isolated from this library by hybridization of the recombinant phage clones with a gpd-specific gene probe generated by polymerase chain reaction. the complete nucleotide sequence encodes ...	2004	15280645
absence of intrinsic electric conductivity in single dsdna molecules.	the intrinsic dc conductivity of long, individual lambda phage dsdna molecules has been investigated by ultrasensitive low current-voltage-spectroscopy (iv) under ambient conditions and controlled low humidity inert gas atmosphere on microfabricated metal-insulator-metal gap structures. we found a strong dependence of the measured conductivity on the apparent humidity, which we attribute to capillary condensation of water to the immobilized dna molecules, giving rise to additional ionic currents ...	2004	15288944
evidence of bar minigene expression and trna2ile sequestration as peptidyl-trna2ile during lambda bacteriophage development.	lambda bacteriophage development is impaired in escherichia coli cells defective for peptidyl (pep)-trna hydrolase (pth). single-base-pair mutations (bar(-)) that affect translatable two-codon open reading frames named bar minigenes (bari or barii) in the lambda phage genome promote the development of this phage in pth-defective cells (rap cells). when the bari minigene is cloned and overexpressed from a plasmid, it inhibits protein synthesis and cell growth in rap cells by sequestering trna(2)( ...	2004	15292158
light-induced molecular cutting: localized reaction on a single dna molecule.	a short focused pulse of light was used to selectively cut lambda-phage dna molecules at specific restriction sites. lambda dna (48.5 kbp) was stretched and placed in a solution containing a restriction enzyme (sma 1), caged magnesium ions (using a dm-nitrophen complex), and a chelating agent (edta). when a pulse of uv light was directed at a particular location on the stretched dna molecule, magnesium ions were released into solution. a series of binding reactions then occur in which the enzyme ...	2003	14632134
lipoplex thermodynamics: determination of dna-cationic lipoid interaction energies.	an experimental study of the cationic lipid-dna binding affinity is presented. the binding free energy was determined by monitoring lipoplex dissociation under conditions of increasing salt concentration. the primary procedure was based on the extent of quenching by energy transfer of fluorophores on dna molecules by fluorophore on a lipid as these molecules came into close association in the lipoplex. titration calorimetry on the dickerson dodecamer was also done, with results that were in agre ...	2003	14645086
crystallization and preliminary analysis of a dsdna bacteriophage capsid intermediate: prohead ii of hk97.	hk97 prohead ii is an early intermediate in the maturation of hk97, a t = 7 dsdna-tailed bacteriophage related to bacteriophage lambda. previously, selected capsid-protein genes of hk97 were expressed in escherichia coli and spontaneously assembled to form an icosahedral capsid that followed a maturation pathway closely similar to the authentic virion. the crystal structure of the mature hk97 capsid (head ii) made in this way was reported at 3.5 a resolution. additional high-resolution structure ...	2003	14646062
solution structure and stability of the full-length excisionase from bacteriophage hk022.	heteronuclear high-resolution nmr spectroscopy was employed to determine the solution structure of the excisionase protein (xis) from the lambda-like bacteriophage hk022 and to study its sequence-specific dna interaction. as wild-type xis was previously characterized as a generally unstable protein, a biologically active hk022 xis mutant with a single amino acid substitution cys28-->ser was used in this work. this substitution has been shown to diminish the irreversibility of xis denaturation an ...	2003	14653811
tracking ecoki and dna fifty years on: a golden story full of surprises.	1953 was a historical year for biology, as it marked the birth of the dna helix, but also a report by bertani and weigle on 'a barrier to infection' of bacteriophage lambda in its natural host, escherichia coli k-12, that could be lifted by 'host-controlled variation' of the virus. this paper lay dormant till nobel laureate arber and phd student dussoix showed that the lambda dna was rejected and degraded upon infection of different bacterial hosts, unless it carried host-specific modification o ...	2003	14654681
site-specific recombination by the dde family member mobile element is30 transposase.	dna rearrangements carried out by site-specific recombinases and transposases (tpases) show striking similarities despite the wide spectrum of the catalytic mechanisms involved in the reactions. here, we show that the bacterial insertion sequence (is)30 element can act similarly to site-specific systems. we have developed an inversion system using is30 tpase and a viable lambda phage, where the integration/excision system is replaced with is30. both models have been proved to operate analogously ...	2003	14665688
[recombineering and its application].	driven by the need of functional genomics, a homologous recombination-based, highly efficient genetic engineering system that termed "recombineering" has recently been developed. recombineering has been defined as a genetic engineering with phage-encoded recombination function that utilizes short homologies, a convenient term to describe homologous-dependent, recombination-mediated, genetic engineering. the bacteriophage lambda red recombination system has critical differences from standard e. c ...	2003	14669518
tumor-specific immunological recognition of frameshift-mutated peptides in colon cancer with microsatellite instability.	colorectal cancers with microsatellite instability (msi+ crcs) caused by dysfunction of dna mismatch repair have unique clinicopathological characteristics including good prognosis with t-cell infiltration in tumor. to identify tumor antigens that induce immune response against msi+ crc, serex (serological analysis of recombinant cdna expression cloning) was applied. by screening a lambda phage cdna library constructed from three msi+ crc cell lines with serum from a patient with msi+ crc with a ...	2003	14500396
genetics of cosq, the dna-packaging termination site of phage lambda: local suppressors and methylation effects.	the cos site of the bacteriophage lambda chromosome contains the sites required for dna processing and packaging during virion assembly. cos is composed of three subsites, cosq, cosn, and cosb. cosq is required for the termination of chromosome packaging. previous studies have shown cosq mutations to be suppressed in three ways: by a local suppressor within cosq; by an increase in the length of the lambda chromosome; and by missense mutations affecting the prohead's portal protein, gpb. in the f ...	2003	14504214
purification, biochemical characterization, and cdna cloning of a glutathione s-transferase from the red imported fire ant, solenopsis invicta.	a glutathione s-transferase (gst) was purified 266-fold from adult workers of the red imported fire ant, solenopsis invicta (hymenoptera: formicidae) by affinity chromatography and preparative isoelectric focusing. the purified enzyme appeared as a single band on sds-page and had a mr of 25.5 kda. steady state kinetics assays of the enzyme with 1-chloro-2,4-dinitrobenzene as substrate were conducted. the vmax, km cdnb, km gsh, kcat, kcat/km cdnb, and kcat/km gsh for the purified fire ant gst wer ...	2003	14505691
the molecular basis of co-operative dna binding between lambda integrase and excisionase.	higher-order nucleoprotein complexes often stabilize catalytic proteins in appropriate conformations for optimal activity and contribute to regulation during reactions requiring association of proteins and dna. formation of such complexes, known as intasomes, is required for site-specific recombination catalysed by bacteriophage lambda integrase protein (int). int-catalysed recombination is regulated by a second bacteriophage-encoded protein, excisionase (xis), which both stimulates excision and ...	2003	14507366
general strategy for broadening adenovirus tropism.	in spite of its broad host range, adenovirus type 5 (ad5) transduces a number of clinically relevant tissues and cell types inefficiently, mostly because of low expression of the coxsackievirus-adenovirus receptor (car). to improve gene transfer to such cells, we modified the ad5 fiber knob to recognize novel receptors. we expressed a functional ad5 fiber knob domain on the capsid of phage lambda and employed this display system to construct a large collection of ligands in the hi loop of the ad ...	2003	14512557
subtraction of cap-trapped full-length cdna libraries to select rare transcripts.	the normalization and subtraction of highly expressed cdnas from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cdna encyclopedia, but these methods have not been suitable for limited rna materials. to normalize and subtract full-length cdna libraries derived from limited quantities of total rna, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cdna libraries that avoi ...	2003	14513556
sequence dependent dna-mediated conduction.	we report on coherent charge transport studies in periodic poly(dg)-poly(dc) and aperiodic lambda-phage dna sequences. the extent and efficiency of charge transfer is discussed as a function of sequence dependent energetics, of temperature dependent base-base couplings, and in relation with experiments.	2003	14525509
the n-terminus is unstructured, but not dynamically disordered, in the complex between hk022 nun protein and lambda-phage boxb rna hairpin.	the nun protein of lambdoid phage hk022 excludes lambda-phage superinfection by blocking expression of genes downstream from the lambda nut sequences. heteronuclear nmr studies have been performed on a nun peptide comprising residues 1-49 bound to the nutr boxb rna. the pattern of (13)c chemical shifts indicates that the arginine-rich motif of nun forms an induced alpha-helix, consisting of residues 23-43, when bound to boxb rna, consistent with the structure of a shorter (residues 22-44) nun pe ...	2003	14550553
mini-lambda: a tractable system for chromosome and bac engineering.	the bacteriophage lambda (lambda) recombination system red has been used for engineering large dna fragments cloned into p1 and bacterial artificial chromosomes (bac or pac) vectors. so far, this recombination system has been utilized by transferring the bac or pac clones into bacterial cells that harbor a defective lambda prophage. here we describe the generation of a mini-lambda dna that can provide the red recombination functions and can be easily introduced by electroporation into any e. col ...	2003	14557065
nucleic acid purification using microfabricated silicon structures.	a microfluidic device has been designed, fabricated and tested for its ability to purify bacteriophage lambda dna and bacterial chromosomal dna, a necessary prerequisite for its incorporation into a biosensor. this device consists of a microfabricated channel in which silica-coated pillars were etched to increase the surface area within the channel by 300-600%, when the etch depth is varied from 20 to 50 microm. dna was selectively bound to these pillars in the presence of the chaotropic salt gu ...	2003	14558999
genome sequences of two closely related vibrio parahaemolyticus phages, vp16t and vp16c.	two bacteriophages of an environmental isolate of vibrio parahaemolyticus were isolated and sequenced. the vp16t and vp16c phages were separated from a mixed lysate based on plaque morphology and exhibit 73 to 88% sequence identity over about 80% of their genomes. only about 25% of their predicted open reading frames are similar to genes with known functions in the genbank database. both phages have cos sites and open reading frames encoding proteins closely related to coliphage lambda's termina ...	2003	14563879
bacteriophage st64b, a genetic mosaic of genes from diverse sources isolated from salmonella enterica serovar typhimurium dt 64.	the complete sequence of the double-stranded dna (dsdna) genome of the salmonella enterica serovar typhimurium st64b bacteriophage was determined. the 40,149-bp genomic sequence of st64b has an overall g+c content of 51.3% and is distinct from that of p22. the genome architecture is similar to that of the lambdoid phages, particularly that of coliphage lambda. most of the putative tail genes showed sequence similarity to tail genes of mu, a nonlambdoid phage. in addition, it is likely that these ...	2003	14563886
the product of the bacteriophage lambda w gene: purification and properties.	gene w is one of the 10 genes that control the morphogenesis of the bacteriophage lambda head. the morpho genesis of the phage lambda head proceeds through the synthesis of an intermediate assembly called the prohead. this is an empty shell into which the bacteriophage dna is introduced--packaged--by the phage enzyme dna terminase. the product of w (gpw) acts after dna packaging, but before the addition of another phage product, gene product fii, and before the addition of tails. the role of gpw ...	2003	14569303
twinned crystals and anomalous phasing.	merohedral or pseudomerohedral twinning of crystals cannot be identified from inspection of the diffraction patterns. several methods for the identification of twinning and the estimation of the twin fraction are suitable for macromolecular crystals and all are based on the statistical properties of the measured diffraction intensities. if the crystal twin fraction is estimated and is not too close to 0.5, the diffraction data can be detwinned; that is, related to the individual crystal specimen ...	2003	14573956
analysis of noise in quorum sensing.	noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. like the lambda switch, bacterial quorum sensing (qs) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in qs circuit operation. therefore, a detailed analysis of the noise behavior of qs systems is needed. we have developed a set of tools generally applicable to the analysis of gene circ ...	2003	14583119
cosmid-based system for transient expression and absolute off-to-on transcriptional control of escherichia coli genes.	cosmids are plasmids that contain the phage lambda sequences (cos) required for packaging of the phage dna into the virion. induction of a lambda prophage in an escherichia coli strain carrying a cosmid results in lysates containing phage particles that are filled with cosmid dna. however, the lysates also contain a large excess of infectious phage particles which complicate use of the packaged cosmids. i report that cosmids packaged by induction of a strain carrying a prophage with an altered c ...	2003	14594824
use of acridine orange staining for the detection of rotavirus rna in polyacrylamide gels.	acridine orange is a metachromatic intercalator used extensively in histochemistry to differentiate double- from single-stranded (ds, ss) nucleic acid by the emission of green and red fluorescence, respectively, under ultraviolet light. in the present study we standardised a protocol in order to use acridine orange to detect rotavirus ds rna in polyacrylamide gels and compared it to silver and ethidium bromide staining. we demonstrated that the simplest and best condition was attained when gels ...	2003	14599676
identification of factors influencing strand bias in oligonucleotide-mediated recombination in escherichia coli.	recombinogenic engineering methodology, also known as recombineering, utilizes homologous recombination to create targeted changes in cellular dna with great specificity and flexibility. in escherichia coli, the red recombination system from bacteriophage lambda has been used successfully to modify both plasmid and chromosomal dna in a highly efficient manner, using either a linear double-stranded dna fragment or a synthetic single-stranded oligonucleotide (sso). the current model for red/sso-me ...	2003	14602928
high-density functional display of proteins on bacteriophage lambda.	we designed a bacteriophage lambda system to display peptides and proteins fused at the c terminus of the head protein gpd of phage lambda. dna encoding the foreign peptide/protein was first inserted at the 3' end of a dna segment encoding gpd under the control of the lac promoter in a plasmid vector (donor plasmid), which also carried lox p(wt) and lox p(511) recombination sequences. cre-expressing cells were transformed with this plasmid and subsequently infected with a recipient lambda phage ...	2003	14607116
improved gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions.	the use of simple theoretical models has provided a considerable contribution to our present understanding of the means by which proteins adopt their native fold from the plethora of available unfolded states. a common assumption in building computationally tractable models has been the neglect of stabilizing non-native interactions in the class of models described as "gō-like." the focus of this study is the characterization of the folding of a number of proteins via a gō-like model, which aims ...	2003	14607121
the role of dna recombination in herpes simplex virus dna replication.	in many organisms the processes of dna replication and recombination are closely linked. for instance, in bacterial and eukaryotic systems, replication forks can become stalled or damaged, in many cases leading to the formation of double stranded breaks. replication restart is an essential mechanism in which the recombination and repair machinery can be used to continue replication after such a catastrophic event. dna viruses of bacteria such as lambda and t4 also rely heavily on dna recombinati ...	2003	14609200
disorder-order transition of lambda cii promoted by low concentrations of guanidine hydrochloride suggests a stable core and a flexible c-terminus.	the cii protein of bacteriophage lambda, which activates the synthesis of the lambda repressor, plays a key role in the lysis-lysogeny switch. cii has a small in vivo half-life due to its proteolytic susceptibility, and this instability is a key component for its regulatory role. the structural basis of this instability is not known. while studying guanidine hydrochloride-assisted unfolding of cii, we found that low concentrations of the chaotrope (50-500 microm) have a considerable effect on th ...	2003	14622272
molecular recognition in helix-loop-helix and helix-loop-helix-leucine zipper domains. design of repertoires and selection of high affinity ligands for natural proteins.	helix-loop-helix (hlh) and helix-loop-helix-leucine zipper (hlhzip) are dimerization domains that mediate selective pairing among members of a large transcription factor family involved in cell fate determination. to investigate the molecular rules underlying recognition specificity and to isolate molecules interfering with cell proliferation and differentiation control, we assembled two molecular repertoires obtained by directed randomization of the binding surface in these two domains. for thi ...	2003	12514181
mismatch repair in the antimutator escherichia coli mud.	antimutators are genetic mutants that produce mutations at reduced rates compared to the wild type strain. they are interesting because they may provide insights into the mechanisms by which spontaneous mutations occur. we have investigated a reported antimutator strain of escherichia coli termed mud for its possible mechanism. the mud strain exhibits a decrease in both spontaneous mutagenesis and mutability with alkylated agents and base analogs. these types of dna lesions are known to be the s ...	2003	12517409
genomic and molecular characterization of cl-43 and its proximal promoter.	collectins are part of the innate immune system as they bind nonself glycoconjugates on the surface of microorganisms and inhibit infection by direct neutralization, agglutination or opsonization of the invaders. conglutinin and cl-43 are serum proteins that have only been found and characterized in bovidae. we have studied molecular and genomic characteristics of cl-43 to identify polymorphisms that might be associated with disease-susceptible phenotypes or other traits in cattle, and to elucid ...	2003	12527419
cloning and characterization of a novel member of the human atf/creb family: atf2 deletion, a potential regulator of the human dna polymerase beta promoter.	the solitary camp response element (cre)1 in the human dna polymerase beta (beta-pol) core promoter plays a key role in both basal expression and the dna-alkylating agent response of the promoter. to further understand the role of the cre in the regulation of this promoter, we searched for novel cre-binding proteins by using a 32p-labeled beta-pol cre oligodeoxynucleotide and a human cdna expression library constructed in phage lambda. a total of fourteen phage clones were isolated, correspondin ...	2003	12909347
activation of site-specific dna integration in human cells by a single chain integration host factor.	the heterodimeric integration host factor (ihf) is a site-specific dna-binding and dna-bending protein from escherichia coli. it plays essential roles in a variety of dna transactions including recombination, transcription and dna replication. ihf's ability for concerted binding and bending of dna is key to its biological function. here we report the design, characterization and application of a single polypeptide chain ihf, termed scihf2. in a novel approach for protein engineering, we inserted ...	2003	12930965
transposition and targeting of the prokaryotic mobile element is30 in zebrafish.	we provide evidence that a prokaryotic insertion sequence (is) element is active in a vertebrate system. the transposase of escherichia coli element is30 catalyzes both excision and integration in extrachromosomal dna in zebrafish embryos. the transposase has a pronounced target preference, which is shown to be modified by fusing the enzyme to unrelated dna binding proteins. joining the transposase to the ci repressor of phage lambda causes transposition primarily into the vicinity of the lambda ...	2003	12935884
single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder.	we used a multiplexed approach based on flow-stretched dna to monitor the enzymatic digestion of lambda-phage dna by individual bacteriophage lambda exonuclease molecules. statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate dna. by relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the dna ...	2003	12947199
the mobile element is1207 of brevibacterium lactofermentum atcc21086: isolation and use in the construction of tn5531, a versatile transposon for insertional mutagenesis of corynebacterium glutamicum.	is1207 is the insertion most frequently found among the spontaneous mutations that abolish the activity of an escherichia coli phage lambda ci gene integrated in the corynebacterium brevibacterium lactofermentum atcc21086 genome. we examined the transposition of transposon-like structures composed of a selective kanamycin resistance gene (aph3), and one or two is1207 sequences. one of these, the tn5531 transposon, transposed efficiently in corynebacterium glutamicum. a replicative and a non-repl ...	2003	12948647
real-time pcr provides improved detection and titer determination of bacteriophage.	the plaque assay is the traditional method for the quantification of bacteriophage, particularly for lambda cloning vectors. unfortunately, this technique is fraught with procedural difficulties, and the quality of the data obtained from this "gold standard" assay may be inaccurate due to the subjective interpretation of the results. the application of quantitative real-time pcr (qpcr) technology can address these issues and be a more accurate platform to evaluate phage growth conditions and qua ...	2003	12951778
toxicity of the bacteriophage lambda cii gene product to escherichia coli arises from inhibition of host cell dna replication.	the bacteriophage lambda cii gene codes for a transcriptional activator protein which is a crucial regulator at the stage of the "lysis-versus-lysogeny" decision during phage development. the cii protein is highly toxic to the host, escherichia coli, when overproduced. however, the molecular mechanism of this toxicity is not known. here we demonstrate that dna synthesis, but not total rna synthesis, is strongly inhibited in cii-overexpressing e. coli cells. the toxicity was also observed when th ...	2003	12954227
baculovirus alkaline nuclease possesses a 5'-->3' exonuclease activity and associates with the dna-binding protein lef-3.	alkaline nuclease (an) of the autographa californica multiple-capsid nucleopolyhedrovirus (acmnpv) (open reading frame 133) was expressed in recombinant baculovirus as a his(6)-tagged fusion and purified by sequential chromatography on ni-nta-agarose, deae-toyopearl, and heparin-sepharose. at all stages of purification, acmnpv an was found to copurify with a 44-kda polypeptide which was identified as the baculovirus single-stranded dna (ssdna)-binding (ssb) protein, lef-3. sedimentation analysis ...	2003	12551981
generation and characterization of cdna clones from sarcoptes scabiei var. hominis for an expressed sequence tag library: identification of homologues of house dust mite allergens.	molecular studies on scabies, a disease of considerable human and veterinary significance, have been limited because of the difficulty of obtaining the causative organism sarcoptes scabiei, the "itch mite." we have used skin from the bedding of crusted scabies patients as a source of mites for the construction of libraries of cdnas from s. scabiei var. hominis in the bacteriophage lambda vector lambdazap express. sequences of 145 clones established that the libraries predominantly contain sequen ...	2003	12556150
design of peptide that recognizes double-stranded dna.	a novel molecular tool for double-stranded (ds) dna detection using synthetic peptide is described. the peptide was designed based on the dna binding domain of the lambda phage cro repressor (cro). the designed peptides contain helix-turn-helix (hth), which is dna binding motif. a cyclic peptide and a mutant peptide based on cro were also designed, and the resulting affinity for dsdna was increased. furthermore, native amino acids of the peptide were replaced with arginine to increase the affini ...	2003	12558048
genetically modified filamentous phage as bactericidal agents: a pilot study.	to evaluate the ability of a filamentous phage encoding lethal proteins to kill bacteria without host-cell lysis.	2003	12969496
rapid detection of yersinia pestis with multiplex real-time pcr assays using fluorescent hybridisation probes.	the objective of the present study was to establish a system of real-time polymerase chain reactions (pcrs) for the specific detection of yersinia pestis using the lightcycler (lc) instrument. twenty-five strains of y. pestis, 94 strains of other yersinia species and 33 clinically relevant bacteria were investigated. assays for the 16s rrna gene target and the plasminogen activator gene (resides on the 9.5-kb plasmid) and for the y. pestis murine toxin gene and the fraction 1 antigen gene (both ...	2003	13129646
chromatographic behaviour and purification of linear lambda phage and plasmid dna molecules on 2-hydroxyethyl methacrylate-ethylene dimethacrylate-based supports.	the hema-bio 1000 support, which is based on a copolymer of 2-hydroxyethyl methacrylate and ethylene dimethacrylate, was used for separation of lambda dna and its fragments and plasmid pbr322 dna. the separation of fragments greater than 6.6 kbp was demonstrated according to the slalom chromatography mechanism on column for size-exclusion chromatography in the case of linear lambda dna fragments. the influence of particle size of column packing, mobile phase rate, and kcl concentration in mobile ...	2003	13677661
biochemical characterization of bacteriophage lambda genome packaging in vitro.	bacteriophage lambda has been extensively studied, and the abundance of genetic and biochemical information available makes this an ideal model system to study virus dna packaging at the molecular level. limited in vitro packaging efficiency has hampered progress toward this end, however. it has been suggested that limited packaging efficiency is related to poor activity of purified procapsids. we describe the construction of a vector that expresses lambda procapsids with a yield that is 40-fold ...	2003	12573573
dna unzipped under a constant force exhibits multiple metastable intermediates.	single molecule studies, at constant force, of the separation of double-stranded dna into two separated single strands may provide information relevant to the dynamics of dna replication. at constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. here, we report previously uncharacterized observations of this striki ...	2003	12574500
comparative analysis of chloroplast dna in pyrus species: physical map and gene localization.	a physical map of chloroplast dna (cpdna) of pear [pyrus ussuriensis var. hondoensis (nakai et kikuchi) rehder] was constructed using five restriction enzymes, sali, xhoi, bamhi, saci and psti. this information will make it possible to investigate the phylogenetic relationships between pyrus species. pear cpdna was found to be a circular molecule with a total size of about 156 kb in which two inverted repeats of 24.8 kb divide the molecule into small (17 kb) and large (90 kb) single-copy regions ...	2003	12582856
molecular characterization of mitomycin c-induced large deletions and tandem-base substitutions in the bone marrow of gpt delta transgenic mice.	deletion mutations constitute an important class of mutations that may result in a variety of human diseases, including cancer. although many chemicals and ionizing radiations induce deletions, this class of mutation has been poorly characterized at the molecular level, particularly in vivo. here we report the molecular nature of deletions as well as base substitutions induced by antitumor antibiotic mitomycin c (mmc) in the bone marrow using a novel transgenic mouse, gpt delta. in this mouse mo ...	2003	12588188
protein folding coupled to dna binding in the catalytic domain of bacteriophage lambda integrase detected by mass spectrometry.	bacteriophage lambda integrase (lambda-int) is the prototypical member of a large family of enzymes that catalyze site-specific dna recombination via single-strand cleavage and the formation of a holliday junction intermediate. crystallographic and biochemical evidence indicate that substantial conformational change (i.e., folding) in the catalytic domain of the protein is required for substrate recognition and catalysis. we have examined the solution conformation of the catalytic domain (c170) ...	2003	12592032
new restriction enzymes discovered from escherichia coli clinical strains using a plasmid transformation method.	the presence of restriction enzymes in bacterial cells has been predicted by either classical phage restriction-modification (r-m) tests, direct in vitro enzyme assays or more recently from bacterial genome sequence analysis. we have applied phage r-m test principles to the transformation of plasmid dna and established a plasmid r-m test. to validate this test, six plasmids that contain bamhi fragments of phage lambda dna were constructed and transformed into escherichia coli strains containing ...	2003	12595571
retroevolution of lambda cro toward a stable monomer.	the cro protein from bacteriophage lambda has a dimeric alpha+beta fold that evolved from an ancestral all-alpha monomer. the sequence mutations responsible for this dramatic structural evolution are unknown. here we use analysis of sequence alignments to show that ala-33, a small side chain in the hydrophobic "ball-and-socket" dimer interface of lambda cro, was a much larger tryptophan side chain at a previous point in evolution. the retroevolutionary lambda cro-a33w mutant shows a 10-fold redu ...	2003	12598646
a spring-loaded state of nusg in its functional cycle is suggested by x-ray crystallography and supported by site-directed mutants.	transcription factor nusg is present in all prokaryotes, and orthologous proteins have also been identified in yeast and humans. nusg contains a 27-residue kow motif, found in ribosomal protein l24 where it interacts with rrna. nusg in escherichia coli (ecnusg) is an essential protein and functions as a regulator of rho-dependent transcription termination, phage lambda n and rrna transcription antitermination, and phage hk022 nun termination. relative to ecnusg, aquifex aeolicus nusg (aanusg) an ...	2003	12600194
forces and pressures in dna packaging and release from viral capsids.	in a previous communication (kindt et al., 2001) we reported preliminary results of brownian dynamics simulation and analytical theory which address the packaging and ejection forces involving dna in bacteriophage capsids. in the present work we provide a systematic formulation of the underlying theory, featuring the energetic and structural aspects of the strongly confined dna. the free energy of the dna chain is expressed as a sum of contributions from its encapsidated and released portions, e ...	2003	12609865
genetic fate of recombinant adeno-associated virus vector genomes in muscle.	recombinant adeno-associated virus (raav) vectors are promising human gene transfer vectors, because they mediate long-term gene expression in vivo. the vector dna form responsible for sustained gene expression has not been clearly defined, but it has been presumed that the vector integrates to some degree and persists in this manner. using two independent methods, we were unable to identify raav integrants in mouse muscle. in the first approach, we were unable to recover host cell-vector dna ju ...	2003	12610125