Heterogeneity in Deoxyribonucleic Acids: I. Dependence on Composition of the Configurational Stability of Deoxyribonucleic Acids

Marmur, Julius; Doty, Paul

doi:10.1038/1831427a0

Cited by 450 publications

(68 citation statements)

References 6 publications

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“…The nature of the polymorphs requires further analysis. with three hydrogen bonds, gave higher thermal stability than the A-T pairing, which has only two such bonds (Marmur and Doty, 1959).…”

Section: Consmentioning

confidence: 99%

Standard methods for virus research inApis mellifera

Miranda

Bailey

Ball

et al. 2013

Journal of Apicultural Research

264

229

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SummaryHoney bee virus research is an enormously broad area, ranging from subcellular molecular biology through physiology and behaviour, to individual and colony-level symptoms, transmission and epidemiology. The research methods used in virology are therefore equally diverse.This article covers those methods that are very particular to virological research in bees, with numerous cross-referrals to other BEEBOOK papers on more general methods, used in virology as well as other research. At the root of these methods is the realization that viruses at their most primary level inhabit a molecular, subcellular world, which they manipulate and interact with, to produce all higher order phenomena associated with virus infection and disease. Secondly, that viruses operate in an exponential world, while the host operates in a linear world and that much of the understanding and management of viruses hinges on reconciling these fundamental mathematical differences between virus and host. The article concentrates heavily on virus propagation and methods for detection, with minor excursions into surveying, sampling management and background information on the many viruses found in bees. Métodos estándar para la investigación de virus en Apis mellifera ResumenLa investigación de los virus de la abeja de la miel es un área sumamente amplia, que abarca desde la biología molecular subcelular hasta la fisiología y el comportamiento, desde síntomas al nivel de individuo hasta al nivel de la colmena, transmisión y epidemiología. Los métodos de investigación en virología son, por tanto, diversos. Este artículo incluye aquellos métodos específicos de la investigación virológica en las abejas, con numerosas referencias cruzadas con otros artículos del BEEBOOK y otros más generales, usados tanto en virología como en otras disciplinas. La base de estos métodos es la comprensión de los virus en su nivel primario de hábitat molecular, ambiente subcelular, que manipulan y con el que interactúan, para producir otros fenómenos de orden superior asociados a la infección del virus y la enfermedad. En segundo lugar, estos virus actúan en un mundo exponencial, mientras que los hospedadores actúan en un mundo lineal y gran parte del entendimiento y manejo de los virus depende de los fundamentos matemáticos de las diferencias entre el virus y el hospedador. El artículo se centra principalmente en la propagación de virus y en los métodos para su detección, con inclusiones menores en su estudio, el manejo del muestreo y la información general sobre los numerosos virus que se encuentran en las abejas.

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Section: Consmentioning

confidence: 99%

Standard methods for virus research inApis mellifera

Miranda

Bailey

Ball

et al. 2013

Journal of Apicultural Research

264

229

View full text Add to dashboard Cite

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“…Since poly(dA-dT) sequences have a melting temperature of about 65°C at physiologic ionic strength (28) [about 10°C…”

Section: Methodsmentioning

confidence: 99%

Foreign DNA introduced by calcium phosphate is integrated into repetitive DNA elements of the mouse L cell genome.

Kato¹,

Anderson²,

Camerini‐Otero³

1986

Mol. Cell. Biol.

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We investigated the sites of integration of exogenous DNA fragments introduced by DNA-mediated gene transfer. Mouse Ltk-cells were transformed with the herpes simplex virus thymidine kinase gene and pBR322 DNA by the calcium phosphate precipitation method. Some of the integrated exogenous DNA sequences were recovered from the stable tk+ transformants in the form of plasmids that were capable of propagation in bacteria. Four plasmids derived from two cloned cell lines were analyzed in detail by nucleotide sequencing and hybridization techniques. These plasmids contained a total of seven cellular-exogenous DNA junctions. In all cases, there was no sequence homology between the exogenous and cellular DNA sequences adjacent to the joining sites, and no specific exogenous or cellular sequences occurred at the junctions. Rearrangement or deletion of Ltk-DNA was always associated with the integration of exogenous DNA. All of the assignable cellular sequences at the junctions were repetitive sequences. Two of these sequences were from the MIF-1 repetitive sequence family, and a third consisted of a 40-base pair simple copolymer of alternating deoxyadenosine-deoxythymidine. Our results suggest that repetitive sequences are relatively favorable sites for the integration of exogenous DNA.Homologous recombination of foreign DNA with the host genome is sufficiently frequent in procaryotes (33) and lower eucaryotes (18) that it is possible to confidently predict the integration site of the introduced DNA. Since such efficient "targeting" of DNA into homologous sequences has not yet been demonstrated in mammalian cells (41), we asked whether the foreign DNA is integrated randomly or at some preferred sites other than the homologous sequences. Although a number of workers have reported on the DNA sequences at the integration sites of viral DNAs that have been introduced into mammalian cells (3,11,37,39), there have been no reports of a similar analysis for the integration of nonviral DNAs. Even though it has been established that at the level of chromosome analysis foreign, nonviral DNAs are integrated randomly (36), there is no information on the DNA sequences at the integration sites of exogenous nonviral DNAs.Since the site of integration may be influenced by proteins encoded by the DNA in question (as appears to be the case for the genomes of some eucaryotic viruses [34]) as opposed to DNA which relies solely on the cellular machinery for its integration, we examined integration sites resulting from the transfer of purified gene fragments and procaryotic DNA. Following transformation of mouse Ltk-cells with a herpes simplex virus thymidine kinase gene (tk) fragment and pBR322 DNA, individual colonies of stable tk+ transformants were isolated and expanded. A plasmid rescue technique was used to recover the integrated exogenous DNA and flanking cellular sequences from the genomic DNA of these cell lines (1, 2). We analyzed the sequences encompassing seven cellular-exogenous DNA junctions. MATERIALS AND METHODSDNA-mediated ge...

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“…It is known that the melting temperatures depend logarithmically on the sodium concentration [N a + ] in the solvent [51,52]. As the melting temperatures scale essentially linearly with the Morse potential barrier, also the latter can be assumed to vary logarithmically with [N a + ] [16].…”

Section: Hamiltonian Modelmentioning

confidence: 99%

Thermodynamics of twisted DNA with solvent interaction

Zoli

2011

The Journal of Chemical Physics

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The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over ∼ 10 7 − 10 8 base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.

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Heterogeneity in Deoxyribonucleic Acids: I. Dependence on Composition of the Configurational Stability of Deoxyribonucleic Acids

Cited by 450 publications

References 6 publications

Standard methods for virus research inApis mellifera

Standard methods for virus research inApis mellifera

Foreign DNA introduced by calcium phosphate is integrated into repetitive DNA elements of the mouse L cell genome.

Thermodynamics of twisted DNA with solvent interaction

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