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Biomedical subjects

J D Griffith

Publications and source records attributed to J D Griffith.

At least 73 records · Page 4Linked to original sources
PubMed1989

UvsY protein of bacteriophage T4 is an accessory protein for in vitro catalysis of strand exchange.

The uvsX and uvsY genes are essential to genetic recombination, recombination-dependent DNA synthesis and to the repair of DNA damage in bacteriophage T4. Purified UvsX protein has been shown to catalyze strand exchange and D-loop formation in vitro, but the role of UvsY protein has been unclear. We report that UvsY protein enhances strand exchange by UvsX protein by interacting specifically with UvsX protein: gene 32 protein (gp32) is not necessary for this effect and UvsY protein has no similar effect on the RecA protein of E. coli. UvsY protein, like UvsX protein, protects single-stranded DNA from digestion by nucleases, but, unlike UvsX protein, shows no ability to protect double-stranded DNA. UvsY protein enhances the rate of single-stranded-DNA-dependent ATP hydrolysis by UvsX protein, particularly in the presence of gp32 or high concentrations of salt, factors that otherwise reduce the ATPase activity of UvsX protein. The enhancement of ATP hydrolysis by UvsY protein is shown to result from the ability of UvsY protein to increase the affinity of UvsX protein for single-stranded DNA.

Adenosine Triphosphatases↗
PubMed1989

Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: possible relevance to the folding of single-stranded nucleic acids.

A 32-base-pair (bp) DNA duplex with deletions in one strand, and thus extra bases in the opposing strand, was ligated head-to-tail to produce linear and circular multimers. The electrophoretic mobility of the linear multimers was analyzed in polyacrylamide gels and the size of the circular DNA was determined by electron microscopy. A 1-base deletion produced a marked retardation in the mobility of the linear multimers coincident with the formation of a population of multimeric circles of a smaller average size than the deletionless 32-mer; 2-, 3-, or 4-base deletions at the same site produced proportionately greater effects. Two 1-base deletions separated by 10 bp on the same strand produced a greater reduction in mobility than a 1-base deletion, whereas two 1-base deletions spaced by 5 bp on the same strand yielded a molecule that behaved more like the deletionless DNA. We conclude that deletions of 1-4 bases at a single site on duplex DNA produce molecules that behave as if they contain sharp bends or kinks. In contrast, single mismatches in the 32-bp duplex produced no abnormality in behavior relative to normally base-paired DNA in the gel mobility and electron microscopic assays. The possible role of such structures in organizing the three-dimensional folding of single-stranded nucleic acids is considered.

Base Composition↗
PubMed1988

RecA protein self-assembly. Multiple discrete aggregation states.

Light scattering, sedimentation and electron microscopy have been used to investigate the aggregation states of highly purified RecA protein in solution. We show that RecA protein will self-assemble into a discrete series of quaternary structures depending upon protein concentration, ionic environment, and nucleotide cofactors. In a stock solution at moderate concentration (10 to 50 microM) RecA protein exists as small particles approximately 4 nm in diameter, larger particles approximately 12 nm in diameter (most probably rings of RecA protein), 10 nm diameter rods varying from 50 to 200 nm in length, and finally as much larger bundles of rods. The addition of monovalent salt shifts the distribution of RecA protein between its various oligomeric states. Increasing protein concentration favors more highly aggregated structures. At a given protein concentration, addition of mM levels of MgCl2 promotes the rapid formation of rods and slow formation of bundles. Under conditions typical of in vitro strand exchange reactions, RecA protein was found to exist as a mixture of rods and 12 nm particles with relatively few monomers.

Adenosine Triphosphate↗
PubMed1988

Formation of D loops by the UvsX protein of T4 bacteriophage: a comparison of the reaction catalyzed in the presence or absence of gene 32 protein.

The UvsX protein of T4 bacteriophage will catalyze the formation of D loops between linear single-stranded DNA (ssDNA) and homologous supercoiled double-stranded DNA (dsDNA) in the absence of T4 gene 32 protein (gp32). This reaction requires one monomer of UvsX protein per three nucleotides of ssDNA so that the ssDNA is completely covered with UvsX protein. Under these conditions, high rates of ATP hydrolysis are observed, and one-third of the products are joined paranemically. The reaction proceeds through a mechanism that creates homology-independent coaggregates of UvsX protein, dsDNA, and ssDNA. When UvsX protein is added to only 1 monomer per 8 nucleotides, but with 1 monomer of gp32 per 12 nucleotides, the rate of ATP hydrolysis is depressed, but D-loop formation is enhanced. Nearly all of the product is bound in plectonemic joints, and no coaggregated intermediates are formed. Coaggregate formation at high concentrations of UvsX protein is not inhibited by the presence of gp32; gp32 simply allows for efficient formation of D loops at such low concentrations of UvsX protein that coaggregates are not constructed. Electron microscopic visualization of the joint structures in this reaction reveals that both gp32 and UvsX protein are bound to the ssDNA. The single-stranded DNA binding (SSB) protein of Escherichia coli will substitute only partially for gp32: in the presence of SSB protein, D-loop formation can be catalyzed at one UvsX protein monomer per eight nucleotides, and it is accomplished without the formation of coaggregates, but a major portion of the product is joined paranemically.

Adenosine Triphosphatases↗
PubMed1988

Assembly of presynaptic filaments. Factors affecting the assembly of RecA protein onto single-stranded DNA.

We have previously shown that the assembly of RecA protein onto single-stranded DNA (ssDNA) facilitated by SSB protein occurs in three steps: (1) rapid binding of SSB protein to the ssDNA; (2) nucleation of RecA protein onto this template; and (3) co-operative polymerization of additional RecA protein to yield presynaptic filaments. Here, electron microscopy has been used to further explore the parameters of this assembly process. The optimal extent of presynaptic filament formation required at least one RecA protein monomer per three nucleotides, high concentrations of ATP (greater than 3 mM in the presence of 12 mM-Mg2+), and relatively low concentrations of SSB protein (1 monomer per 18 nucleotides). Assembly was depressed threefold when SSB protein was added to one monomer per nine nucleotides. These effects appeared to be exerted at the nucleation step. Following nucleation, RecA protein assembled onto ssDNA at net rates that varied from 250 to 900 RecA protein monomers per minute, with the rate inversely related to the concentration of SSB protein. Combined sucrose sedimentation and electron microscope analysis established that SSB protein was displaced from the ssDNA during RecA protein assembly.

Adenosine Triphosphate↗
PubMed1988

The terminus of SV40 DNA replication and transcription contains a sharp sequence-directed curve.

We have examined nucleosome positioning on two DNA segments containing sharp sequence-directed curvatures. A 223 bp DNA from Crithidia fasciculata was cloned into two sites in pBR325 separated by 28%. These sites were found to selectively reconstitute nucleosomes 5- to 7-fold more effectively than the adjoining straight DNA. The terminus of replication and termini of transcription of SV40 DNA are contained within a region of approximately 200 bp centrally located in a 1216 bp fragment. Visualization of this fragment by electron microscopy revealed a sharp curve of approximately 200 degrees in the terminal region. Reconstitution of histone protein with this fragment revealed a 2- to 5-fold higher probability of assembling nucleosomes in the terminal region over the adjacent DNA.

Animals↗
PubMed1988

Curved helix segments can uniquely orient the topology of supertwisted DNA.

To show that DNA containing sharp sequence-directed curvature can preferentially establish ends of supertwisted domains, a highly curved DNA from Crithidia fasciculata was cloned into two sites separated by 28% in pBR325. When this construct (pJGC2) was examined by electron microscopy, 63% of the supercoiled molecules were branched with three or more arms, and the remaining molecules appeared as linear interwound rods. The distance between the tips of two of the arms for the branched molecules measured within 2% of 28% of the DNA contour for 32% of the pJGC2 molecules, as contrasted with only 6.6% for the poorly branched pBR325 DNA. When one of the curved segments in pJGC2 was replaced by a highly curved fragment from SV40, similar results were obtained.

Animals↗
PubMed1988

A knotted free minicircle in kinetoplast DNA.

Kinetoplast DNA, the mitochondrial DNA of trypanosomes, is a network containing thousands of minicircles that are topologically interlocked. The minicircle replication intermediates are free molecules that have been released from the network. We report here that one form of free minicircles is a trefoil knot. Identification of this knotted structure is based on its electrophoretic and sedimentation properties, its response to treatments with restriction enzymes or topoisomerase II, and its appearance by electron microscopy. Except for its topology, the knotted minicircle closely resembles a previously described replication intermediate with a unique gap in the newly synthesized L strand.

Animals↗
PubMed1988

DNA strand exchanges.

Biochemical and electron microscopic studies of the strand exchange reactions catalyzed by the RecA protein of Escherichia coli and the UvsX protein of T4 phage reveal that these reactions proceed in three distinct steps. The first step, termed joining, involves the assembly of RecA (or UvsX) protein onto a single-stranded DNA (ssDNA) molecule and the subsequent search for homology with a double-stranded DNA (dsDNA) partner and formation of a stable synapsis. In the second step (envelopment/exchange), the exchange of DNA strands occurs fueled by the hydrolysis of ATP. The third step (release of products) entails the resolution of the complexes and dissociation of the protein from the DNAs. The structure of the intermediates in the in vitro reactions catalyzed by the RecA and UvsX proteins is emphasized in this review. The results of pairing different DNA molecules in vitro (such as linear ssDNA pairing with linear or supertwisted dsDNA) are described. Paranemic joints represent a major pathway of joining between two DNA molecules which may involve, in some cases, most of the DNA substrate molecules. Since the nature of paranemic joints has only recently begun to be understood, the nature, role, and possible in vivo function of paranemic joining are considered.

DNA↗
PubMed1987

Cationic metals promote sequence-directed DNA bending.

A DNA segment of approximately 200 base pairs (bp) from Crithidia fasciculata kinetoplast minicircles was previously shown by electron microscopy (EM) to bend into a small circle due to its unique nucleotide sequence containing repeated blocks of 4-6 A's. When this segment was flanked by 207 bp of plasmid DNA on one side and 460 bp on the other, the resulting 890-bp DNA was found to appear either relatively straight or extremely bent as visualized by EM. The bend was located one-third the distance from one end. The fraction of molecules with the most extreme bend increased from approximately 2% to 50-60% following incubation of the DNA with increasing concentrations of Zn2+, Co2+, Ba2+, and Mn2+. These observations suggest that sequence-directed bending in DNA is an inducible and not a static phenomenon. Possible roles of transitions between the bent and straight conformations in the control of gene expression are discussed.

Animals↗
PubMed1986

Investigation of the abuse liability of buspirone in alcohol-dependent patients.

By use of the Addiction Research Center Inventory, the Amphetamine Self-Rating Scale, the Single-Dose Questionnaire, and selected physiologic measures (blood pressure, pulse and respiratory rates, oral temperature, and pupil diameter), the abuse liability of buspirone (10, 20, and 40 mg) was compared with that of diazepam (10 and 20 mg) and placebo in 19 subjects who were hospitalized for the treatment of alcohol dependency. Each treatment was given as a single dose at intervals of at least three days according to a double-blind, six-period, crossover Latin square design. Neither buspirone nor diazepam had any effect on blood pressure, pulse and respiratory rates, or body temperature. A small, transient pupillary constriction was evident in the 20- and 40-mg buspirone groups, but it dissipated within two hours after dosing. Both buspirone and diazepam had only a small stimulating effect on appetite. On the Pentobarbital-Chlorpromazine-Alcohol Group and Sedation subscales of the Addiction Research Center Inventory, the 40-mg dose of buspirone yielded effects suggestive of a mild sedative-type drug. Only the 20-mg dose produced a significant effect on the Euphoria scale. Diazepam appeared to be more active as a sedative-hypnotic type of drug, by virtue of its effects on both the Amphetamine and Euphoria subscales and its greater effects on the Morphine-Benzedrine Group, Pentobarbital-Chlorpromazine-Alcohol Group, and Sedation subscales, suggesting euphoria. Not only does the lack of effect of buspirone on the Amphetamine and Morphine-Benzedrine Group subscales indicate lack of a euphorigenic property, but the score on the Lysergic Acid Diethylamide subscale, especially in the 40-mg group, suggests a dysphorigenic property at high doses. On the Amphetamine Self-Rating Scale, buspirone and diazepam affected only the sleep factor and only the 40-mg buspirone dose was distinguishable from placebo. On the Single-Dose Questionnaire, both buspirone and diazepam tended to be rated more as sedative-type drugs, but buspirone was generally less well liked than diazepam. Overall, the results, which suggest a lack of euphoria and the presence of dysphoria at high doses, indicate that buspirone has only limited, if any, abuse liability.

Administration, Oral↗
PubMed1985

Genetic rearrangement of DNA induces knots with a unique topology: implications for the mechanism of synapsis and crossing-over.

We have determined the topological sign of the knots produced by a cycle of phage lambda integrative recombination. To insure that these knots reflect intrinsic features of the reaction mechanism, the substrate was constructed so that random interwrapping of segments of DNA played a minimal role in the topological outcome. The knotted DNA was coated with the bacteriophage T4 uvsX gene product and examined in the electron microscope to determine the nature of each crossing point or node. All of the knots were identical; they were trefoils with three nodes of positive sign. We interpret this result to mean that one recombination site, which previous work had indicated is organized into a nucleosome-like structure, is wrapped with a handedness identical to that found in nucleosomes. Therefore, this wrapping may explain the dependence of recombination on supercoiling of the substrate DNA. Moreover, we show that the topological result sharply limits acceptable mechanisms for the details of strand exchange.

Bacteriophage lambda↗
PubMed1984

Visualization of SSB-ssDNA complexes active in the assembly of stable RecA-DNA filaments.

We have demonstrated that SSB binds to ssDNA in a complex manner, producing two fundamentally different structures: one that appears as a nucleosomal chain of beads and linkers, and the other as a smooth-contoured, extended nucleoprotein filament. Under physiologic salt conditions, only the beaded complexes were observed. Experiments indicate that the highly beaded forms are the most active in the assembly of the stable RecA-ssDNA filaments. These results further support our previous suggestion (Chrysogelos and Griffith 1982) that the protein-free linker regions are important in two ways. First, they provide access to the DNA template, and second, they provide a means for the two proteins to associate one with the other when bound to ssDNA. We suggest here that SSB should be considered as an assembly factor for RecA in its binding to ssDNA. Furthermore, our results argue that once RecA has associated with both the ssDNA template and SSB, some structural alteration in the (ATP-primed) RecA must occur that nucleates the formation of the very ordered, helical RecA filament along the ssDNA.

DNA, Bacterial↗
PubMed1983

Gyrase . DNA complexes visualized as looped structures by electron microscopy.

Gyrase bound to duplex DNA in the absence of ATP is seen by electron microscopy as a nearly spherical particle frequently located at the intersection of two duplex DNA strands. Such looped structures with gyrase situated at the base of the loops are observed with both linear and circular DNA substrates, and two or three individual DNA molecules bound to the same protein are also seen at high DNA concentrations. Addition of the nonhydrolyzable beta,gamma-imido analog of ATP to the gyrase . DNA reaction mixture prior to sample fixation for microscopy reduces the frequency of gyrase molecules found at DNA intersections. Looped structures similar to those of the gyrase . DNA complex are also seen with the complex of DNA and the A subunit of gyrase. When negatively supercoiled DNA which has been partially relaxed by gyrase in the absence of ATP is fixed for electron microscopic examination, intermediate forms are observed that contain both supercoiled and relaxed loops in a single DNA molecule, with the enzyme located at the common base of the loops. These results suggest that gyrase possesses multiple DNA-binding sites, a feature which allows the enzyme to hold DNA in constrained loops. The relation of these observations to the mechanism of gyrase action is discussed.

Base Composition↗
PubMed1983

Bupropion: clinical assay for amphetamine-like abuse potential.

Bupropion hydrochloride (100, 200, and 400 mg), d-amphetamine sulfate (15 and 30 mg), and placebo were compared in 13 volunteers who had histories of amphetamine abuse. Each dose was given orally at intervals of 3 or more days according to a double-blind, randomized crossover design. Bupropion had little or no effect on blood pressure, pulse rate, respiration, body temperature, pupil diameter, subjective appetite, food intake, sleep, or selected subscales of the Addiction Research Center Inventory and Single Dose Questionnaire. Conversely, d-amphetamine was active on most measures. It is concluded that, despite bupropion's reinforcing properties in animals, the compound is not amphetamine-like and is unlikely to give rise to such abuse in humans.

Adult↗
PubMed1982

Filamentous structures associated with Epstein-Barr virus-infected cells.

After the onset of Epstein-Barr virus DNA and protein synthesis 10 h after superinfection of Raji cells (a cell line containing Epstein-Barr virus DNA but not producing virus), filamentous structures 25 nm in diameter and 0.2 to 1.4 micrometers in length could be detected in the cell cytoplasm by electron microscopy. These structures banded in metrizamide gradients with viral DNA and proteins, but at a density different from that of virions or nucleocapsids. These filaments, enriched in a 155,000-dalton protein similar in size to a major nucleocapsid protein of Epstein-Barr virus, may represent intermediates in viral nucleocapsid assembly.

Acyclovir↗