Quantitation of polymerase chain reaction products by capillary electrophoresis using laser fluorescence.
AuthorsButler JM, McCord BR, Jung JM, Wilson MR, Budowle B, Allen RO
JournalJ Chromatogr B Biomed Appl
PubMed ID7820255
In samples where the amount of DNA is limited, the polymerase chain reaction (PCR) can amplify specific regions of the DNA. A quantitative analysis of the PCR product would be desirable to ensure sufficient DNA is available for analysis. In this study, we examine the use of capillary electrophoresis (CE) ... More
Role of diacylglycerol kinase alpha in the attenuation of receptor signaling.
AuthorsSanjuán MA, Jones DR, Izquierdo M, Mérida I
JournalJ Cell Biol
PubMed ID11285286
'Diacylglycerol kinase (DGK) is suggested to attenuate diacylglycerol-induced cell responses through the phosphorylation of this second messenger to phosphatidic acid. Here, we show that DGKalpha, an isoform highly expressed in T lymphocytes, translocates from cytosol to the plasma membrane in response to two different receptors known to elicit T cell ... More
Flow cytometric monitoring of antibiotic-induced injury in Escherichia coli using cell-impermeant fluorescent probes.
AuthorsMortimer FC, Mason DJ, Gant VA
JournalAntimicrob Agents Chemother
PubMed ID10681337
'Three fluorescent nucleic acid binding dyes-propidium iodide, TO-PRO-1, and SYTOX green-were evaluated, and their abilities to distinguish between bacterial cells with and without an intact cytoplasmic membrane were compared. Each dye was readily able to discriminate between healthy and permeabilized cells of Escherichia coli, although SYTOX green showed a greater ... More
Spectral measurements of intercalated PCR-amplified short tandem repeat alleles.
AuthorsMarino MA, Devaney JM, Davis PA, Smith JK, Girard JE
JournalAnal Chem
PubMed ID9823710
'Short tandem repeat (STR) alleles are popular for use as forensic markers due to their highly polymorphic nature. Commonly they are separated by gel electrophoresis and visualized using intercalation dyes. The purpose of this study was to determine the changes in absorbance and fluorescence of DNA-intercalation dye complexes as a ... More
TOTO and YOYO: new very bright fluorochromes for DNA content analyses by flow cytometry.
AuthorsHirons GT, Fawcett JJ, Crissman HA
JournalCytometry
PubMed ID7513274
'Flow cytometric (FCM) studies were performed on nuclei, ethanol-fixed CHO cells, and isolated human GM130 chromosomes stained with two new cyanine dyes, TOTO and YOYO. These fluorochromes, which are dimers of thiazole orange and oxazole yellow, respectively, have high quantum efficiencies and exhibit specificities for both DNA and RNA. Bound ... More
Phosphatidylethanolamine mediated destabilization of lipid-based pDNA delivery systems.
'We have previously reported the development of lipid-DNA particles (LDPs) formed, via a hydrophobic cationic lipid-DNA complex intermediate, when detergent-solubilized cationic lipids are mixed with DNA. This study investigates the influence of zwitterionic co-lipid headgroups on the formation and stability of this intermediate and the subsequent DNA protection and transfection ... More
Versatile low-viscosity sieving matrices for nondenaturing DNA separations using capillary array electrophoresis.
AuthorsMadabhushi RS, Vainer M, Dolnik V, Enad S, Barker DL, Harris DW, Mansfield ES
JournalElectrophoresis
PubMed ID9059830
'The high-resolution separation of double-stranded DNA (dsDNA) has important applications in physical mapping strategies and in the analysis of polymerase chain reaction (PCR) products. Although high-resolution separations of dsDNA by capillary electrophoresis (CE) have been reported, pulsed fields were required to achieve complete resolution of DNA fragments beyond 23 kilobase ... More
Assessment of the anti-microbial agent C31G as a spermicide: comparison with nonoxynol-9.
AuthorsThompson KA, Malamud D, Storey BT
JournalContraception
PubMed ID8724622
'The broad-spectrum anti-microbial agent, C31G, containing an equimolar mixture of n-dodecyl-dimethylamine-N-oxide (C12-N-O) and N-(n-dodecyl), N-dimethyl-glycine (C12-betaine), was tested for spermicidal activity in comparison with the currently used spermicide, nonoxynol-9 (N-9). The rate of sperm cell permeabilization by the spermicides, as assayed with the fluorescent probe, TO-PRO-1, increased as the cube ... More
Microchip device for cell lysis, multiplex PCR amplification, and electrophoretic sizing.
AuthorsWaters LC, Jacobson SC, Kroutchinina N, Khandurina J, Foote RS, Ramsey JM
JournalAnal Chem
PubMed ID9463271
'The steps of cell lysis, multiplex PCR amplification, and electrophoretic analysis are executed sequentially on a monolithic microchip device. The entire microchip is thermally cycled to lyse cells and to amplify DNA, and the products are then analyzed using a sieving medium for size separation and an intercalating dye for ... More
A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA.
AuthorsProdhomme S, Demaret JP, Vinogradov S, Asseline U, Morin-Allory L, Vigny P
JournalJ Photochem Photobiol B
PubMed ID10672530
'The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)3-N+(CH3)3 and -(CH2)6-I)) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, ... More
Self-assembling DNA-lipid particles for gene transfer.
AuthorsZhang YP, Reimer DL, Zhang G, Lee PH, Bally MB
JournalPharm Res
PubMed ID9090708
'PURPOSE: We have demonstrated that a heteromolecular complex consisting of cationic lipids and DNA can be prepared and isolated (1). Cationic lipids bind DNA through electrostatic interactions. However, when sufficient lipids are bound to DNA the physical and chemical properties of the complex are governed by hydrophobic effects. Here we ... More
Characteristics of different nucleic acid staining dyes for DNA fragment sizing by flow cytometry.
AuthorsYan X, Grace WK, Yoshida TM, Habbersett RC, Velappan N, Jett JH, Keller RA, Marrone BL
JournalAnal Chem
PubMed ID10624155
'An efficient and reliable double-stranded DNA (dsDNA) staining protocol for DNA fragment sizing by flow cytometry is presented. The protocol employs 0.8 microM of PicoGreen to label a wide range of DNA concentrations (0.5 ng/mL to 10,000 ng/mL) without regard to the solution dye/bp ratios and without initial quantification of ... More
Multiple sample PCR amplification and electrophoretic analysis on a microchip.
AuthorsWaters LC, Jacobson SC, Kroutchinina N, Khandurina J, Foote RS, Ramsey JM
JournalAnal Chem
PubMed ID9868915
'Polymerase chain reactions (PCRs) were carried out on as many as four DNA samples at a time on a microchip device. The PCR products were then analyzed, either individually or together on the same device, by microchip gel electrophoresis. A standard PCR protocol was used to amplify 199- and 500-base ... More
A modified fluorescent intercalator displacement assay for RNA ligand discovery.
AuthorsAsare-Okai PN, Chow CS,
JournalAnal Biochem
PubMed ID20863807
'Fluorescent intercalator displacement (FID) is a convenient and practical tool for identifying new nucleic acid-binding ligands. The success of FID is based on the fact that it can be fashioned into a versatile screening assay for assessing the relative binding affinities of compounds to nucleic acids. FID is a tagless ... More
Detection of bromodeoxyuridine incorporation by alteration of the fluorescence emission from nucleic acid binding dyes using only an argon ion laser.
AuthorsFrey T
JournalCytometry
PubMed ID7875038
'A method was developed that uses paired DNA dyes to detect the incorporation of bromodeoxyuridine (BrdUrd) into cellular DNA and requires only 488 nm excitation. The fluorescence of thiazole blue, TO-PRO-3, and LDS-751 was found to be enhanced by the presence of BrdUrd in DNA. Pairing LDS-751, thiazole blue, or ... More
PCR amplification and analysis of simple sequence length polymorphisms in mouse DNA using a single microchip device.
AuthorsDunn WC, Jacobson SC, Waters LC, Kroutchinina N, Khandurina J, Foote RS, Justice MJ, Stubbs LJ, Ramsey JM
JournalAnal Biochem
PubMed ID10610701
Staining of DNA in live and fixed cells.
AuthorsCrissman HA, Hirons GT
JournalMethods Cell Biol
PubMed ID7532262
Antibiotic preparations contain DNA: a source of drug resistance genes?
AuthorsWebb V, Davies J
JournalAntimicrob Agents Chemother
PubMed ID8285621
Fluorescence measurements and polymerase chain reaction amplification of streptomycete 16S ribosomal DNA sequences were used to show that a number of antibiotic preparations employed for human and animal use are contaminated with chromosomal DNA of the antibiotic-producing organism. The DNA contains identifiable antibiotic resistance gene sequences; the uptake of this ... More
Control of a genetic regulatory network by a selector gene.
AuthorsGuss KA, Nelson CE, Hudson A, Kraus ME, Carroll SB
JournalScience
PubMed ID11303087
The formation of many complex structures is controlled by a special class of transcription factors encoded by selector genes. It is shown that SCALLOPED, the DNA binding component of the selector protein complex for the Drosophila wing field, binds to and directly regulates the cis-regulatory elements of many individual target ... More
Bacterial adhesion to and viability on positively charged polymer surfaces.
AuthorsTerada A, Yuasa A, Kushimoto T, Tsuneda S, Katakai A, Tamada M,
JournalMicrobiology
PubMed ID17159210
Secondary and tertiary amino groups were introduced into polymer chains grafted onto a polyethylene flat-sheet membrane to evaluate the effects of surface properties on the adhesion and viability of a strain of the Gram-negative bacterium Escherichia coli and a strain of the Gram-positive bacterium Bacillus subtilis. The characterization of the ... More
The polarization of fluorescence of DNA stains depends on the incorporation density of the dye molecules.
AuthorsUy JL, Asbury CL, Petersen TW, van den Engh G,
JournalCytometry A
PubMed ID15351985
BACKGROUND: The fluorescence induced by polarized light sources, such as the lasers that are used in flow cytometry, is often polarized and anisotropic. In addition, most optical detector systems are sensitive to the direction of polarization. These two factors influence the accuracy of fluorescence intensity measurements. The intensity of two ... More
Use of pulsed-field gel electrophoresis to investigate factors influencing the measurement of DNA double-strand breaks in human brain tumour specimens.
AuthorsWang J, Delgado DA, Deen DF
JournalInt J Radiat Biol
PubMed ID7884283
We used pulsed-field gel electrophoresis combined with densitometry to investigate variables influencing the measurement of DNA double-strand breaks (dsb) in human brain tumour cells and frozen tissue. Our studies showed that this system worked best when we ran the gel at 60 V for 22-25 h at 18 degrees C ... More
Microfabricated porous membrane structure for sample concentration and electrophoretic analysis.
AuthorsKhandurina J, Jacobson SC, Waters LC, Foote RS, Ramsey JM
JournalAnal Chem
PubMed ID10330910
A microfabricated injection valve incorporating a porous membrane structure is reported that enables electrokinetic concentration of DNA samples using homogeneous buffer conditions followed by injection into a channel for electrophoretic analysis. The porous membrane was incorporated in the microchannel manifold by having two channels separated from each other by 3-12 ... More
Cell death in the CNS of the Wnt-1 mutant mouse.
AuthorsSerbedzija GN, Dickinson M, McMahon AP
JournalJ Neurobiol
PubMed ID8910786
Using the benzothiazolium-4-quinolium dye, TO-PRO-1, to detect cell death in live embryos, we labeled a developmental series of Wnt-1 null mutant and wild type embryos to determine if cell death contributed to the absence of the midbrain and rostral metencephalon observed in Wnt-1 mutant embryos. We found that there is ... More
Enumeration of small ciliates in culture by flow cytometry and nucleic acid staining.
AuthorsLindström ES, Weisse T, Stadler P
JournalJ Microbiol Methods
PubMed ID11830303
We developed a fast and simple protocol for accurate quantification of small freshwater ciliates by flow cytometry (FCM). The ciliates were stained with several nucleic acid stains such as TO-PRO-1, YO-YO-1 and PicoGreen, and analysed by a commercially available flow cytometer. The method was tested with cultures of the prostomatid ... More
Homogeneous fluorescence detection method for human leukocyte antigen-DR typing following polymerase chain reaction amplification with sequence-specific primer.
AuthorsOkamoto N, Lee A, Kano T, Lee TD
JournalAnal Biochem
PubMed ID7810876
A fluorescent homogeneous method for the detection of sequence-specific amplification of human leukocyte antigen (HLA) alleles has been developed. In this approach, polymerase chain reaction sequence-specific primers (PCR-SSP) are used to amplify DRB1, DRB3, and DRB4 alleles. Lambda exonuclease and Exonuclease I are added to reduce background by digesting template ... More
Neuronal death is an active, caspase-dependent process after moderate but not severe DNA damage.
AuthorsGobbel GT, Chan PH
JournalJ Neurochem
PubMed ID11208915
Mild insults to neurons caused by ischemia or glutamate induce apoptosis, whereas severe insults induce non apoptotic death, such as necrosis. The molecular targets that are damaged by these insults and ultimately induce cell death are not fully established. To determine if DNA damage can induce apoptotic or non apoptotic ... More
Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications.
AuthorsZipper H, Brunner H, Bernhagen J, Vitzthum F
JournalNucleic Acids Res
PubMed ID15249599
The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure-property relationships that affect methods applying SG. These studies ... More
Ultrasonically targeted delivery into endothelial and smooth muscle cells in ex vivo arteries.
AuthorsHallow DM, Mahajan AD, Prausnitz MR
JournalJ Control Release
PubMed ID17291619
This study tested the hypothesis that ultrasound can target intracellular uptake of drugs into vascular endothelial cells (ECs) at low to intermediate energy and into smooth muscle cells (SMCs) at high energy. Ultrasound-enhanced delivery has been shown to enhance and target intracellular drug and gene delivery in the vasculature to ... More
Microbial analysis at the single-cell level: tasks and techniques.
AuthorsShapiro HM
JournalJ Microbiol Methods
PubMed ID11000426
The heterogeneity of microorganisms themselves is orders of magnitude greater than the heterogeneity of perspectives from which they are contemplated by human observers. Even closely related species may exhibit marked differences in biochemistry and behavior, and, under many conditions, similar, striking heterogeneity may exist within a clonal population of organisms ... More
Fluorescence enhancement of DNA-bound TO-PRO-3 by incorporation of bromodeoxyuridine to monitor cell cycle kinetics.
AuthorsBeisker W, Weller-Mewe EM, Nüsse M
JournalCytometry
PubMed ID10520203
BACKGROUND:The detection of DNA-incorporated bromodeoxyuridine (BrdUrd) in mammalian cells is a well-known and important technique to study cell cycle. The use of TO-PRO-3 for detection of BrdUrd substitution of DNA by dual-laser flow cytometry has been investigated. METHODS:Fluorescence enhancement of TO-PRO-3 in BrdUrd-labeled cells is registered in combination with the ... More
Effects of intercalators on complexation of RecA with duplex DNA.
AuthorsTuite E, Kim SK, Nordén B, Takahashi M
JournalBiochemistry
PubMed ID8845362
To elucidate the binding mode of recombination protein A (RecA) to double-stranded (ds) DNA, the effects on the RecA-DNA interaction of several mono- and bisintercalators of the acridine, phenanthridine, and cyanine classes have been investigated by linear dichroism spectroscopy. Simple monointercalators lacking side chains efficiently promoted the binding of RecA ... More
Optimization of intercalation dye concentration for short tandem repeat allele genotyping using capillary electrophoresis with laser-induced fluorescence detection.
AuthorsMarino MA, Devaney JM, Davis PA, Girard JE
JournalJ Chromatogr B Biomed Sci Appl
PubMed ID10517359
DNA analysis using capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection requires that polymerase chain reaction products either be prepared using primers with fluorescent molecules covalently bonded to them, or stained with a fluorescent intercalation dye following amplification. The intercalation technique has the advantage of allowing fluorescence detection of any ... More
Stains, labels and detection strategies for nucleic acids assays.
AuthorsKricka LJ
JournalAnn Clin Biochem
PubMed ID11928759
Selected developments and trends in stains, labels and strategies for detecting and measuring nucleic acids (DNA, RNA) and related molecules [e.g. oligo(deoxy)nucleotides, nucleic acid fragments and polymerase chain reaction products] are surveyed based on the literature in the final decade of the 20th century (1991-2000). During this period, important families ... More
Formation of novel hydrophobic complexes between cationic lipids and plasmid DNA.
AuthorsReimer DL, Zhang Y, Kong S, Wheeler JJ, Graham RW, Bally MB
JournalBiochemistry
PubMed ID7548044
An ability to generate a well defined lipid-based carrier system for the delivery of plasmid DNA in vivo requires the characterization of factors governing DNA/lipid interactions and carrier formation. We report that a hydrophobic DNA/lipid complex can be formed following addition of cationic lipids to DNA in a Bligh and ... More
Characterization of lipid DNA interactions. I. Destabilization of bound lipids and DNA dissociation.
AuthorsHarvie P, Wong FM, Bally MB
JournalBiophys J
PubMed ID9675205
We have recently described a method for preparing lipid-based DNA particles (LDPs) that form spontaneously when detergent-solubilized cationic lipids are mixed with DNA. LDPs have the potential to be developed as carriers for use in gene therapy. More importantly, the lipid-DNA interactions that give rise to particle formation can be ... More
Antigenic and Functional Properties of the Human Red Blood Cell Urea Transporter hUT-B1.
The Kidd (JK) blood group locus encodes the urea transporter hUT-B1, which is expressed on human red blood cells and other tissues. The common JK*A/JK*B blood group polymorphism is caused by a single nucleotide transition G838A changing Asp-280 to Asn-280 on the polypeptide, and transfection of erythroleukemic K562 cells with ... More
A Human IPS Model Implicates Embryonic B-Myeloid Fate Restriction as Developmental Susceptibility to B Acute Lymphoblastic Leukemia-Associated ETV6-RUNX1.
Authors
JournalDev Cell
PubMed ID29290585
The Hairpin Form of r(G4C2)exp in c9ALS/FTD Is Repeat-Associated Non-ATG Translated and a Target for Bioactive Small Molecules.
Authors
JournalCell Chem Biol
PubMed ID30503283
Midkine promotes selective expansion of the nephrogenic mesenchyme during kidney organogenesis.
Authors
JournalOrganogenesis
PubMed ID19521555
Differential expression of unconventional myosins in apoptotic and regenerating chick hair cells confirms two regeneration mechanisms.