On the processivity of polymerases.
Explore the source record for details and available documents.
DNA Replication↗
Biomedical subjects
F R Fairfield
Publications and source records attributed to F R Fairfield.
Rapid DNA sequencing based upon single molecule detection.
We are developing a laser-based technique for the rapid sequencing of 40-kb or larger fragments of DNA at a rate of 100 to 1000 bases per second. The approach relies on fluorescent labeling of the bases in a single fragment of DNA, attachment of this labeled DNA fragment to a support, movement of the supported DNA fragment into a flowing sample stream, and detection of individual fluorescently labeled bases as they are cleaved from the DNA fragment by an exonuclease. The ability to sequence large fragments of DNA will significantly reduce the amount of subcloning and the number of overlapping sequences required to assemble megabase segments of sequence information.
Base Sequence↗
Studies on mitochondrial type I topoisomerase and on its function.
We have reported previously that rat liver mitochondria contain a topoisomerase and have shown it to be distinct from the nuclear enzyme by its sensitivity to Berenil and ethidium bromide. We report here some additional characterization. The enzyme differs further from its nuclear counterpart in its failure to bind to ssDNA cellulose and its chromatographic behavior on Sephadex; the latter procedure yields an Mr of 44 000 for the mitochondrial and 70 000 for the nuclear enzyme. The topoisomerase is strongly associated with mitochondrial membranes; only 10% of the activity could be extracted. The pH optimum of the enzyme falls between 6.0 and 8.5, with an NaCl optimum of 0.13 M in 0.1 M Tris (pH 8.3). Dithiothreitol is required, while N-ethylmaleimide is inhibitory. Tosylphenylalanine chloromethyl ketone, a serine proteinase inhibitor, abolishes activity; another, phenylmethanesulfonyl fluoride, has no effect. Berenil, a non-intercalating drug, and four of its analogues all inhibit with up to 100-fold differences in potency. No dependence on ATP, Mg2+, or both together could be shown. Neither novobiocin nor oxolinic acid shows any inhibitory effect. Nicked circles are generated in the presence of DMSO. These three observations are consistent with the topoisomerase being of the Type I class. Positively supercoiled pBR322 DNA, whose 6-8 positive turns were generated by altering solution conditions, is relaxed by the enzyme, indicating a lack of requirement for a negatively supercoiled substrate. We have also examined a partially purified preparation of the corresponding mitochondrial enzyme from mouse L cells. This enzyme is largely similar in properties to the rat liver enzyme. In isolated mitochondria, Berenil causes biphasic alterations in [3H]dATP incorporation into DNA, 10(-4) mM stimulating 2-fold, while higher concentrations inhibit. [3H]UTP incorporation into mitochondrial RNA also follows this pattern.
Animals↗
Coupling with packaging explains apparent nonreciprocality of Chi-stimulated recombination of bacteriophage lambda by RecA and RecBC functions.
Chi (chi, 5'-GCTGGTGG) is a recombinator in RecA- and RecBC-mediated recombination in Escherichia coli. In vegetative recombination between two bacteriophage lambda strains, one with and the other without Chi (a+ chi +b- X a- chi 0b+), the chi-containing recombinant (a- chi +b-) is less abundant than the non-chi-containing recombinant (a+ chi 0b+). Previously this was taken was evidence for nonreciprocality of chi-stimulated exchange. This inequality, however, is now seen to result from an event at cos (lambda's packaging origin) that both activates Chi and initiates DNA packaging. An event at rightward cos leads to activation of leftward chi on the same chromosome for an exchange to its left. From the resulting circulating dimer (--cos-a+- chi 0-b+-cos-a-- chi +-b- --), the cos that activated chi is more likely to be used for rightward packaging initiation than is the cos from the other parent. Consistent with this coupling model is "biased packaging" in lambda carrying two cos sites per monomer genome. When their maturation is dependent on dimerization by chi-stimulated exchange, the phage particles result more often from packaging from the cos that activates chi than from packaging from the other cos. Since Chi activation and packaging can be uncoupled, we infer that some early and reversible step in packaging activates chi. A strong candidate for this step is a double-strand break at cos that provides an oriented entry site for a recombinase.
Bacterial Proteins↗
On the processivity of DNA replication.
In this paper we describe the nature and importance of processive enzymatic reactions in biological processes. A model is set up to describe the processive synthetic process in DNA replication, and experiments are presented to define and test the model, using the components of the T4 phage-coded five-protein (in vitro) DNA replication system of Alberts. Nossal and coworkers. These experiments are performed either with a homogeneous oligo dT-poly dA primer-template system, or with a natural primer-template system using phage M13 DNA. The results are used to define some molecular aspects of the microscopic "processivity cycle".
Base Sequence↗
A staining procedure for identifying viable cell hybrids constructed by somatic cell fusion, cybridization, or nuclear transplantation.
A general procedure for identifying viable hybrid cells was developed. One cell type was labeled by a brief incubation in the Kodak laser dye rhodamine 123, which accumulates in the mitochondria; a second cell type was labeled by a brief incubation in the Hoechst fluorochrome 33258, which binds to chromatin. The substances which are eventually lost from the organelles, appeared to be nontoxic; the plating efficiencies of numerous cell lines tested was unaffected. Either whole cells or cytoplasts labeled with rhodomine 123 were fused, using inactivated Sendai virus, to whole cells or karyoplasts labeled with Hoechst 33258. When living cells were illuminated with ultraviolet light, individual whole cell hybrids, cybrids or cytoplasmic- nuclear hybrid cells could be rapidly identified by the appropriate staining pattern.
Animals↗
Mitochondria contain a distinct DNA topoisomerase.
A topoisomerase (nicking-closing enzyme) has been isolated from rat liver mitochondria. It has purified by double-stranded DNA-cellulose chromatography approximately 50,000-fold, based on the crude mitochondrial extract. It possesses a minimum specific activity of 1.9 x 10(5) units/mg. The enzyme has been shown to be distinctly mitochondrial, differentiated from the nuclear topoisomerase by its sensitivity to the intercalating drug, ethidium bromide, and to the non-intercalating trypanocidal drug, Berenil.
Animals↗