Publications

mutation affecting head antigen of bacteriophage t3.		1962	14490971
sonis reactivation of antiserum-neutralized bacteriophage t3.		1952	14938310
characterization of bacteriophage t3 dna ligase.	dna ligases of bacteriophage t4 and t7 have been widely used in molecular biology for decades, but little is known about bacteriophage t3 dna ligase. here is the first report on the cloning, expression and biochemical characterization of bacteriophage t3 dna ligase. the polyhistidine-tagged recombinant t3 dna ligase was shown to be an atp-dependent enzyme. the enzymatic activity was not affected by high concentration of monovalent cations up to 1 m, whereas 2 mm atp could inhibit its activity by ...	2004	15113838
transcription arrest caused by long nascent rna chains.	the transcription process is highly processive. however, specific sequence elements encoded in the nascent rna may signal transcription pausing and/or termination. we find that under certain conditions nascent rna chains can have a strong and apparently sequence-independent inhibitory effect on transcription. using phage t3 rna polymerase (t3 rnap) and covalently closed circular (cccdna) dna templates that did not contain any strong termination signal, transcription was severely inhibited after ...	2004	15716026
transcriptional inhibition by an oxidized abasic site in dna.	2-deoxyribonolactone (dl) is an oxidized abasic site in dna that can be induced by gamma-radiolysis, ultraviolet irradiation, and numerous antitumor drugs. although this lesion is incised by ap endonucleases, suggesting a base-excision repair mechanism for dl removal, subsequent excision and repair synthesis by dna polymerase beta is inhibited due to accumulation of a protein-dna cross-link. this raises the possibility that additional repair pathways might be required to eliminate dl from the ge ...	2006	16485899
compensatory evolution in response to a novel rna polymerase: orthologous replacement of a central network gene.	a bacteriophage genome was forced to evolve a new system of regulation by replacing its rna polymerase (rnap) gene, a central component of the phage developmental pathway, with that of a relative. the experiment used the obligate lytic phage t7 and the rnap gene of phage t3. t7 rnap uses 17 phage promoters, which are responsible for all middle and late gene expression, dna replication, and progeny maturation, but the enzyme has known physical contacts with only 2 other phage proteins. t3 rnap wa ...	2007	17220516
visualization of bacteriophage t3 capsids with dna incompletely packaged in vivo.	the tightly packaged double-stranded dna (dsdna) genome in the mature particles of many tailed bacteriophages has been shown to form multiple concentric rings when reconstructed from cryo-electron micrographs. however, recent single-particle dna packaging force measurements have suggested that incompletely packaged dna (ipdna) is less ordered when it is shorter than approximately 25% of the full genome length. the study presented here initially achieves both the isolation and the ipdna length-ba ...	2008	18952096
a likely pathway for formation of mobile group i introns.	mobile group i introns are rna splicing elements that have been invaded by endonuclease genes. these endonucleases facilitate intron mobility by a unidirectional, duplicative gene-conversion process known as homing [1]. survival of the invading endonuclease depends upon its ability to promote intron mobility. therefore, the endonuclease must either quickly change its cleavage specificity to match the site of intron insertion, or it must already be preadapted to cleave this sequence. here we show ...	2009	19200727
compensatory evolution for a gene deletion is not limited to its immediate functional network.	genetic disruption of an important phenotype should favor compensatory mutations that restore the phenotype. if the genetic basis of the phenotype is modular, with a network of interacting genes whose functions are specific to that phenotype, compensatory mutations are expected among the genes of the affected network. this perspective was tested in the bacteriophage t3 using a genome deleted of its dna ligase gene, disrupting dna metabolism.	2009	19445716
dna packaging-associated hyper-capsid expansion of bacteriophage t3.	evidence that in vivo bacteriophage t3 dna packaging includes capsid hyper-expansion that is triggered by lengthening of incompletely packaged dna (ipdna) is presented here. this evidence includes observation that some of the longer ipdnas in t3-infected cells are packaged in ipdna-containing capsids with hyper-expanded outer shells (he ipdna-capsids). in addition, artificially induced hyper-expansion is observed for the outer shell of a dna-free capsid. detection and characterization of he ipdn ...	2010	20122936
metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity.	the human oropharynx is a reservoir for many potential pathogens, including streptococcal species that cause endocarditis. although oropharyngeal microbes have been well described, viral communities are essentially uncharacterized. we conducted a metagenomic study to determine the composition of oropharyngeal dna viral communities (both phage and eukaryotic viruses) in healthy individuals and to evaluate oropharyngeal swabs as a rapid method for viral detection. viral dna was extracted from 19 p ...	2011	20547834
the rnase protection assay.	a sensitive method for quantitation of mrna in gene transfer studies is mrna protection using end-labeled dna probes. in addition, this technique also provides structural information about the transcript under study (1). in vitro labeled antisense rnacan be used as an alternative to end-labeled dna probes (2,3. rna probes have attained wide popularity because of the ease of synthesis and high yield of probe in a labeling reaction. this has been made possible by the recent characterization of sin ...	1991	21416363
a hypothesis for bacteriophage dna packaging motors.	the hypothesis is presented that bacteriophage dna packaging motors have a cycle comprised of bind/release thermal ratcheting with release-associated dna pushing via atp-dependent protein folding. the proposed protein folding occurs in crystallographically observed peptide segments that project into an axial channel of a protein 12-mer (connector) that serves, together with a coaxial atpase multimer, as the entry portal. the proposed cycle begins when reverse thermal motion causes the connector' ...	2010	21994710
agarose gel electrophoresis reveals structural fluidity of a phage t3 dna packaging intermediate.	we find a new aspect of dna packaging-associated structural fluidity for phage t3 capsids. the procedure is (i) glutaraldehyde cross-linking of in vivo dna packaging intermediates for the stabilization of structure and then (ii) determining effective radius by two-dimensional agarose gel electrophoresis (2d-age). the intermediates are capsids with incompletely packaged dna (ipdna) and without an external dna segment; these intermediates are called ipdna-capsids. we initially increase the product ...	2012	22222979