Propidium Iodide and PicoGreen as Dyes for the DNA Fluorescence Correlation Spectroscopy Measurements

Many experimental designs, in which nucleic acid conformational changes are of interest, require reliable fluorescence labeling. The appropriate fluorescence probe should have suitable optical properties and, more importantly, should not interfere with the investigated processes. In order to avoid chemical modifications the fluorescence label needs to be associated with nucleic acid via weak non-covalent interactions. There are a number of fluorescent probes that change their fluorescent properties (i.e. their quantum yield and/or spectral characteristics) upon association with nucleic acid. Such probes are frequently used to detect, visualize and follow processes involving nucleic acid and its conformational changes. In order to obtain reliable data regarding macromolecule or aggregate topology a detailed knowledge of probe–nucleic acid interactions on the molecular level is needed. In this paper we show that the association of propidium iodide with DNA alters its conformation and that it selectively labels plasmid fragments and/or its subpopulations in a concentration-dependent meaner. Another dye, PicoGreen, exhibits better properties. It labels nucleic acid uniformly and without any concentration-dependent artifacts.     

The frequency characteristics analysis of series photodetector frequency circuit system based on circuit parameters of quartz crystal and its application for bacterial DNA identification

The circuit parameters of quartz crystal were employed for frequency sensitivity analysis of series photodetector frequency circuit system. The influence of circuit parameters of quartz crystal on the oscillation frequency and response sensitivity were theoretically derived and experimentally verified. On the basis of optimal circuit parameters, the DNA probe detection limit 2 pmol/L can be measured by 49.4 MHz sensor system. In comparison with the conventional fluorescence technique, the frequency method showed that the detection limits of DNA probe AH642 with Cy5 fluorescence dye and DNA probe VA180 with Cy5 fluorescence dye were lower than the conventional fluorescence technique by 2–3 orders; meanwhile, through the feature of probe uniqueness, Aeromonas hydrophila DNA and fluorescence probe AH642-Cy5 can be successfully judged for hybridization reaction. Moreover, Vibro alginolyticus DNA and fluorescence probe VA180-Cy5 can be successfully judged for hybridization reaction.     

Methylene blue as a DNA probe for a comparative study of Cd, Pb and Cr ions binding to calf thymus DNA

Methylene blue (MB) was developed as a sensitive DNA probe for a comparative study of Cd²⁺, Pb²⁺ and Cr³⁺ ions binding with calf thymus DNA (ctDNA). The fluorescence intensity of the MB-ctDNA system increased dramatically when heavy metal ions (Cd²⁺, Pb²⁺ and Cr³⁺ ions) were added, which indicated that some of the bound MB molecules were released from the ctDNA base pairs. To compare the binding affinity of these three different heavy metal ions with ctDNA, the relationships between the fluorescence intensity of the MB-ctDNA-M (Metal ions) system and the concentration ratio of [M]/[DNA(p)] were investigated. The results showed that the order of the binding affinity of heavy metal ions with ctDNA had the following sequence: Cr³⁺> Cd²⁺>Pb²⁺. This order was further proved by the effects of heavy metal ions on the number of MB bound to ctDNA, the measurements of binding constants of these heavy metal ions to ctDNA, and the effects of heavy metal ions on the absorption of the MB-ctDNA system. In addition, the interaction mechanisms of Cd²⁺, Pb²⁺ and Cr³⁺ ions with ctDNA were also discussed in detail. These results indicated that their interaction mechanisms are related to the concentration ratios of heavy metal ions to DNA.     

One-step aqueous synthesis of CdS nanoparticles as a novel fluorescence probe for the ultrasensitive detection of DNA

One-step aqueous synthesis of CdS nanoparticles as a novel fluorescence probe for sensitive and selective determination of DNA with synchronous fluorescence spectrometric method has been developed. Different from the traditional organometallic route, in which toxic precursors or solvents might be used, the wet chemical approach demonstrated in this paper is superior in terms of simplicity, using of nontoxic materials, mild synthetic condition and good reproducibility. When Δλ=255 nm, maximum synchronous fluorescence is produced at 264 nm, the synchronous fluorescence intensity of the composite nanoparticles is significantly decreased in the presence of trace DNA at PH 0.91. Under optimal conditions, the linear ranges of the calibration curves are 0.08-30.0 μg mL⁻¹ for ctDNA and 0.05-35.0 μg mL⁻¹ for hsDNA, respectively. The detection limits are 1.5 ng mL⁻¹ for ctDNA and 2.2 ng mL⁻¹ for hsDNA, respectively. Furthermore, the method is successfully applied to the quantification of DNA in synthetic samples. The results show that this proposed method is stable, sensitive and practical for the determination of trace DNA.     

Synthesis,Characterization and DNA Interaction Study of a New Oxovanadium (IV) Complex Containing Acetylacetone and Dicyandiamide as Ligands

ABSTRACT

A new oxovanadium (IV) complex [VO(acac)₂DCDA]H₂O (where acac = acetylacetonate; DCDA = dicyandiamide) was synthesized and characterized by elemental analysis, IR, UV, ESR, TG-DTA analysis and powdered XRD. The electronic and ESR spectral studies indicate the monomeric nature of the complex having distorted octahedral structure. The complex shows prominent emission peak at 485 nm and excitation peak at 355 nm. The cyclic voltammetry study shows irreversible process. DNA binding study of the complex with CT-DNA indicates nonintercalative mode with binding constant 2.063 × 10² M^?1.     

Spectroscopic Study of 2-(2-pyridyliminomethyl)phenol as a Novel Fluorescent Probe for Superoxide Anion Radicals and Superoxide Dismutase Activity

A novel spectrofluorometric method, using 2-(2-pyridyliminomethyl)phenol as a fluorescent probe, was developed for the determination of superoxide anion radical (O₂ ^•−) and superoxide dismutase activity (SOD). The new fluorescent probe was synthesized and characterized with elemental analysis and IR spectra. It was oxidized by O₂ ^•− to form a less fluorescence product. Based on this reaction, a spectrofluorometric method was proposed and successfully used to determine superoxide anion radicals and SOD activity. The effects of interferences were studied. The reaction was simple, precise and sensitive. It was applied to determine SOD activity in garlic, papaya and spinach successfully.     

新型离子液体预富集-石墨炉原子吸收法测定透析液中超痕量铅

设计合成了新型室温离子液体—1-丁基-3-三甲基硅烷咪唑六氟磷酸,并用于透析液中超痕量铅的预富集。从双硫腙作为螯合剂使透析液(1 000 mL或更大体积)中存在的铅(Ⅱ)形成中性的铅-双硫腙配合物,摒弃传统的有机萃取剂—四氯化碳,代以1-丁基-3-三甲基硅烷咪唑六氟磷酸为绿色萃取剂来萃取铅配合物。收集含有配合物的下层离子液体相,加入硝酸分解铅配合物从而使铅(Ⅱ)进入水相,其水溶液中的铅含量直接用石墨炉原子吸收法测定。实验表明此富集体系明显优于传统有机溶剂四氯化碳和经典离子液体1-丁基-3-甲基咪唑六氟磷酸萃取体,铅的一次萃取率和富集倍数分别在99%和200以上。预富集结合石墨炉原子吸收法应用于透析液中超痕量铅的测定,结果令人满意。     

The new HMQC-based technique for the quantitative determination of heteronuclear coupling constants. Application for the measurement of 3J(H'(i),P(i+1)) in DNA oligomers

A new general J-HMQC-based technique is presented, which allows an accurate determination of heteronuclear coupling constants. The most important feature of this new approach includes acquisition of the two data sets with and without the additional pi(S)-pulse at the end of coupling evolution period. This enables preservation and separation of the two orthogonal terms of coupling evolution, which are manifested by in- and antiphase cross-peaks, respectively. The coupling magnitudes are evaluated by the nonlinear least-squares fitting of the ratios of integrated signal volumes for both kinds of signals. The effectiveness of the new sequence is demonstrated by determination of the 3J(H3'(i),P(i+1)) couplings in DNA octamer duplex d(GCGTACGC)(2) sample. Additionally, the ability of the new method for the measurement at the natural abundance level of 13C nuclei is presented for the beta-cyclodextrin.