DNA probe for Aeromonas salmonicida.

A DNA fragment that is specific to Aeromonas salmonicida has been isolated from a genomic DNA library by differential hybridization. The specificity of this fragment as a DNA probe for A. salmonicida was shown by hybridization against reference strains and clinical isolates of A. salmonicida, related aeromonads, and species from several other bacterial genera. The sensitivity of detection by a polymerase chain reaction test, based on this fragment, was approximately two A. salmonicida cells.     

DNA probe for Aeromonas salmonicida.

A DNA fragment that is specific to Aeromonas salmonicida has been isolated from a genomic DNA library by differential hybridization. The specificity of this fragment as a DNA probe for A. salmonicida was shown by hybridization against reference strains and clinical isolates of A. salmonicida, related aeromonads, and species from several other bacterial genera. The sensitivity of detection by a polymerase chain reaction test, based on this fragment, was approximately two A. salmonicida cells.     

Comparison of radio-labeled DNA probe with a nonisotopic probe for assay of serum hepatitis B virus DNA

A biotin-labeled DNA probe was compared to a 32P radio-labeled DNA probe for the detection of serum hepatitis B virus (HBV) DNA. Serum specimens were treated with proteolytic enzyme and detergent. DNA was extracted using phenol, denatured in sodium hydroxide and applied to a nitrocellulose filter paper using a vacuum filter device. The nitrocellulose filters were then incubated with either the biotin-labeled or the radio-labeled probe. Annealing of the probe, indicating the presence of HBV-DNA in the sample, was detected either by autoradiography for the 32P-labeled probe or by measuring the presence of an acid phosphatase attached to a streptavidin molecule for the biotin-labeled probe. Using the same 2-day time to complete the assays, excellent correlation of the qualitative and semiquantitative measurements were obtained using 20 HBsAg-positive and 9 HBsAg-negative sera. The nonisotopic assay detected 1.0 pg of HBV-DNA, a sensitivity comparable to reported sensitivities of 32P-labeled HBV-DNA probes when similar assay times are used. 0.02 pg/microliter of HBV-DNA was detected in a normal serum to which HBV-DNA in a recombinant plasmid was added. Our results indicate that the biotin-labeled HBV-DNA probe is approximately as sensitive as the radio-labeled probe for the detection of HBV-DNA using a similar assay time. Isotopic probe assays are more sensitive with longer assay times. The biotin-labeled probe offers the advantage of a longer shelf life and a nonisotopic assay procedure.     

An oligonucleotide probe to assay lysis and DNA hybridization of a diverse set of bacteria

A computer bank of 16 S rRNA bacterial sequences was searched to determine a consensus sequence expected to hybridize with DNA from a wide variety of bacteria. An oligonucleotide probe, named a panprobe, containing this sequence was used to assay the degree of lysis of bacterial colonies on filter paper heated in a microwave oven and subsequently treated with NaOH. As determined by colony hybridization with the panprobe, lysis was achieved for 51 of 59 different species of bacteria tested. DNA, isolated from the eight bacteria not detected by colony hybridization, did hybridize with the panprobe in slot blot hybridizations.     

Brownian dynamics simulation of probe diffusion in DNA: effects of probe size, charge and DNA concentration

We have used Brownian dynamics simulation to study probe diffusion in solutions of short chain DNA using our previously developed simulation algorithm. We have examined the effect of probe size, charge, and DNA concentration on the probe diffusion coefficient, with the aim of gaining insight into the diffusion of proteins in a concentrated DNA environment. In these simulations, DNA was modeled as a worm-like chain of hydrodynamically equivalent spherical frictional elements while probe particles were modeled as spheres of given charge and hydrodynamic radius. The simulations allowed for both short range Lennard-Jones interactions and long ranged electrostatic interactions between charged particles. For uncharged systems, we find that the effects of probe size and DNA concentration on the probe diffusion coefficient are consistent with excluded volume models and we interpret our results in terms of both empirical scaling laws and the predictions of scaled particle theory. For charged systems, we observe that the effects of probe size and charge are most pronounced for the smallest probes and interpret the results in terms of the probe charge density. For an ionic strength of 0.1 M we find that, below a critical probe surface charge density, the probe diffusion coefficient is largely independent of probe charge and only weakly dependent on the DNA charge. These effects are discussed in terms of the interactions between the probe and the DNA matrix and are interpreted in terms of both the underlying physics of transport in concentrated solutions and the assumptions of the simulation model.     

Applications of universal probe on DNA hybridization

A convenient method for DNA hybridization termed "Universal probe" is described which is based on the principle of sandwich hybridization. This system consists of two probes: primary probe which is single-stranded DNA prepared from a chimeric phage-plasmid vector containing the complementary sequence to a target; and labeled secondary probe which has an opposite strand of the primary probe without the complementary sequence. By use this universal probe human beta-globin gene was able to be detected on Southern blots of genomic DNA. A potential advantage of this method is that the single-stranded primary probe is prepared easily by the chimeric phage-plasmid vector system and tedious labeling is not needed each time.     

The fluorescence properties of a DNA probe

Steady-state and dynamic fluorescence measurements have been performed on DAPI in solution and in complexes formed with a number of synthetic and natural polydeoxynucleotides. The decay of DAPI in buffer at pH 7 was decomposed using two exponentials having lifetime values of approximately 2.8 ns and 0.2 ns. The double exponential character of the decay was maintained over a large pH range from 3 to 9. At pH 1 the short component dominated, whereas at pH 12, only the long component was detectable. Two distinct spectra were associated with the two lifetime components; the short component was shifted to the red. The short lifetime component occurs in the presence of water. In water the excitation spectra depended on the emission wavelength and there was no viscosity dependence of the two forms. To explain these results we propose that there is a ground state conformer in which preferential solvation of the indole ring allows proton transfer in the excited state. DAPI complexed with polydeoxynucleotides retained most of the features of the decay of DAPI in solution. However, the complexes with fuly AT-containing polymers stabilized the longer lifetime form of DAPI because the stronger binding enhanced solvent shielding. A gradual increase of the short lifetime component, which monitors dye solvent exposure, was obtained as the AT content was decreased. For polyd(GC) the decay was similar to that of free DAPI.Abbreviations DAPI 4-6-diamidino-2-phenylindole - POPOP 1,4-bis(5-phenyl-2-oxazolyl)-benzene; 2,2-p-phenylene-bis(5-phenyloxazole) Financial support for this work was provided by a M.P.I. grant 1984, Roma, Italy for M.L.B. and NSF-PCM 84-03107 and PHS-IP41RR03155 for E.G.     

Specific DNA probe for detecting Legionella pneumophila

A fragment of the gene for cytolysin has been cloned. The product of the gene has been earlier identified as an immunoserological marker of Legionella pneumophila. Clones were selected by immunodetection of cytolysin gene product expression. An EcoRI 3.8 kb fragment of the genomic DNA from Legionella pneumophila strain Philadelphia-1 was used as a DNA probe that hybridized with the bacterial colonies of 20 Legionella pneumophila strains but not with the colonies of 10 other Legionella species or 8 other bacterial genera. The cloned fragment has been shown to be unique for Legionella pneumophila. The region of homology is suggested to be longer than a possible dimension of the cytolysin gene.     

Preparation of enzyme-conjugated DNA probe and application to the universal probe system.

A general procedure for the cross-linking of enzyme to DNA has been developed for use as a nonradioactive probe. In this method, DNA is transaminated with diaminopropane to introduce primary amino groups into the cytosine residues. Then the amino groups are converted to thiol groups using a heterobifunctional cross-linker. The thiolated DNA is conjugated with the maleimide-introduced enzyme. With this method, alkaline phosphatase was cross-linked to a single-stranded DNA (sspUCRf1). The conjugate was able to detect 5 pg of target DNA (pUCf1 plasmid, 3.2 kbp) fixed onto the nitrocellulose membrane, using a colorimetric assay. The enzyme-conjugated DNA was applied to "the universal probe system," which consisted of two single-stranded DNA probes (a primary probe and a labeled secondary probe). Using alkaline phosphatase-conjugated sspUCRf1 DNA as the secondary probe, the c-myc gene and HBV DNA were detected effectively on Southern and dot-blot hybridization.     

纳米粒子标记DNA探针在电化学DNA生物传感器中的应用

介绍了纳米电化学DNA生物传感器的基本概念和分类,并介绍了用于DNA标记的纳米粒子的六种类型及其三大检测方法,在此基础上对纳米电化学DNA生物传感器在基因检测、疾病诊断、DNA检测等方面的最新进展进行了综述与讨论.     

纳米粒子标记DNA 探针在电化学DNA 生物传感器中的应用

介绍了纳米电化学DNA生物传感器的基本概念和分类,并介绍了用于DNA标记的纳米粒子的六种类型及其三大检测方法,在此基础上对纳米电化学DNA生物传感器在基因检测、疾病诊断、DNA检测等方面的最新进展进行了综述与讨论。     

Evolving DNA motifs to predict GeneChip probe performance

Background  

Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe.     

Identification of Mycoplasma hyopneumoniae with a DNA probe

From a genomic library of Mycoplasma hyopneumoniae a 1.3 kb DNA fragment was cloned which showed specific Southern hybridization and dot hybridization with the type strain of several porcine and bovine Mycoplasma species. This probe selectively recognized M. hyopneumoniae sequences in purified DNA or in broth-grown organisms. The 35S-labelled probe could detect as little as 100 pg of DNA or 10(5) colour changing units. This is a possible alternative diagnostic procedure for enzootic pneumonia of pigs.