Fluorometric Determination Of DNA Research Articles

Graphene oxide and enzyme-assisted dual-cycling amplification method for sensitive fluorometric determination of DNA.

A fluorometric method is described for the determination of DNA. It involves the use of graphene oxide (GO), exonuclease III (Exo III), and two specially designed fluorophore-labeled hairpin probes (HP1 and HP2). Different from other GO-based DNA assays, the method takes advantage of the distinct binding abilities of GO with hairpin DNA probes and single nucleotides. GO serves as a strong quencher for fluorescent labels to ensure a very low background signal. Two reaction cycles mediated by Exo III are employed to enhance the signals. The combination of GO-induced quenching and Exo III-mediated dual regeneration of analytes leads to a detection limit as low as 1 pM for the model analyte human hemochromatosis protein (HFE) gene. The method is also applicable for the determination of HFE gene spiked into fetal bovine serum. Graphical abstract Schematic representation of a GO-based, Exo III-assisted method for dual-signal amplified detection of DNA, for which human haemochromatosis protein (HFE) gene is designed as the model target. The assay involves graphene oxide (GO), exonuclease (Exo III), and two specially designed, fluorophore-labelled hairpin probes (HP1 and HP2).

Fluorometric determination of DNA using nano-SiO2 particles as an effective dispersant and stabilizer for acridine orange

A sensitive fluorometric method for the determination of ctDNA (calf thymus DNA) is presented. It has good selectivity and sensitivity and uses nano-SiO2 particles as an effective dispersant and stabilizer for acridine orange (AO). Compared to resonance light scattering (RLS) and the conventional method that uses organic dyes as fluorescence probe, the new method is more tolerant towards coexisting foreign substances and also more stable. With 20 mg nano-SiO2 particles, 10 µmol L−1 AO, at pH 8.01 and an ionic strength of 0.02 mol L−1, the interaction of AO with nano-SiO2 and ctDNA results in fluorescent signal enhancement. The extent of enhancement was in good proportion to the concentration of ctDNA at excitation/emission wavelengths of 490/523 nm, respectively. The calibration curve was linear over 0.66–55.60 µg mL−1. The determination limit (3σ) was 15 ng mL−1. The method was applied to the determination of ctDNA in synthetic samples with satisfactory results.

Fluorometric determination of DNA using a new ruthenium complex Ru(bpy)2PIP(V) as a nucleic acid probe.

A new ligand, 2-phenyl(5-fluoro)imidazo[f]-1,10-phenanthroline (PIP(V)), and its coordination compounds, Ru(bpy)2PIP(V), were synthesized. The fluorescence spectrum of the interaction between Ru(bpy)2PIP(V) and DNA was studied, and a very strong fluorescence peak at a wavelength of 589 nm appeared. The optimum condition of analyzing DNA was decided. The method is simple, convenient and fast, and also has high sensitivity and good selectivity. It has been satisfactorily employed for determinations in synthesized samples.

Fluorometric determination of DNA in mammalian cell cultures by PicoGreen

An intercalating fluorochrome, PicoGreen, was assessed for its ability to determine the concentration of DNA in clarified mammalian cell culture broths containing monoclonal antibodies. Fluorescent signal suppression was ameliorated by sample dilution or by performing the assay above the pI of secreted IgG. The source of fluorescence in clarified culture broth was validated by incubation with RNase A and DNase I. At least 91.8% of fluorescence was attributable to nucleic acid and pre-digestion with RNase A was shown to be a requirement for successful quantification of DNA in such samples.

Fluorometric Determination of DNA in Agarose Gels: Usefulness for Measurement of Double-Strand Breaks in Nonlabeled Cells by Pulsed-Field Gel Electrophoresis

Quantitative measurement of DNA in agarose gels, particularly as needed for measurement of double-strand breaks induced by agents such as radiation, usually involves the use of radioactively labeled DNA. Thus its usefulness is usually limited to growing cells which incorporate radiolabeled thymidine into DNA. To circumvent this problem, we have developed a fluorometric technique for quantitative estimation of DNA in the presence of large amounts of agarose. Gel slices are solubilized with concentrated sodium perchlorate and DNA is selectively precipitated with cadmium chloride. The amount of DNA can then be estimated with 3,5-diaminobenzoic acid. Determination of DNA is linear in the range 10 ng to 1 microgram or more. We describe the application of this technique to the measurement of 60Co gamma-ray-induced double-strand breaks by pulsed-field gel electrophoresis. Our results are essentially identical to those obtained using radiolabeled DNA.

No change in DNA damage or repair of single- and double-strand breaks as human diploid fibroblasts age in vitro

Using the in vitro human diploid fibroblast model, we tested theories of aging which hypothesize that either accumulation of DNA damage or decreased DNA repair capacity is causally related to cellular senescence. Between population doubling level (PDL) 32 and 71, fetal lung-derived normal diploid human fibroblasts (IMR 90) were assayed for both DNA single-strand breaks (SSBs, spontaneous and induced by 6 Gy) and DNA double-strand breaks (DSBs, spontaneous and induced by 100 Gy). After gamma-irradiation cells were kept on ice unless undergoing repair incubation at 37 °C for 7.5–120 min or 18–24 h. To assay DNA strand breaks we used the filter elution technique in conjunction with a fluorometric determination of DNA which is not biased in favor of proliferating aging cells as are radioactive labelling methods. We found no change with in vitro age in the accumulation of spontaneous SSBs or DSBs, nor in the kinetics or completeness of DNA strand rejoining after gamma-irradiation. Cells at varying PDLs rejoined approx. 90% of SSBs and DSBs after 60 min repair incubation and 100% after 18–24 h repair incubation. We conclude that aging and senescence as measured by proliferative lifespan in IMR 90 cells are neither accompanied nor caused by accumulation of DNA strand breaks or by diminished capacity to rejoin gamma-radiation-induced SSBs or DSBs in DNA.

Direct fluorometric determination of DNA in human leukocyte homogenates

Direct fluorometric determination of DNA in human leukocyte homogenates

Improved Microfouling Assay Employing a DNA-Specific Fluorochrome and Polystyrene as Substratum

With a direct count assay, 10 fouling bacterial isolates have been characterized for their ability to adhere to glass cover slips and polystyrene dishes. Although most adhered in greater numbers to polystyrene, the preference was statistically significant for only seven isolates at the 95% confidence level, due in part to the greater variability in cell attachment to glass (coefficient of variation, 32.3% for glass compared with 10.0% for polystyrene). Employing polystyrene dishes, a novel microfouling assay was developed, based on the extraction and fluorometric determination of DNA. The assay was rapid, enabled the detection of as little as 0.15 mug of DNA per dish ( approximately 5,000 cells per mm), and showed good agreement with the direct count assay. The DNA method resulted in less variability among three replicates (average coefficient of variation, 7.06%) and allowed for estimation of bacterial density over a larger surface area per sample (1.89 x 10 mm) than was feasible with epifluorescence microscopy (0.06 to 0.1 mm).

Fluorometric Determination of DNA in Aquatic Microorganisms by Use of Hoechst 33258

A method for the determination of microbial DNA in aquatic environments by the use of Hoechst 33258 has been developed. With unsophisticated instrumentation and simple extraction procedures, it is possible to detect from 0.05 to 10 mug of DNA in bacterial cultures or natural water samples. The method is specific for DNA; DNase I treatment of extracts of natural microbial populations removed 95 to 100% of the observed fluorescence. DNA content ranged from 165 ng ml for relatively eutrophic Potomac River water to 27 ng ml for coastal Atlantic Ocean water and was correlated to an acridine orange direct count (r = 0.90).

Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258 : Paul, J.H. and Brenda Myers, 1982. Appl. environ. Microbiol., 43(6): 1393–1399

Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258 : Paul, J.H. and Brenda Myers, 1982. Appl. environ. Microbiol., 43(6): 1393–1399

Fluorometric determination of DNA and RNA in Chlamydomonas using ethidium bromide.

By using the fluorescence enhancement of ethidium bromide bound to nuclei acid, a very rapid, simple and sensitive assay of DNA in the green alga Chlamydomonas has been devised. Total fluorescence (DNA + RNA) was determined by complex formation with ethidium bromide in a cell lysate made by mixing cell samples with lauroyl sarcosinate, EDTA and NaOH and incubating the mixture for 5 min at room temperature followed by neutralization. For determination of DNA the RNA was digested by incubating the cell sample in te alkaline lysis solution for 45 min at 60 degrees C followed by neutralization, and complex formation with ethidium bromide. Quenching of the fluorescence due to cellular pigments was corrected for using an internal DNA standard.

Fluorometric determination of DNA in fixed tissue using ethidium bromide

The measurement of DNA in tissue samples fixed in ethanol/acetic acid is described. Small, fixed tissue samples are digested by warm alkaline treatment followed by neutralization with HCl, and DNA is determined by complex formation with the dye ethidium bromide (EB). When standard DNA from calf thymus was treated similarly, a hyperchromicity of 8–12% and a reduction in fluorescence intensity of the EB-DNA complex to 55% was observed. The NaOH concentration (0.5–2.0 mol/liter) or the temperature (50–60°C) used for the digestion of tissue, as well as subsequent ribonuclease or protease treatment had no effect on the observed tissue DNA concentrations.

Fluorometric determination of DNA in Chlamydomonas

The diaminobenzoic acid dihydrochloride fluorescence method has been examined to determine optimal conditions for the assay of DNA in perchloric acid extracts and in pretreated Chlamydomonas cells on glass-fiber filters. Maximal fluorescence yield was obtained by allowing: (a) the perchloric acid extract to react with 4–6% diaminobenzoic acid dihydrochloride for 20–40 min at 60–80°C at about pH 3.0; (b) the pretreated cells on glass-fiber filters to react with a 20% solution of diaminobenzoic acid dihydrochloride for 40 min at 60°C.