Green-light transilluminator for the detection without photodamage of proteins and DNA labeled with different fluorescent dyes

The excitation spectra of Nile red and SYPRO red, two currently used dyes for the fluorescent staining of protein bands in sodium dodecyl sulfate (SDS)-polyacrylamide gels, show an excitation peak in the UV region and another in the visible region (maximum at about 550 nm). Ethidium bromide and other intercalating dyes, e.g. propidium iodide, ethidium dimers, and benzoxazolium-4-quinolinium dimer-3 (YOYO), used for the fluorescent staining of DNA bands in agarose gels also show an excitation peak in the same region of the visible spectrum. We have designed and constructed a green-light transilluminator with an emission maximum at 542 nm. This visible transilluminator allows the detection of protein bands stained with Nile red and SYPRO red with the same sensitivity obtained with a 300 nm UV transilluminator. The green-light transilluminator also allows the detection of about 2 ng of DNA per band in gels stained with ethidium bromide and the other intercalating dyes indicated above. In contrast to the UV transilluminators, the green-light transilluminator does not produce photodamage of DNA even after long exposures (10 min). This makes this transilluminator very useful for preparative work. Furthermore, the green-light transilluminator does not require UV safety equipment and, consequently, it can be very convenient for teaching laboratories.     

New asymmetric monomethine cyanine dyes for nucleic-acid labelling: absorption and fluorescence spectral characteristics

Absorption spectra and fluorescence properties of a series of newly synthesized asymmetric monomethine cyanine dyes are studied. The dyes carry one or two positive charges. They are devoid of their own fluorescence in solution and become fluorescent upon binding to nucleic acids only. The fluorescence maxima of the new dyes are localized between 530 and 650 nm. The wavelength and intensity of fluorescence are dependent on molecular structure of the dye, type of nucleic acid and the concentration of both nucleic acid and salts. Some of the dyes are capable of distinguishing between single-stranded and double-stranded (ds) polynucleotides giving fluorescence maxima localized at different wavelengths. Detection threshold for dsDNA for most of the dyes is comparable to that of ethidium bromide. The sensitivity of the dye-dsDNA complexes to NaCl concentrations show that the new dyes interact with dsDNA by both intercalation and electrostatically.     

Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution.

The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA strains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4',6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye-DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye-DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA-cyanine dye complexes were small. Broadening of dye-ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye-dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.     

Synthesis and Verification of 9,10-Diphenylanthracene and Its Utility as a Fluorescer in a Peroxyoxalate Chemiluminescence System. An Organic Laboratory Project Integrating Synthesis with Fluorescence and Chemiluminescence

A project for the organic laboratory integrating the organic synthesis of 9,10-diphenylanthracene with fluorescence and chemiluminescence is described. The fluorescent compound is synthesized from anthraquinone by reaction with phenyllithium and subsequent hydrolysis and reduction with KI and NaH₂PO₂ in acetic acid. The structure of the product is verified by its melting point and by IR, ¹H NMR, and fluorescence spectroscopy. A peroxyoxalate chemiluminescent reaction using bis(2-butoxycarbonyl-3,4,6-trichlorophenyl) oxalate and hydrogen peroxide as the energy source is tested. The chemiluminescence emittance spectrum of the prepared diphenylanthracene is found to be essentially identical to that of the fluorescence spectrum of the same compound. Finally, the kinetics of the chemiluminescent reactions using different intensity-modifiers are monitored by measuring intensity-versus-time decay curves.     

Relative DNA binding affinity of helix 3 homeodomain analogues, major groove binders, can be rapidly screened by displacement of prebound ethidium bromide. A comparative study

The binding affinity for a 12-bp dsDNA of Antennapedia helix 3 analogues, major groove binders, has been measured by displacement of prebound ethidium bromide, a fluorescent displacement assay proposed for minor groove binders by Boger et al.(J. Am. Chem. Soc., 2000, 122, 6382-6394). Relative binding affinities determined by this method were compared to those obtained by gel mobility shift and footprinting assays for the 12-bp dsDNA and a 178-bp DNA fragment. The present work demonstrates that the fluorescence displacement assay is suitable for rapid screening of major groove binders, even though about 60 to 70% of the prebound ethidium bromide is displaced by these peptides. Total (100%) displacement of ethidium bromide was serendipitously achieved by addition in the peptide sequence, at the N-terminus, of a S-3-nitro-2-pyridinesulfenyl-N-acetyl-cysteine residue. S-3-nitro-2-pyridinesulfenylcysteine was shown to (i) bind to dsDNA with a micromolar affinity and (ii) direct within DNA grooves a peptide with no affinity for dsDNA.     

AuCl4-H2O2化学发光体系研究

本文发现, AuCl4^-在KOH和H2O2存在下会产生弱化学发光信号; 在此基础上建立了AuCl4^-H2O2-KOH-CTMAB体系测定金的新的简单的化学发光分析法; 方法的检测限为5.5ppbAn; 线性范围为10-800pph; 测定100ppb金溶液的相对标准偏差为6.5%; 并初步探讨了AuCl4^-化学发光的可能过程及表面活性剂的影响作用。     

Evaluation of fluorescent compounds for peroxyoxalate chemiluminescence detection

The behaviour of 19 fluorescent compounds of various types in peroxyoxalate chemiluminescence reactions was studied in terms of the relation of their excitation efficiency to their singlet excitation energy and oxidation potential. Compounds having low singlet excitation energy and low oxidation potential were excited effectively. As a result of the study, 3-aminoperylene was selected as a fluorophore for derivatization of simple car?ylic acids. The derivatives were separated by reversed-phase microbore h.p.l.c. and were detected by a peroxyoxalate chemiluminescence reaction detector. The detection limit was 0.1 fmol.     

A study of the chemiluminescence of some acidic triphenylmethane dyes

Chemiluminescence was observed when some acidic triphenylmethane dyes were oxidized with hydrogen peroxide in alkaline solution. Trace amounts of Co(II) catalysed this chemiluminescent reaction strongly, especially in the presence of the cationic surfactant cetyltrimethylammonium bromide. The chemiluminescence spectra of some compounds and the absorption spectra of some products of the chemiluminescent reactions were investigated, and some acidic triphenylmethane dyes were studied by the Hückel molecular orbital method. On the basis of these investigations, a possible mechanism for this chemiluminescent reaction, and an initial explanation for the relationship between the structure of the reagents and their chemiluminescent behaviour were proposed. The optimum conditions for use of some of the chemiluminescent reaction systems were selected by means of the modified simplex method, and a chemiluminescent analytical method for determination of ultratrace amounts of cobalt was established, with a detection limit of 5 pg/ml. It was used for analysis of natural water samples, and good results were obtained.     

Thiazole orange as an everyday replacement for ethidium bromide and costly DNA dyes for electrophoresis

DNA gel electrophoresis is a standard tool of biochemistry and molecular biology laboratories. The common dye ethidium bromide suffers from toxicity concerns and requires the use of damaging ultraviolet light. We observe that exposing plasmid DNA to a UV transilluminator for only 1 s results in detectable loss of colonies following transformation, suggesting rapid accumulation of DNA damage. SYBR Safe, a commercial product, is marketed as a safe alternative to ethidium bromide and has excellent sensitivity with nondamaging blue light, but suffers from prohibitively high costs. We show that thiazole orange, the parent compound of SYBR Safe, is an excellent, simple, and inexpensive alternative to these dyes. It is excitable with safe blue light or UV light, with DNA detection limits in agarose gels similar to ethidium bromide and SYBR Safe (1–2 ng/lane). Thiazole orange safely allows the use of nondamaging blue light at the same cost as ethidium bromide.     

Flow and evaporation cells for the detection of proteins on membranes with the peroxyoxalate chemiluminescent reaction in organic media

The high-energy intermediates generated in the reaction of bis(2,4,6-trichlorophenyl)oxalate (TCPO) with H2O2 can excite electronically different fluorophores with a high quantum yield in organic solvents. We have previously applied this peroxyoxalate chemiluminescent reaction to the detection of proteins labeled with the fluorescent dye 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF) on polyvinylidene difluoride (PVDF) membranes. In this work, we have investigated the possibility to enhance the sensitivity of this detection method using specially designed cells in which the reagents TCPO and H2O2 in acetone are continuously renewed. In the flow cell, two syringes are used to renew the reagents in the reaction chamber containing the PVDF membrane with blotted proteins labeled with MDPF. In the evaporation cell, a fresh solution of reagents continuously replaces the volume of acetone evaporated in the reaction chamber. Both cells show a low emission background but the observed elution of proteins from the membrane produced by the flow of reagents in acetone limits the maximum sensitivity attainable with these cells. The best result (detection of 1 ng of MDPF-labeled protein) has been obtained with the evaporation cell.     

Studies on Mechanism of Chemiluminescence Reaction of 2, 6, 7-Trihydroxyl-9-(4'-chlorophenyl )-3-fluorone

1INTRoDUCTIONPhenylfluoroneisanimportanttypeofreagentinanalytica1chemistry"~'>.Themoleculesofthisreagenthavearigidplanarstructuret5'6i,sotheenergyofmolecularorbitsofthereagentscanbecalculatedbyHuckelmolecularorbitalmethod(HMO).WehadtriedtoassigndissociationconstantsforsomesuchreagentsbyacombinedspectrophotometricandHMOmethodt7'8i.Them.thodissimpleandtheresultsaresatisfactory.Inthispaper,apossiblemechanismforcatalyticchemiluminescencere-actionofCl-PFisproposedonthebasisofstudyingchemil…     

A fluorescent and chemiluminescent difunctional mesoporous silica nanoparticle as a label for the ultrasensitive detection of cancer cells

A new kind of ultrabright fluorescent and chemiluminescent difunctional mesoporous silica nanoparticle (FCMSN) is reported. A luminescent dye, Rhodamine 6G or tris(2,2′-bipyridyl)dichlororuthenium(II) hexahydrate (Rubpy), is doped inside nanochannels of a silica matrix. The hydrophobic groups in the silica matrix avoid the leakage of dye from open channels. The amines groups on the surface of the FCMSN improve the modification performance of the nanoparticle. Because the nanochannels are isolated by a network skeleton of silica, fluorescence quenching based on the inner filter effect of the fluorescent dyes immobilized in nanochannels is weakened effectively. The Quantum Yield of obtained 90 nm silica particles was about 61%. Compared with the fluorescent core–shell nanoparticle, the chemiluminescence reagents can freely enter the nanoparticles to react with fluorescent dyes to create chemiluminescence. The results show that the FCMSN are both fluorescent labels and chemiluminescent labels. In biological applications, the NaIO₄ oxidation method was proven to be superior to the glutaraldehyde method. The amount of amino could affect the specificity of the FCMSN. The fluorescence microscopy imaging demonstrated that the FCMSN is viable for biological applications.     

Properties of nucleic acid staining dyes used in gel electrophoresis

Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed? was the most sensitive and safest dye to use with UV light excitation, and both GelGreen? and Diamond? Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.     

Supramolecular Reassembly of Self‐Exfoliated Ionic Covalent Organic Nanosheets for Label‐Free Detection of Double‐Stranded DNA

Ionic covalent organic nanosheets (iCONs), a member of the two‐dimensional (2D) nanomaterials family, offer a unique functional platform for a wide range of applications. Herein, we explore the potential of an ethidium bromide (EB)‐based covalent organic framework ( EB‐TFP ) that self‐exfoliates in water resulting in 2D ionic covalent organic nanosheets ( EB‐TFP‐iCONs ) for the selective detection of double‐stranded DNA (dsDNA). In an aqueous medium, the self‐exfoliated EB‐TFP‐iCONs reassemble in the presence of dsDNA resulting in hybrid EB‐TFP‐iCONs‐DNA crystalline nanosheets with enhanced fluorescence at 600 nm. Detailed steady‐state and time‐resolved emission studies revealed that the reassembly phenomenon was highly selective for dsDNA when compared to single‐stranded DNA (ssDNA), which allowed us to use the EB‐TFP‐iCONs as a 2D fluorescent platform for the label‐free detection of complementary DNA strands.     

Quadruplex-to-duplex transition of G-rich oligonucleotides probed by cationic water-soluble conjugated polyelectrolytes

G-quartet DNA converts to duplex form in the presence of its complementary strand. This conformational change can be detected in real time by a homogeneous assay method based on the signal amplification of conjugated polyelectrolytes and the specific interaction of intercalating dyes with double-stranded DNA (dsDNA). The probe solution contains a cationic, conjugated polymer (CCP), G-quadruplex labeled with a fluorescein at the 5'-terminus (G-quadruplex-Fl), and ethidium bromide (EB). The addition of a complementary target results in the transition from G-quadruplex to duplex (dsDNA-Fl) and EB intercalation within the duplex structure. Excitation of the CCP leads to energy transfer from CCP to dsDNA-Fl (FRET-1) and then energy transfer from dsDNA-Fl to EB (FRET-2). Increasing the number of mismatched bases discourages dsDNA formation, which is detected in the assay.     

Mono- and bis-intercalating dyes for multiplex fluorescence lifetime detection of DNA restriction fragments in capillary electrophoresis

The use of novel intercalating dyes as labels in DNA restriction fragment analysis by capillary electrophoresis with frequency-domain fluorescence lifetime detection is described. The dyes, including one mono-intercalating dye with three positive charges and three bis-intercalating, homodimeric dyes with four positive charges, were excited by the 488 nm line of an argon ion laser and exhibited lifetimes in the range of 1-3 ns. The separations were performed using a gel containing 1% high-molecular-weight (HMW) hydroxyethylcellulose (HEC) (90,000-105,000) and 0.3% low-molecular-weight (LMW) HEC (24,000-27,000) in Tris-borate-EDTA buffer (TBE). Multiplex lifetime detection of mixtures of dye-labeled DNA restriction fragment digests and size standard fragments was achieved. Compared to previous results obtained with several mono-intercalating dyes of lesser charge (McIntosh, S. L., Nunnally, B. K., Nesbit, A. R., Deligeorgiev, T. G., Gadjev, N. I., McGown, L. B., Anal. Chem. 2000, 72, 5444-5449), the present dyes provided a wider range of lifetimes and better lifetime discrimination in multiplex detection. There was no evidence of dye exchange during the capillary electrophoresis experiment.     

Direct determination of single-to-double stranded DNA ratio in solution using steady-state fluorescence measurements

We report a simple and rapid method for quantitation of single-to-double stranded (ss : ds) DNA ratios in solution, using steady-state measurements of fluorescence from two simultaneously excited intercalated dyes; the ratio of fluorescence intensities from PicoGreen (525 nm) and ethidium bromide (610 nm) is directly proportional to the ss : ds DNA ratio.     

CO2/NIR light dual-controlled nanoparticles for dsDNA unzipping

Both of carbon dioxide(CO2)and near-infrared(NIR)light as triggers for non-invasive remotely control are attracting wide attentions due to their good biocompatibility and easy operation.Here,CO2/NIR light dual controlled nanoparticles are proposed to remotely regulate the unzipping of dsDNA by using imidazole functionalized conjugated polymer nanoparticles(imidazole-CPNs).The dsDNA successfully coats on the shell of imidazole-CPNs to form imidazole-CPNs/dsDNA assembly due to intensively electrostatic interaction triggered by CO2.Furthermore,the unzipping process of dsDNA is remotely controlled by NIR light based on the photothermal effect,and it can be readily monitored by the fluorescence intensity of ethidium bromide(EB)and CD spectra of dsDNA.Thus,dual stimulation responsive imidazole-CPNs effectively control dsDNA unzipping under CO2 stimulus and NIR light,promising a new direction in the biological applications of DNA,such as the treatments of diseases caused by gene duplication abnormality.     

邻硝基苯基荧光酮化学发光性能和机理研究

研究了在碱性介质中金属离子催化邻硝基苯基荧光酮（ｏ－ＮＰＦ）－Ｈ２Ｏ２体系的化学发光行为。结果表明，在研究的２０多种金属离子中，只有Ｃｏ２＋离子对ｏ－ＮＰＦ－Ｈ２Ｏ２体系有较强的催化发光作用，Ｃｏ２＋的浓度与发光强度在２．５×１０－９～３．０×１０－６ｇ／ｍＬ范围内呈良好的线性关系。通过对化学发光光谱、荧光光谱的研究以及用Ｈｕｃｋｅｌ分子轨道法（ＨＭＯ）计算了ｏ－ＮＰＦ的π电子分布和键级，提出了ｏ－ＮＰＦ可能的化学发光机理．     

Improvement of ways to obtain ethidium bromide and synthesis of ethidium ethyl sulfate,a new fluorescent dye for detection of nucleic acids

Two methods for synthesis of ethidium bromide, a fluorescent dye widely used in molecular biology, were improved. An analog of ethidium bromide, ethidium ethyl sulfate, was synthesized.