Publications

site-specific mutagenesis of t4 gene 32: the role of tyrosine residues in protein-nucleic acid interactions.	bacteriophage t4 gene 32 encodes a single-stranded dna (ssdna) binding protein (gp32) required for t4 dna replication, recombination, and repair. previous physicochemical studies on gp32 and other ssdna binding proteins have suggested that binding may involve hydrophobic interactions that result from the close approach of several aromatic amino acid side chains with the nucleic acid bases. in the case of gp32, five tyrosines and two phenylalanines have previously been implicated in gp32.ssdna co ...	1989	2684276
evidence for a net-like organization of lipopolysaccharide particles in the escherichia coli outer membrane.	cell wall lps of escherichia coli are organized as particles which are visible in the electron microscope, after treatment of the wall with alkali. we now describe alkali treated walls of three e. coli strains with differences in susceptibility to the t4 phage infection. strain cr63, a usual host for the t4 phage, shows the lps particles on the murein layer. these particles are absent in alkali treated cell walls of the strain w. walls of this strain are broken during t4 infection and phages can ...	1989	2689280
dna polymerase alpha activity is not affected by protein kinases or alkaline phosphatase.	recent studies with crude or partially purified cell extracts have suggested that dna polymerase alpha activity may be regulated by enzymatic phosphorylation. to further investigate these findings, we have examined the effects of protein kinases and phosphatases on highly purified dna polymerase alpha from mouse cells. incubation of dna polymerase alpha with a variety of protein kinases, including protein kinase c, had no effect on polymerase activity. in addition, treatment of the polymerase wi ...	1989	2930569
transcript analyses of the uvsx-40-41 region of bacteriophage t4. changes in the rna as infection proceeds.	the bacteriophage t4 genes uvsx (recombination protein), 40 (stimulates head formation), and 41 (dna replication protein, part of the primase-helicase) are located together on the t4 genome (5'----3' uvsx-40-41). previous analyses have indicated that all three proteins are expressed within 5 min after infection and that the level of 41 protein is less than that of uvsx. the mapping of transcripts from this region (reported here) shows that this expression arises from polycistronic messages detec ...	1989	2668289
site-directed mutagenesis of the t4 endonuclease v gene: mutations which enhance enzyme specific activity at low salt concentrations.	previous structure/function analyses of the dna repair enzyme, t4 endonuclease v, have suggested that the extreme carboxyl portion of the enzyme is associated with pyrimidine dimer-specific binding (recinos and lloyd, and stump and lloyd, biochemistry 27:1832-1838 and 1839-1843, 1988, respectively). within the final 11 amino acids there are 5 aromatic, 2 basic, and no acidic residues and it has been proposed that these residues stack with and electrostatically interact with the kinked dna at the ...	1989	2695926
monofunctional angular furocoumarins: sequence specificity in dna photobinding of 6,4,4'-trimethylangelicin and other angelicins.	the sequence specificity in the photoreaction (365 nm) of 6,4,4'-trimethylangelicin (tma) with dna fragments of the lac i gene of escherichia coli was studied by using dna sequencing methodology. in order to map the sites of tma photoaddition, we took advantage of the (3'-5') exonuclease activity associated with t4 dna polymerase, which is blocked by bulky adducts, such as furocoumarin photoadducts. a quantitative analysis of the sites of photoaddition is reported. tma was demonstrated to photor ...	1989	2762383
bacteriophage t4 early promoter regions. consensus sequences of promoters and ribosome-binding sites.	twenty-nine early promoters from bacteriophage t4 and 14 early promoters from bacteriophage t6 were isolated using vector m13hdl17, a promoterless derivative of m13mp8 carrying a linker sequence, the bacteriophage lambda-terminator tr1, and the lacz' gene including part of its ribosome-binding site. the consensus sequence for the t4 promoters is: (sequence; see text). ribosome-binding sites of t4 share the sequence: 5'...g.ggaga..aa.atgaa.a...3' the consensus sequence of the t4 early promoter re ...	1989	2810355
bacteriophage t4 nrda and nrdb genes, encoding ribonucleotide reductase, are expressed both separately and coordinately: characterization of the nrdb promoter.	we examined the expression of the bacteriophage t4 nrda and nrdb genes, which encode the alpha 2 and beta 2 subunits, respectively, of ribonucleoside diphosphate reductase, the first committed enzyme in the pathway of synthesis of the deoxyribonucleoside triphosphates. t4 nrda, located 700 bp upstream from nrdb, has been shown previously to be transcribed by two major transcripts: a prereplicative, polycistronic message, tu, orginating at an immediate-early promoter, pe, that is 3.5 kb upstream ...	1990	2228963
selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (mad): a vehicle for direct determination of three-dimensional structure.	an expression system has been established for the incorporation of selenomethionine into recombinant proteins produced from plasmids in escherichia coli. replacement of methionine by selenomethionine is demonstrated at the level of 100% for both t4 and e. coli thioredoxins. the natural recombinant proteins and the selenomethionyl variants of both thioredoxins crystallize isomorphously. anomalous scattering factors were deduced from synchrotron x-ray absorption measurements of crystals of the sel ...	1990	2184035
stable albicidin resistance in escherichia coli involves an altered outer-membrane nucleoside uptake system.	albicidin blocked dna synthesis in intact cells of a pola- enda- escherichia coli strain, and in permeabilized cells supplied with all necessary precursor nucleotides, indicating a direct effect on prokaryote dna replication. replication of phages t4 and t7 was also blocked by albicidin in albicidin-sensitive (albs) but not in albicidin-resistant (albr) e. coli host-cells. all stable spontaneous albr mutants of e. coli simultaneously became resistant to phage t6. the locus determining albicidin ...	1990	2191080
electron microscopic analysis of dna forks generated by escherichia coli dna helicase ii.	t7 phage dna eroded with lambda exonuclease (to create 3'-protruding strands) or exonuclease iii (to create 5'-protruding strands) was treated under unwinding assay conditions with dna helicase ii. single-stranded dna-binding protein (of escherichia coli or phage t4) was added to disentangle the denatured dna and the complexes were examined in the electron microscope. dna helicase ii complexes filtered through a gel column before assay retain the ability to generate forks suggesting that dna hel ...	1990	2170129
acute endotoxin-induced lymphocyte subset sequestration in sheep lungs.	endotoxemia is associated with an early phase of pulmonary hypertension and a later increase in microvascular permeability. these physiologic changes are attended by peripheral blood and lung lymph leukopenia and a rapid accumulation of both granulocytes and lymphocytes in the peripheral lung. in the present study, the numbers of lymphocytes in blood, lung lymph, and lung tissue after infusion of endotoxin were determined by fluorescent labeling of lymphocyte populations with monoclonal antibodi ...	1990	2179624
dna polymerase ii is encoded by the dna damage-inducible dina gene of escherichia coli.	the structural gene for dna polymerase ii was cloned by using a synthetic inosine-containing oligonucleotide probe corresponding to 11 amino acids, which were determined by sequencing the amino terminus of the purified protein. the labeled oligonucleotide hybridized specifically to the lambda clone 7h9 from the kohara collection as well as to plasmid pgw511 containing the sos-regulated dina gene. approximately 1400 base pairs of dina sequence were determined. the predicted amino-terminal sequenc ...	1990	2217198
mechanistic studies of ionizing radiation and oxidative mutagenesis: genetic effects of a single 8-hydroxyguanine (7-hydro-8-oxoguanine) residue inserted at a unique site in a viral genome.	t4 rna ligase was used to construct a deoxypentanucleotide containing a single 8-hydroxyguanine (7-hydro-8-oxoguanine; g8-oh) residue, which is one of the putatively mutagenic dna adducts produced by oxidants and ionizing radiation. the pentamer d(gctag8-oh)p was prepared by the ligation of a chemically synthesized acceptor molecule, d(gcta), to an adducted donor, 8-hydroxy-2'-deoxyguanosine 5',3'-bisphosphate. the acceptor was efficiently converted to the reaction product (greater than 95%), an ...	1990	2223758
comparison of chemical reactivity, cytotoxicity, interstrand cross-linking and dna sequence specificity of bis(platinum) complexes containing monodentate or bidentate coordination spheres with their monomeric analogues.	the properties of a new bis(platinum) complex containing two monodentate coordination spheres, [(trans-ptcl(nh3)2)2h2n(ch2)4nh2]cl2 (1,1/t,t), are reported. comparison is made with respect to chemical reactivity, in vitro biological activity in murine and tumor cells, dna conformational changes, cross-linking efficiency, and sequence specificity between this complex and the previously reported complex containing two bidentate platinum atoms, [(pt(mal)(nh3))2h2n(ch2)4nh2] (2,2/c,c), as well as wi ...	1990	2271599
selection for lysis inhibition in bacteriophage.	for escherichia coli cells that have been infected by t-even bacteriophages (phages t2, t4, and t6), the adsorption of a second t-even phage results in an increase in the length of the original phage infection and an associated increase in the number of phages produced by the same infected cell. this is a phage encoded response called lysis inhibition. in this study the ecological significance of lysis inhibition is explored. in particular it is argued that lysis inhibition is an adaptive respon ...	1990	2273898
intracellular lytic enzyme systems and their use for disruption of escherichia coli.	this article focusses on lytic enzyme systems available in e. coli and their potential use for cellular disruption. in the systems described here the genetic information for lysis would be carried within the microbial host, either integrated or naturally occurring on chromosomal dna, or on extrachromosomal elements such as plasmids. each microbe would carry complete information for endogenous enzymatic lysis, and lysis would occur in a controlled manner after being triggered by an external facto ...	1990	2291440
resolution of holliday junction analogs by t4 endonuclease vii can be directed by substrate structure.	endonuclease vii is an enzyme from bacteriophage t4 capable of resolving four-arm holliday junction intermediates in recombination. since natural holliday junctions have homologous (2-fold) sequence symmetry, they can branch migrate, creating a population of substrates that have the branch point at different sites. we have explored the substrate requirements of endonuclease vii by using immobile analogs of holliday junctions that lack this homology, thereby situating the branch point at a fixed ...	1990	2199447
a proposed structure of bacteriophage t4 gene product 22--a major prohead scaffolding core protein.	gene 22 of bacteriophage t4 encodes a major prohead scaffolding core protein of 269 amino acid residues. from its nucleotide sequence the gene product (gp) 22 has a predicted mr of 29.9 and a pi of 4.3. the protein is rich in charged residues (glutamic acid and lysine) and contains low amounts of proline and glycine and no cysteine residues. we suggest that gp22 undergoes limited proteolytic processing which eliminates the short c-terminal piece from the molecule during the early steps of prohea ...	1990	2088448
a self-splicing group i intron in the dna polymerase gene of bacillus subtilis bacteriophage spo1.	we report a self-splicing intron in bacteriophage spo1, whose host is the gram-positive bacillus subtilis. the intron contains all the conserved features of primary sequence and secondary structure previously described for the group ia introns of eukaryotic organelles and the gram-negative bacteriophage t4. the spo1 intron contains an open reading frame of 522 nucleotides. as in the t4 introns, this open reading frame begins in a region that is looped out of the secondary structure, but ends in ...	1990	2119891
the uvsy protein of bacteriophage t4 modulates recombination-dependent dna synthesis in vitro.	an in vitro system containing the t4 gene 43, 45, 44/62, 32, dda, and uvsx proteins catalyzes dna synthesis that is dependent on the synapsis step of homologous genetic recombination. the rate of dna synthesis in this system is highly dependent on the concentration of the uvsx recombinase (a reca-like protein). here we report the effect of the t4 uvsy protein, a recombination accessory protein, on this reaction. low concentrations of uvsy protein greatly stimulate dna synthesis at low concentrat ...	1990	2144282
effects of the bacteriophage t4 gene 41 and gene 32 proteins on rna primer synthesis: coupling of leading- and lagging-strand dna synthesis at a replication fork.	we have demonstrated previously that the template sequences 5'-gtt-3' and 5'-gct-3' serve as necessary and sufficient signals for the initiation of new dna chains that start with pentaribonucleotide primers of sequence pppapcpnpnpn or pppgpcpnpnpn, respectively. normally, the complete t4 primosome, consisting of the t4 gene 41 (dna helicase) and gene 61 (primase) proteins, is required to produce rna primers. however, a high concentration of the 61 protein alone can prime dna chain starts from th ...	1990	2158814
sequence analysis of conserved rega and variable orf43.1 genes in t4-like bacteriophages.	bacteriophage t4 rega protein is a translational repressor of several phage mrnas. in the t4-related phages examined, rega nucleotide sequences are highly conserved and the inferred amino acid sequences are identical. the exceptional phage, rb69, did not produce a rega protein reproducibly identifiable by western blots (immunoblots) nor did it produce mrna that hybridized to t4 rega primers. nucleotide sequences of either 223 or 250 base pairs were identified immediately 3' to rega in rb18 and r ...	1990	2168375
recombination hotspots in bacteriophage t4 are dependent on replication origins.	bacteriophage t4 recombination "hotspots" were first detected by the rescue of genetic markers from uv-irradiated phage particles. these hotspots have since been detected following treatments that yield other forms of dna damage, and at least one is active in the absence of damage. the previous mapping of phage replication origins near the peaks of two recombination hotspots suggested that the origins cause the localized enhancement of recombination. here we show that deletion of one origin elim ...	1991	2068082
lanthanide accumulation in the periplasmic space of escherichia coli b.	treatment of growing escherichia coli b with lanthanide ions [lanthanum(iii), terbium(iii), and europium(iii)] and subsequent aldehyde-oso4 fixation caused areas of high contrast to appear within the periplasm (the space between inner and outer membrane of the cell envelope). x-ray microanalysis of ultrathin sections of epon-embedded or acrylic resin-embedded cells revealed the presence of the lanthanide and of phosphorus in the areas, whose contrast greatly exceeded that of other stained struct ...	1991	1987113
effects of mutations of the bulged nucleotide in the conserved p7 pairing element of the phage t4 td intron on ribozyme function.	the p7 element of group i introns contains a semiconserved "bulged" nucleotide, a c in group ia introns (nt 870 in the td intron) and an a in group ib introns [cech, t.r. (1988) gene 73, 259-271]. variants u870, g870, and a870, isolated by a combination of in vitro and in vivo genetic strategies, indicate that c and a at position 870 are consistent with splicing whereas u and g are not. although mutants g870 and u870 could be activated in vitro by increasing the mg2+ concentration, their km for ...	1991	2009267
physiological, morphological, and physicochemical characterization of a novel escherichia coli bacteriophage, phage mm.	a double-stranded dna containing, t even-like, escherichia coli bacteriophage, called mm, has been isolated from the local sewage and purified by polyethylene glycol precipitation followed by banding on a cesium chloride three-step gradient. it yields a burst size of 75 particles per infected cell, and has an adsorption coefficient of 3.3 x 10(-10) cm3/min and a latent period of 45 min. electron microscopy of phage mm reveals an isometric icosahedral head, 92 nm long and 81 nm wide, and a 112-nm ...	1991	2059549
stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in dna: endonuclease iii from escherichia coli, sodium hydroxide, and lys-trp-lys.	the dna strand cleavage reaction catalyzed by endonuclease iii from escherichia coli (endo iii) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-s proton and formation of a trans alpha,beta-unsaturated aldose product; we previously reported the same stereochemical course for the reaction catalyzed by uv endonuclease v from bacteriophage t4 (uv endo v) [mazumder, a., gerlt, j. a., rabow, l., absalon, m. j., stubbe, j., & bolton, p. h. ...	1991	1846560
immunoanalysis of ultraviolet radiation induced dna damage and repair within specific gene segments of plasmid dna.	the region-specific heterogeneity of repairing dna damage has been established in several biological systems. a flexible and sensitive approach, based upon dna damage specific antibodies, is described to monitor the repair of specific lesions within discrete genomic segments. membrane transblotted dna restriction fragments are immunoanalyzed for the initial formation and repair of 254 nm radiation induced pyrimidine dimers. sensitivity of dimer immunodetection increases proportional to fragment ...	1991	1657185
oligonucleotide site directed mutagenesis of all histidine residues within the t4 endonuclease v gene: role in enzyme-nontarget dna binding.	in order to evaluate the contributions that histidine residues might play both in the catalytic activities of endonuclease v and in binding to nontarget dna, the technique of oligonucleotide site directed mutagenesis was used to create mutations at each of the four histidine residues in the endonuclease v gene. although none of the histidines were shown to be absolutely required for the pyrimidine dimer specific dna glycosylase activity or the apurinic lyase activity, conservative amino acid cha ...	1991	1868080
in vivo restriction. sequence and structure of endonuclease ii-dependent cleavage sites in bacteriophage t4 dna.	endonuclease ii of bacteriophage t4 is required for in vivo restriction of cytosine-containing dna from its host, escherichia coli, (as well as from phage mutants lacking cytosine modification), normally the first step in the reutilization of host dna nucleotides for synthesis of phage dna in infected cells. the phage cytosine-dna is fragmented incompletely to yield genetically defined fragments. this restriction is different from that of type i, ii, or iii restriction enzymes. we have located s ...	1991	1744134
folding of group i introns from bacteriophage t4 involves internalization of the catalytic core.	fe(ii)-edta, a solvent-based cleavage reagent that distinguishes between the inside and outside surfaces of a folded rna molecule, has revealed some of the higher-order folding of the group ib intron from tetrahymena thermophila pre-rrna. this reagent has now been used to analyze the bacteriophage t4 suny and td introns, both of which are members of the group ia subclass. significant portions of the phylogenetically conserved secondary structure are protected from fe(ii)-edta cleavage. however, ...	1991	1763026
[the role of temperature as a factor of structure and functional fit of a "prey" virus based on the example of phage t4].	by means of high-precision acoustic measurements and by the methods of fluorescent and electron microscopy investigations were performed of thermoinduced conformational changes in t4 bacteriophage and its thermolabile mutants altered in baseplate proteins (gene products "7", "8", "10"). a relationship was found between the conformational changes in t4 bacteriophage structure in the temperature range of 33-45 degrees c and the efficiency of bacteriophage adsorption and changes in the orientation ...	1991	1809394
the human homologous pairing protein hpp-1 is specifically stimulated by the cognate single-stranded binding protein hrp-a.	homologous pairing and strand exchange of dna are catalyzed by the human homologous pairing protein hpp-1 in a magnesium-dependent, atp-independent reaction that requires homologous dna substrates and stoichiometric quantities of hpp-1. here we show that the addition of the purified human single-strand binding (ssb) protein hrp-a to the reaction mixture stimulates the rate of homologous pairing 70-fold and reduces the amount of hpp-1 required for the reaction at least 10-fold. the identification ...	1991	1924369
phage t4 expression vector: protection from proteolysis.	we have developed an efficient method for the expression of heterologous genes during infection by t4, a bacteriophage known to inhibit the proteolytic systems of escherichia coli. this system enables us to clone genes in a plasmid expression vector and move them readily into t4. we have used lacz as a reporter gene to show that both plasmid and phage exhibit low basal expression or high-level expression under the control of a t7 promoter. this system promises a possible solution to the problem ...	1991	1937029
cleavage reaction of a synthetic oligoribonucleotide corresponding to the autocleavage site of a precursor rna from bacteriophage t4.	a fragment (guuucguacaaac) having a consensus sequence for the self-cleavage domain in a precursor of an rna molecule from t4-infected escherichia coli cells (p2sp1; precursor of species 1) was chemically synthesized and found to be cleaved either between ca (139-140) or between ua (137-138) in the presence of monovalent cations and a non-ionic detergent. the cleaved products had 5'-hydroxyl and 3'-phosphate groups, of which some were in the form 2',3'-cyclic phosphates.	1991	1959662
cloning, sequencing, overproduction, and purification of m. cvibi (gantc) methyltransferase from chlorella virus nc-1a [corrected].	we have cloned and sequenced the cvibim gene from chlorella virus nc-1a by selecting for the modification phenotype. the modification gene was cloned on a 7-kb bamhi fragment inserted into the bamhi site of the puc13 plasmid. the cvibim gene was localized at the 3' end of this fragment. sequencing of this region revealed a large open reading frame that codes for methyltransferase (mtase; symbol m.) (predicting 260 amino acids). m.cvibi (gantc) aa sequence is homologous to m.dam(gatc), m.dpnii(ga ...	1992	1427082
consequences of molecular engineering enhanced dna binding in a dna repair enzyme.	facilitated one-dimensional diffusion is a general mechanism utilized by several dna-interactive proteins as they search for their target sites within large domains of nontarget dna. t4 endonuclease v is a protein which scans dna in a nonspecifically bound state and processively incises dna at ultraviolet (uv)-induced pyrimidine dimer sites. an electrostatic contribution to this mechanism of target location has been established. previous studies indicate that a decrease in the affinity of endonu ...	1992	1567866
improved band shift assay for the simultaneous analysis of protein-dna interactions and enzymatic functions of dna polymerases.	a simple method to assay the major properties of dna polymerases such as template binding, polymerase and exonuclease activities in one step is exemplified with the dna polymerases of e. coli, bacteriophage t4 and herpes simplex virus. combining the advantages of the band-shift assay with the resolving power of polyacrylamide gradient gel electrophoresis, the procedure is particularly useful for a rapid functional analysis of mutant polymerases as well as inhibitors of dna replication.	1992	1314195
evidence that recbc-dependent degradation of duplex dna in escherichia coli recd mutants involves dna unwinding.	infection of escherichia coli with phage t4 gene 2am was used to transport 3h-labeled linear duplex dna into cells to follow its degradation in relation to the cellular genotype. in wild-type cells, 49% of the dna was made acid soluble within 60 min; in recb or recc cells, only about 5% of the dna was made acid soluble. remarkably, in recd cells about 25% of the dna was rendered acid soluble. the dna degradation in recd cells depended on intact recb and recc genes. the degradation in recd cells ...	1992	1322885
ligation-independent cloning of glutathione s-transferase fusion genes for expression in escherichia coli.	a plasmid vector has been constructed that allows the ligation-independent cloning of cdnas in any reading frame and directs their synthesis in escherichia coli as glutathione s-transferase-linked fusion proteins. the cloning procedure does not require restriction enzyme digestion of the target sequence and does not introduce any additional sequences between the thrombin cleavage site and the foreign protein. extended single-stranded tails complementary between the vector and insert, generated b ...	1992	1339364
three-dimensional structure of the beta subunit of e. coli dna polymerase iii holoenzyme: a sliding dna clamp.	the crystal structure of the beta subunit (processivity factor) of dna polymerase iii holoenzyme has been determined at 2.5 a resolution. a dimer of the beta subunit (m(r) = 2 x 40.6 kd, 2 x 366 amino acid residues) forms a ring-shaped structure lined by 12 alpha helices that can encircle duplex dna. the structure is highly symmetrical, with each monomer containing three domains of identical topology. the charge distribution and orientation of the helices indicate that the molecule functions by ...	1992	1349852
the distribution of uv damage in the laci gene of escherichia coli: correlation with mutation spectrum.	we have determined the uv (254 nm) damage distribution in the transcribed and non-transcribed strands of the i-d region of the escherichia coli laci gene. the locations of replication blocking lesions were revealed as termination sites of t7 dna polymerase and/or t4 dna polymerase 3'-5' exonuclease. termination products, i.e. both cyclobutane pyrimidine dimers and 6-4 photoproducts, were resolved and analysed on an automated dna sequencer. these two major photoproducts are not randomly distribut ...	1992	1383713
roles of cys148 and asp179 in catalysis by deoxycytidylate hydroxymethylase from bacteriophage t4 examined by site-directed mutagenesis.	the proposed roles of cys148 and asp179 in deoxycytidylate (dcmp) hydroxymethylase (ch) have been tested using site-directed mutagenesis. ch catalyzes the formation of 5-(hydroxymethyl)-dcmp, essential for dna synthesis in phage t4, from dcmp and methylenetetrahydrofolate. ch resembles thymidylate synthase (ts), an enzyme of known three-dimensional structure, in both amino acid sequence and the reaction catalyzed. conversion of cys148 to asp, gly, or ser decreases ch activity at least 10(5)-fold ...	1992	1420151
in vitro characterization of repair synthesis initiated by t4 endonuclease v on a synthetic dna substrate.	the size of the repair patch produced by e. coli dna polymerase (pol i) following the removal of a pyrimidine dimer from dna in response to the nicking activity of t4 endonuclease (t4 endo v) was determined. a 48-bp dna containing a pyrimidine dimer at a defined location was labelled in the damaged strand and incubated with t4 endo v and e. coli endonuclease iv. subsequently, dna synthesis by dna pol i was carried out in the presence of four dntps, atp and dna ligase. analysis of the reaction pr ...	1992	1512008
critical functional role of the cooh-terminal ends of longitudinal hydrophobic strips in alpha-helices of t4 lysozyme.	the sensitivity of bacteriophage t4 lysozyme function to amino acid substitutions at defined positions in and around the longitudinal, hydrophobic strips of 9 alpha-helices was assessed after systematic replacement of each residue in the protein with a series of 13 amino acids. the hydrophobic strips were defined by identifying the longitudinal sectors in the helices with the highest mean residue hydrophobicities. sensitivity to mutation (the percentage of replacements leading to loss of functio ...	1992	1517218
are there highly conserved dna polymerase 3'----5' exonuclease motifs?	it was proposed by bernad et al. [cell 59 (1989) 219-228] and blanco et al. [gene 100 (1991) 27-38] that the 3'----5' exonuclease (exo) domain of escherichia coli dna polymerase i (poli) is structurally and functionally conserved among prokaryotic and eukaryotic dna polymerases. the basis for this claim is the presence of three short peptide sequences in many dna polymerases that resemble poli sequences that have been shown by x-ray crystallographic and genetic engineering studies to be metal io ...	1992	1551593
recombinant human immunodeficiency virus type 1 nucleocapsid (ncp7) protein unwinds trna.	the nucleocapsid protein (nc) of all animal retroviruses, encoded by the gag gene, is the major structural protein of the core ribonucleoprotein complex, bound to genomic rna in mature virions. nc is also thought to play one or more accessory roles in reverse transcription. mature nc (p7nc) from human immunodeficiency virus type 1 (hiv-1) is a 71-amino acid, basic protein which contains two cys3his zn(ii) retroviral-type zinc finger domains. herein, we describe the subcloning and expression of h ...	1992	1551877
processive proofreading is intrinsic to t4 dna polymerase.	dna replication occurs in vivo with very high processivity, meaning that the replication complex assembles at the origin(s) of replication and then performs template-directed synthesis of dna over virtually the entire genome without dissociation. such processivity also characterizes reconstituted replication holoenzyme complexes in vitro. however, the isolated dna polymerases are much less processive, especially under physiological conditions. in this paper we monitor the degree of processivity ...	1992	1629215
replication inhibition and translesion synthesis on templates containing site-specifically placed cis-diamminedichloroplatinum(ii) dna adducts.	a series of site-specifically plantinated, covalently closed circular m13 genomes (7250 bp) was constructed in order to evaluate the consequences of dna template damage induced by the anticancer drug cis-diamminedichloroplatinum(ii) (cis-ddp). here are reported the synthesis and characterization of genomes containing the intrastrand cross-linked adducts cis-[pt(nh3)2[d(apg)-n7(1),-n7(2)]], cis-[pt-(nh3)2[d(gpcpg)-n7(1),-n7(3)]], and trans-[pt(nh3)2[d(cpgpcpg)-n3(1),-n7(4)]]. these constructs, as ...	1992	1314653
a system of transposon mutagenesis for bacteriophage t4.	we have developed a system of transposon mutagenesis for bacteriophage t4. the transposon is a plasmid derivative of tn5 which contains the essential t4 gene 24, permitting a direct selection for transposition events into a gene 24-deleted phage. the transposition occurred at a frequency of only 10(-7) per progeny phage, even though a dam- host was used to increase transposition frequency. phage strains with a transposon insert were distinguished from most pseudorevertants of the gene 24 deletio ...	1992	1322484
effect of escherichia coli nusg function on lambda n-mediated transcription antitermination.	the escherichia coli nus factors act in conjunction with the bacteriophage lambda n protein to suppress transcription termination on the lambda chromosome. nusa binds both n and rna polymerase and may also interact with other nus factors. to search for additional components of the n antitermination system, we isolated host revertants that restored n activity in nusa1 mutants. one revertant, nusg4, was mapped to the rif region of the e. coli chromosome and shown to represent a point mutation near ...	1992	1531224
molecular characterisation of a dna ligase gene of the extremely thermophilic archaeon desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases.	a 3382 bp fragment containing a gene for a dna ligase from the extremely thermophilic, acidophilic, and facultatively anaerobic archaeon (archaebacterium) desulfurolobus ambivalens was cloned and sequenced. the deduced amino acid sequence (600 amino acids, 67619 molecular weight) showed 30-34% sequence identity with the atp-dependent eucaryal (eukaryotic) dna ligases of schizosaccharomyces pombe, saccharomyces cerevisiae, the human dna ligase i, and with the vaccinia dna ligase. distant similari ...	1992	1437556
a tightly regulated system for overproduction of bacteriophage t4 lysozyme in escherichia coli.	bacteriophage t4 lysozyme has been purified using the ni-chelate affinity chromatography technique from overexpressing escherichia coli cells by fusion to an n-terminal 6x his tail. regulation of the lysozyme gene expression has been found to be critical during growth phase of the bacteria by comparing different plasmid constructions. whereas a tac-promoter fusion construct alone did not lead to efficient production of t4 lysozyme because of early cell lysis, an improved repressor sequence and c ...	1993	8251753
genetic and biochemical studies of bacteriophage t4 dna polymerase 3'-->5'-exonuclease activity.	dna polymerase exonucleolytic proofreading is important in attaining high fidelity dna replication. one of the most well characterized proofreading activities is the 3'-->5'-exonuclease activity of bacteriophage t4 dna polymerase. we have used genetic analyses and protein sequence comparisons to escherichia coli dna polymerase i to identify amino acids in the n-terminal region of t4 dna polymerase that are required for exonucleolytic proofreading. mutant dna polymerases with amino acid substitut ...	1993	8262948
from the double-helix to novel approaches to the sequencing of large genomes.	elucidation of the structure of dna by watson and crick [nature 171 (1953) 737-738] has led to many crucial molecular experiments, including studies on dna replication, transcription, physical mapping, and most recently to serious attempts directed toward the sequencing of large genomes [watson, science 248 (1990) 44-49]. i am totally convinced of the great importance of the human genome project, and toward achieving this goal i strongly favor 'top-down' approaches consisting of the physical map ...	1993	8276270
enzyme interactions involving t4 phage-coded thymidylate synthase and deoxycytidylate hydroxymethylase.		1993	8304181
dna conformation induced by the bacteriophage t4 uvsx protein appears identical to the conformation induced by the escherichia coli reca protein.	the study of homologous genetic recombination has been dominated by the reca protein of escherichia coli, which is involved in dna recombination and repair, as well as phage induction, in vivo. the active form of the reca protein is a helical filament formed on dna in the presence of atp, and within this filament, the dna is extensively stretched to about 5.1 a rise per base-pair and untwisted to about 19 base-pairs per turn. the bacteriophage t4 uvsx protein is only weakly homologous to reca, b ...	1993	8331653
identification of unusual rna folding patterns encoded by bacteriophage t4 gene 60.	a 50-nucleotide (nt) untranslated region (coding gap sequence) that interrupts the amino acid coding sequence in t4 gene 60, plus an additional 5 nt upstream and another 3 nt downstream from the gap sequence, shows unusual folding patterns according to rna structure prediction. a predicted highly stable and significant hairpin structure in the 5' half of the gap sequence and a plausible tertiary structural element computed in the 3' part of the gap sequence seem significant by statistical tests ...	1993	8382655
a comparative study of scatchard-type and linear lattice models for the analysis of epr competition experiments with spin-labeled nucleic acids and single-strand binding proteins.	an epr competition formalism is developed which provides relative affinities of proteins for nucleic acids. two models for analyzing protein-nucleic acid interactions, one assuming independent binding sites (model 1) and the other considering site overlap (model 2), are examined with respect to their validity and limitations. the models are employed to derive affinity ratio relationships which are used to calculate the relative affinities of gene 32, gene 5, and ssb proteins for various nucleic ...	1993	8382967
structure/function analysis of the ala116-->lys121 region of endonuclease v by random targeted mutagenesis.	endonuclease v is the product of the denv gene of bacteriophage t4 and is responsible for the recognition and repair of pyrimidine dimers due to uv irradiation of dna. this is accomplished by a two-step mechanism involving incision at the site of the lesion followed by cleavage of the phosphate backbone. in order to better understand this molecule, and to validate our new mutagenesis procedure, we have constructed a series of random mutations within the region ala116-->lys121 using a random targ ...	1993	8441681
introduction of ca(2+)-binding amino-acid sequence into the t4 lysozyme.	the 51-62 loop of t4 phage lysozyme was altered by site-directed mutagenesis to obtain maximal homology with the typical ef-hand motif. a ca(2+)-binding site was designed and created by replacing both gly-51 and asn-53 with aspartic acid. the mutant t4 lysozyme (g51d/n53d) was expressed in escherichia coli. the activity of the g51d/n53d-mutant was about 60% of that of the wild-type protein. this mutant can bind ca2+ ions specifically, while the effective dissociation constant was essentially gre ...	1993	8448199
assembly of a functional replication complex without atp hydrolysis: a direct interaction of bacteriophage t4 gp45 with t4 dna polymerase.	the seven-protein bacteriophage t4 dna replication complex can be manipulated in vitro to study mechanistic aspects of the elongation phase of dna replication. under physiological conditions, the processivity of dna synthesis catalyzed by the t4 polymerase (gp43) is greatly increased by the interaction of this enzyme with its accessory proteins (gp44/62 and gp45) and the t4 single-stranded dna binding protein (gp32). the assembly of this t4 holoenzyme requires hydrolysis of atp by the gp44/62 co ...	1993	8475061
concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in stem.	quantitative stem with the imaging mode of ratio-contrast was investigated in order to evaluate the local concentration of dna in situ for different kinds of dna plasms in terms of intracellular packing densities (p.d.). the ability of ratio imaging to suppress thickness variations provided the basis to use unstained sections from cryofixed and freeze-substituted material. the dna p.d. within the nucleoid of e. coli was determined to be about 100 mg ml-1. quantitative data concerning the p.d. of ...	1993	8475602
laser-induced protein-dna cross-links via psoralen furanside monoadducts.	we have developed a technique for cross-linking dna binding proteins to dna using psoralen furanside monoadducts as photoaffinity probes and a continuous-wave argon ion laser (366 nm) as a light source. several dna binding proteins (t7 rna polymerase, uvrb, single-stranded dna binding protein of escherichia coli, t4 gp32, and reca of e. coli) are shown to cross-link to single-stranded psoralen monoadducted dna oligos differing in length and sequence. increasing fluences of laser light on a fixed ...	1993	8504073
mapping transcription start points with t4 dna polymerase.		1993	8386296
identification, isolation, and characterization of the structural gene encoding the delta' subunit of escherichia coli dna polymerase iii holoenzyme.	the gene encoding the delta' subunit of dna polymerase iii holoenzyme, designated holb, was cloned by a strategy in which peptide sequence was used to derive a dna hybridization probe. the gene maps to 24.95 centisomes of the chromosome. sequencing of holb revealed a 1,002-bp open reading frame predicted to produce a 36,936-da protein. the gene has a ribosome-binding site and promoter that are highly similar to the consensus sequences and is flanked by two potential open reading frames. protein ...	1993	8509334
sliding clamps of dna polymerases.	the determination of the structure of the processivity factor (beta subunit) of escherichia coli dna polymerase iii holoenzyme showed that this protein acts to clamp the polymerase onto dna by forming a closed circular structure that can encircle duplex dna (x.-p. kong, r. onrust, m. o'donnell & j. kuriyan. (1992). cell, 69, 425-437). in this review we describe the features of the beta subunit that allow it to be linked tightly but non-specifically to dna, and discuss the surprisingly symmetrica ...	1993	7903401
escherichia coli proteins, including ribosomal protein s12, facilitate in vitro splicing of phage t4 introns by acting as rna chaperones.	to address the effect of host proteins on the self-splicing properties of the group i introns of bacteriophage t4, we have purified an activity from escherichia coli extracts that facilitates both trans- and cis-splicing of the t4 introns in vitro. the activity is attributable to a number of proteins, several of which are ribosomal proteins. although these proteins have variable abilities to stimulate splicing, ribosomal protein s12 is the most effective. the activity mitigates the negative effe ...	1994	7958841
a single stranded dna binding protein isolated from hela cells facilitates ni2+ activation of dna polymerases in vitro.	the divalent nickel ion (ni2+) is one of several metal ions that can substitute for mg2+ in the activation of dna polymerases in vitro, but usually with very low efficiency. we have purified and partially characterized a ni(2+)-binding protein (p40) from hela cell extracts that can specifically enhance the polymerase activity of dna polymerase alpha (pol alpha) and other dna polymerases in response to ni2+. this protein, with a molecular mass of 40 kda, is a single stranded dna binding protein t ...	1994	7999774
sequence-specific cleavage of oligoribonucleotide capable of forming a stem and loop structure.	the precursor of an rna molecule from t4-infected escherichia coli cells (p2sp1 rna) has the capacity to cleave itself at specific positions ((upa (137-138) and cpa (170-171)) within a possible loop and stem structure. this specific cleavage requires at least a monovalent cation and nonionic detergents. to confirm that the sequence-specific cleavage occurs autolytically, we studied the selective hydrolysis of rna using a chemically synthesized 13-mer (guuucguacaaac) having sequences correspondin ...	1994	8051096
the pseudodisaccharides: a novel class of group i intron splicing inhibitors.	lysinomicin, a naturally-occurring pseudodisaccharide, inhibits translation in prokaryotes. we report that lysinomicin (and three related compounds) are able to inhibit the self-splicing of group i introns, thus identifying pseudodisaccharides as a novel class of group i intron splicing inhibitors. lysinomicin inhibited the self-splicing of the suny intron of phage t4 with a ki of 8.5 microm (+/- 5 microm) and was active against other group i introns. inhibition was found to be competitive with ...	1994	7800490
crystal structure of thymidylate synthase from t4 phage: component of a deoxynucleoside triphosphate-synthesizing complex.	thymidylate synthase from phage t4 (t4ts) is part of a complex of several enzymes required for coordinate dna synthesis in infected escherichia coli cells. it has been proposed that similar complexes of enzymes related to dna synthesis are also functional in eukaryotes [pardee, a. b. (1989) science 246, 603-608]. to delineate the role of structure in the function of this complex, we have solved the structure of t4ts as a basis for mapping the complex by mutagenesis. the 3.1 a structure of the un ...	1994	7803410
fibritin encoded by bacteriophage t4 gene wac has a parallel triple-stranded alpha-helical coiled-coil structure.	the bacteriophage t4 late gene wac (whisker's antigen control) encodes a fibrous protein which forms a collar/whiskers complex. whiskers function as a helper protein for the long tail fibres assembly and plays a role in regulating retraction of the long tail fibres in response to environmental conditions. in this work we show that expression of the cloned wac gene in escherichia coli yields a protein oligomer of 53 nm length which we call fibritin, and which is able to complement gpwac t4 partic ...	1994	7932704
intron-containing t4 bacteriophage gene suny encodes an anaerobic ribonucleotide reductase.	the function of the suny protein, encoded by an intron-containing gene of bacteriophage t4, has remained hitherto unknown in contrast to the extensively studied self-splicing reaction of the suny intron. here we show that anaerobic t4 infections of escherichia coli induce a ribonucleoside triphosphate reductase activity that is 10-30-fold higher than the bacterial host level of the corresponding enzyme. inactivation of the t4 suny gene (in this communication renamed nrdd) significantly decreased ...	1994	8051113
site-specific incorporation of biophysical probes into proteins.	biophysical probes which can detect structural changes in proteins and the interaction of proteins with other macromolecules are important tools in studying protein function. many difficulties remain, however, in introducing probes into proteins site-specifically. here we report the successful site-specific incorporation of a spin-labeled, a fluorescent, and a photoactivatible amino acid into a variety of surface and internal sites in bacteriophage t4 lysozyme by using unnatural amino acid mutag ...	1994	8159678
direct pcr sequencing of the ndd gene of bacteriophage t4: identification of a product involved in bacterial nucleoid disruption.	the rapid disruption of the escherichia coli nucleoid after t4 infection requires the activity of the phage-encoded ndd gene. we have genetically identified the sequence encoding ndd. determination of the sequence of a 2.5-kb segment including ndd closed the last significant gap in the sequence of the t4 genome. this analysis was performed on pcr-amplified fragments that were purified by gel-exclusion chromatography and then submitted to linear amplification cycle sequencing. this technology per ...	1994	8163181
synthesis of circular rna in bacteria and yeast using rna cyclase ribozymes derived from a group i intron of phage t4.	studies on the function of circular rna and rna topology in vivo have been limited by the difficulty in expressing circular rna of desired sequence. to overcome this, the group i intron from the phage t4 td gene was split in a peripheral loop (l6a) and rearranged so that the 3' half intron and 3' splice site are upstream and a 5' splice site and 5' half intron are downstream of a single exon. the group i splicing reactions excise the internal exon rna as a circle (rna cyclase ribozyme activity). ...	1994	7512723
lytic infection of escherichia coli biofilms by bacteriophage t4.	escherichia coli 3000 xiii formed biofilms on the surface of polyvinylchloride coupons in a modified robbins device. bacteriophage t4d+ infected cells in the biofilm and replicated. it is commonly held that bacteriophage cannot infect surface-attached bacteria (biofilms) because such bacteria are protected by an exopolymeric matrix that binds macromolecules and prevents their diffusion into the biofilm. to our knowledge this is the first observation that a bacteriophage can infect and multiply w ...	1995	7728652
vaccinia virus gene a18r encodes an essential dna helicase.	the vaccinia virus a18r protein is a dna-dependent atpase that contains the canonical sequence motifs associated with the dexh group of dna and rna helicases. investigation of a18r protein function during infection indicated it functions in the early and late phases of vaccinia virus transcription. the a18r protein shares sequence similarity with the mammalian dna helicase ercc3. the ercc3 protein has a dual function: it is a component of the transcription factor tfiih and is an essential partic ...	1995	7545242
recombination-dependent dna replication stimulated by double-strand breaks in bacteriophage t4.	we analyzed the mechanism of recombination-dependent dna replication in bacteriophage t4-infected escherichia coli using plasmids that have sequence homology to the infecting phage chromosome. consistent with prior studies, a pbr322 plasmid, initially resident in the infected host cell, does not replicate following infection by t4. however, the resident plasmid can be induced to replicate when an integrated copy of pbr322 vector is present in the phage chromosome. as expected for recombination-d ...	1995	7592477
[does taxis exist in bacterial viruses?].	by way of example of interaction of t4 bacteriophage with e. coli bacterium the scenario of enhancement of sorption of phages on bacteria through the remote mechanism of their cyclic interaction has been considered. an enlargement of the typical phage size, when its fibrillae are opened, underlies this mechanism. modification of the structure of phages also occurs through the medium by release of products of bacterial metabolism into it. allied questions related to investigation of physicochemic ...	1995	7703277
phage t4 dna [n6-adenine]methyltransferase. overexpression, purification, and characterization.	the bacteriophage t4 dam gene, encoding the dam dna [n6-adenine]methyltransferase (mtase), has been subcloned into the plasmid expression vector, pjw2. in this construct, designated pint4dam, transcription is from the regulatable phage lambda pr and pl promoters, arranged in tandem. a two-step purification scheme using deae-cellulose and phosphocellulose columns in series, followed by hydroxyapatite chromatography, was developed to purify the enzyme to near homogeneity. the yield of purified pro ...	1995	7782299
the cooh-terminal domain of the rna polymerase alpha subunit in transcriptional enhancement and deactivation at the bacteriophage t4 late promoter.	many activator proteins generate their positive control of transcription through interactions with the cooh-terminal domain of the escherichia coli rna polymerase alpha subunit. we have examined the participation of this alpha-domain in transcriptional enhancement and suppression at bacteriophage t4 late promoters. enhancement is generated by the t4 gene 45 protein, which is the dna-tracking processivity factor of viral dna replication; suppression of unenhanced transcription is generated by the ...	1995	7797594
dependence of frequency of homologous recombination on the homology length.	the frequency of homologous recombination is believed to be a linear function of the length (n bp) of homology between dnas. here, the n intercept is believed to be determined by a threshold length below which some physical constraint is effective. in the mammalian gene targeting systems, however, the frequency depends more steeply than linearly on the homology length. to explain both the linear dependence and the steeper dependence, we propose a model where the branch point of a reaction interm ...	1995	7498755
the catalytic domain of a bacterial lytic transglycosylase defines a novel class of lysozymes.	the 70-kda soluble lytic transglycosylase (slt70) from escherichia coli is a bacterial exo-muramidase that cleaves the cell wall peptidoglycan, producing 1,6-anhydro-muropeptides. the x-ray structure of slt70 showed that one of its domains is structurally related to lysozyme, although there is no obvious similarity in amino acid sequence. to relate discrete structural features to differences in reaction mechanism and substrate/product specificity, we compared the three-dimensional structure of t ...	1995	7479697
protection from proteolysis using a t4::t7-rnap phage expression-packaging-processing system.	dna coding for bacteriophage t7 rna polymerase (t7-rnap) was inserted into a positive selection-vector form of the t4 genome, placing it under the control of bacteriophage t4 ipiii promoters. the recombinant t4::t7-rnap fusion phage retained infectivity and produced t7-rnap in infected cells. fusion genes were constructed by insertion into a plasmid containing an ipiii (encoding internal protein iii) target portion and a bacteriophage t7 promoter region. when escherichia coli cells containing th ...	1995	7557416
binding of the junction-resolving enzyme bacteriophage t7 endonuclease i to dna: separation of binding and catalysis by mutation.	bacteriophage t7 endonuclease i is a resolving enzyme that selectively cleaves four-way dna junctions, and related branched species. we have isolated mutants of this protein that retain full structural selectivity of binding to four-way junctions, but which are completely inactive as nucleases. this is consistent with a divisibility of structure-selective binding and catalysis. the mutations that inactivate endonuclease i as a nuclease are clustered into the second quarter of the primary sequenc ...	1995	7853409
head-on collision between a dna replication apparatus and rna polymerase transcription complex.	an in vitro system reconstituted from purified proteins has been used to examine what happens when the dna replication apparatus of bacteriophage t4 collides with an escherichia coli rna polymerase ternary transcription complex that is poised to move in the direction opposite to that of the moving replication fork. in the absence of a dna helicase, the replication fork stalls for many minutes after its encounter with the rna polymerase. however, when the t4 gene 41 dna helicase is present, the r ...	1995	7855590
t4 endonuclease v protects the dna strand opposite a thymine dimer from cleavage by the footprinting reagents dnase i and 1,10-phenanthroline-copper.	the glycosylase/abasic lyase t4 endonuclease v initiates the repair of ultraviolet light-induced pyrimidine dimers. this enzyme forms an imino intermediate between its n-terminal alpha-nh2 group and c-1' of the 5'-residue within the dimer. sodium borohydride was used to covalently trap endonuclease v to a 49-base pair oligodeoxynucleotide containing a site-specific cyclobutane thymine dimer. the bound and free oligonucleotides were then subjected to nuclease protection assays using dnase i and a ...	1995	7876117
distance determination in proteins using designed metal ion binding sites and site-directed spin labeling: application to the lactose permease of escherichia coli.	as shown in the accompanying paper, the magnetic dipolar interaction between site-directed metal-nitroxide pairs can be exploited to measure distances in t4 lysozyme, a protein of known structure. to evaluate this potentially powerful method for general use, particularly with membrane proteins that are difficult to crystallize, both a paramagnetic metal ion binding site and a nitroxide side chain were introduced at selected positions in the lactose permease of escherichia coli, a paradigm for po ...	1995	8618889
preliminary crystallographic studies of bacteriophage t4 fibritin confirm a trimeric coiled-coil structure.	fibritin, a 52-kda product of gene wac of bacteriophage t4, forms fibrous "whiskers" that connect to the phage tail and facilitate the later stages of phage assembly. preliminary experiments suggest that fibritin is a trimer, and its predominant central part has a parallel alpha-helical coiled-coil structure. to investigate the oligomerization and function of fibritin, we have designed and studied two related deletion mutants, denoted m and e, that consist of its last 75 and 120 amino acids, res ...	1996	8623529
in vitro characterization of transcription termination factor rho from escherichia coli rho(nusd) mutants.	escherichia coli nusd strains are bacteria that carry mutations in rho, the gene for transcription termination factor rho, that block the growth of phages t4 and lambdar32. we have identified the rho mutation in six independent nusd strains, and although five of the strains have different mutations, with one exception the mutations are in the proposed rna-binding domain of rho. we overexpressed, purified, and characterized the five different mutant rho proteins. all show substantial rna-dependen ...	1996	8757797
t4 phage gene 32 protein as a candidate organizing factor for the deoxyribonucleoside triphosphate synthetase complex.	after t4 bacteriophage infection of escherichia coli, the enzymes of deoxyribonucleoside triphosphate biosynthesis form a multienzyme complex that we call t4 deoxyribonucleoside triphosphate (dntp) synthetase. at least eight phage-coded enzymes and two enzymes of host origin are found in this 1.5-mda complex. the complex may shuttle dntps to dna replication sites, because replication draws from small pools, which are probably highly localized. several specific protein-protein contacts within the ...	1996	8626661
carboranyl oligonucleotides. 3. biochemical properties of oligonucleotides containing 5-(o-carboranyl-1-yl)-2'-deoxyuridine.	boronated oligonucleotides are potential candidates for boron neutron capture therapy, antisense technology, and as tools in molecular biology. the biological properties of dodecathymidylic acids containing one or more 5-(o-carboran-1-yl)-2'-deoxyuridine residues at different locations within the oligonucleotide chain were studied. 5-(o-carboran-1-yl)-2'-deoxyuridine containing oligonucleotides manifested marked increased lipophilicity and resistance to 3'- or 5'-phosphodiesterases compared to t ...	1996	8639534
kinetic mechanism of dna binding and dna-induced dimerization of the escherichia coli rep helicase.	the monomeric escherichia coli rep protein undergoes a dna-induced dimerization upon binding either single-stranded (ss) or duplex dna with the dimer being the active form of the rep helicase. using stopped-flow fluorescence, we have determined a minimal kinetic mechanism for this reaction in which rep monomer (p) binds to ss oligodeoxynucleotides (dn(pn)15) (s) by a two-step mechanism to form ps*, which can then dimerize with p to form p2s as indicated: [reaction in text]. this minimal mechanis ...	1996	8652567
prokaryotic dna ligases unwind superhelical dna.	we have studied the effect on dna topology of binding of prokaryotic dna ligases (t4 and e. coli) to superhelical or nicked circular dna. performing topoisomerase i-mediated relaxation in the presence of increasing amounts of t4 ligase led to a shift in the topoisomer distribution to increasingly more negative values. this result suggested that t4 ligase unwound the dna and was further substantiated by ligation of nicked circular molecules by e. coli dna ligase in the presence of increasing amou ...	1996	8806663
an n-terminal mutation in the bacteriophage t4 mota gene yields a protein that binds dna but is defective for activation of transcription.	the bacteriophage t4 mota protein is a transcriptional activator of t4-modified host rna polymerase and is required for activation of the middle class of t4 promoters. mota alone binds to the -30 region of t4 middle promoters, a region that contains the mota box consensus sequence [(t/a)(t/a)tgctt(t/c)a]. we report the isolation and characterization of a protein designated mot21, in which the first 8 codons of the wild-type mota sequence have been replaced with 11 different codons. in gel retard ...	1996	8892810
a common mechanism of action for the n-glycosylase activity of dna n-glycosylase/ap lyases from e. coli and t4.	duplex oligonucleotides containing the base lesion analogs, o-methylhydroxylamine- and o-benzylhydroxylamine-modified abasic (ap) sites, were substrates for the dna n-glycosylases endonuclease iii, formamidopyrimidine dna n-glycosylase and t4 endonuclease v. these n-glycosylases are known to have associated ap lyase activities. in contrast, uracil dna n-glycosylase, a simple n-glycosylase which does not have an associated ap lyase activity, was unable to recognize the modified ap sites. endonucl ...	1996	8960131
tracing the interaction of bacteriophage with bacterial biofilms using fluorescent and chromogenic probes.	phages t4 and e79 were fluorescently-labeled with rhodamine isothiocyanate (ritc), fluoroscein isothiocyanate (fitc), and by the addition of 4'6-diamidino-2-phenylindole (dapi) to phage-infected host cells of escherichia coli and pseudomonas aeruginosa. comparisons of electron micrographs with scanning confocal laser microscope (sclm) images indicated that single ritc-labeled phage particles could be visualized. biofilms of each bacterium were infected by labeled phage. sclm and epifluorescence ...	1996	8987490