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.     

Comparison of benzothiazole-based dyes for sensitive DNA detection

For efficient and quantitative DNA detection, fluorescence staining is the most often explored approach, which relies on non-covalent binding of dyes with double stranded DNA (dsDNA). Ethidium bromide (EB) is the most classic DNA stain, but suffers from its high carcinogenicity. A series of less toxic alternatives were developed, many of which contain the core structure of the benzothiazole ring. However, the relationship between the structure and the DNA detection performance was not illustrated. Herein, five benzothiazole dyes, namely thiazole orange, SYBR Green I, PicoGreen, SYBR Safe, and thioflavine-T, were compared for DNA detection through direct fluorescence and gel electrophoresis, with particular focus on the structure-performance relationship. It turned out that SYBR Green I is currently the best choice for DNA detection. The results in this work may be useful for future DNA-staining dye developments.     

Comparison of benzothiazole-based dyes for sensitive DNA detection

For efficient and quantitative DNA detection, fluorescence staining is the most often explored approach, which relies on non-covalent binding of dyes with double stranded DNA (dsDNA). Ethidium bromide (EB) is the most classic DNA stain, but suffers from its high carcinogenicity. A series of less toxic alternatives were developed, many of which contain the core structure of the benzothiazole ring. However, the relationship between the structure and the DNA detection performance was not illustrated. Herein, five benzothiazole dyes, namely thiazole orange, SYBR Green I, PicoGreen, SYBR Safe, and thioflavine-T, were compared for DNA detection through direct fluorescence and gel electrophoresis, with particular focus on the structure-performance relationship. It turned out that SYBR Green I is currently the best choice for DNA detection. The results in this work may be useful for future DNA-staining dye developments.     

Cell-permeable iminocoumarine-based fluorescent dyes for mitochondria

A class of small molecule fluorophores, 2-iminocoumarin-3-carboxamide derivatives, has been developed by a rapid microwave-assisted process. These fluorescent probes are cell membrane permeable with low cytotoxicity and able to selectively stain organelles in living cells.     

Ortho-functionalized perylenediimides for highly fluorescent water-soluble dyes

Clearly visible: A water-soluble and highly fluorescent perylenediimide is synthesized via ruthenium-catalyzed alkylation with outstanding yields. For the first time, the possibility to use phosphonate derivatives in a Murai-type reaction is demonstrated.     

Synthesis of thiacyanine dyes containing coumarin moieties at benzothiazole rings

New bischromophoric dyes (thiacarbocyanine and thiadicarbocyanine) containing coumarin moieties at each of the two benzothiazole systems, as well as monomethinecyanine containing coumarin moiety at only one heterocyclic system, manifest significant batho-chromic shift compared to relative coumarin-free dyes.     

Polymethine dyes — Furo[2,3-g]benzothiazole derivatives

A new heterocyclic base- 2-methylfuro[2,3-g]benzothiazole — and cyanine dyes with residues of this base were synthesized. It is shown that introduction of a furo[2,3] group in the 6,7 positions of the benzothiazole residue in the cyanines leads to a smaller bathochromic effect than the introduction of a thieno[2,3] and, particularly, a benzo group in the same positions.     

Characterization of acridone dyes for use in four-decay detection in DNA sequencing

Four acridone dyes and dye-labeled primers were characterized for use in four-decay DNA sequencing. In the four-decay scheme, fluorescence lifetime replaces spectral ("color") selectivity for distinguishing between four base-specific labels in a single-lane capillary electrophoresis (CE) separation of the DNA fragments. Prior to the introduction of the acridone dyes, a major obstacle to four-decay detection was the lack of four suitable dyes with resolvable lifetimes. The four acridone dyes, whether free in solution or tethered to DNA primer, exhibit significant differences among their lifetimes and are well-suited to use together in four-decay sequencing. The lifetimes of the four dye-labeled DNA primers that were sequentially injected and detected on-the-fly in a 2% POP6 sequencing gel were 4, 6, 11 and 14 ns. A 405 nm violet laser diode provides optimal excitation of the four dyes.     

Synthesis and fluorescence characteristics of novel asymmetric cyanine dyes for DNA detection

Sixteen new asymmetric monomethine cyanine dyes have been synthesized and their spectral characteristics and interaction with double stranded DNA have been investigated. The dyes absorb in the region 453–519 nm and have molar absorptivities in the range 37.900–93.100 l M^?1 cm^?1. The dyes do not have intrinsic fluorescence, but in the presence of dsDNA they exhibited a significant enhancement in fluorescence. The most pronounced increase was found for D9, D10, D12 and D16 allowing the recommendation of these dyes as the most sensitive DNA markers. Thermodynamic analysis of cyanine–DNA complexation was carried out using the McGhee & von Hippel non-cooperative excluded site model, and binding parameters have been derived. A hypothesis describing the DNA–dye binding mode has been proposed.     

Ultrasensitive DNA detection using highly fluorescent bioconjugated nanoparticles

Sensitive DNA detection is extremely important in clinical diagnostics, gene therapy, and a variety of biomedical studies. We have developed a novel DNA bioanalysis method with a 0.8 fM (0.8 x 10-15 M) detection limit using a bioconjugated fluorescent nanoparticle-based sandwich assay. An organic dye silica nanoparticle is synthesized using a modified reverse microemulsion. The nanoparticles are highly fluorescent, extremely photostable, and easy for bioconjugation for bioanalysis. They exhibit an excellent signaling ability in the presence of trace amounts of DNA targets. With an effective surface modification, nonspecific binding and nanoparticle aggregation are minimized. In addition, the nanoparticle-based DNA bioanalysis assay can effectively discriminate one-base mismatched DNA sequences. We expect this nanoparticle-based assay to be widely useful in a number of biomedical applications where reproducible, selective, and ultrasensitive gene analysis is critical.     

Axially chiral bichromophoric fluorescent dyes

A new life for Kurt Mislow's authentic amines: Diaminobiphenyls were applied as the framework materials for the synthesis of axially chiral bichromophoric systems with strong CD and CPL effects.     

Near-infrared small molecular fluorescent dyes for photothermal therapy

This review aims to provide a summary of the progress in fluorescent dyes for photothermal therapy in recent years and it is classified according to the structure of organic molecules including cyanines, phthalocyanines, rhodamine analogues and BODIPYs.     

Triphenylmethane dyes as fluorescent probes for G-quadruplex recognition

Triphenylmethane (TPM) dyes normally render rather weak fluorescence due to easy vibrational deexcitation. However, when they stack onto the two external G-quartets of a G-quadruplex (especially intramolecular G-quadruplex), such vibrations will be restricted, resulting in greatly enhanced fluorescence intensities. Thus, TPM dyes may be developed as sensitive G-quadruplex fluorescent probes. Here, fluorescence spectra and energy transfer spectra of five TPM dyes in the presence of G-quadruplexes, single- or double-stranded DNAs were compared. The results show that the fluorescence spectra of four TPM dyes can be used to discriminate intramolecular G-quadruplexes from intermolecular G-quadruplexes, single- and double-stranded DNAs. The energy transfer fluorescence spectra and energy transfer fluorescence titration can be used to distinguish G-quadruplexes (including intramolecular and intermolecular G-quadruplexes) from single- and double-stranded DNAs. Positive charges and substituent size in TPM dyes may be two important factors in influencing the binding stability of the dyes and G-quadruplexes.     

Spectroscopic studies of fluorescent perylene dyes

The lowest electronic transition of the fluorescent perylene dye bis-(3,5-di-tertbutylphenyl)-perylene-3, 4:9,10-biscarboximide has been investigated b     

Rotational barriers in perylene fluorescent dyes

Rotational barriers in N-substituted perylene dyes have been determined. Phenyl substituents with tert-butyl groups in the o-position give rigid systems, whereas secondary alkyl groups cause low rotational barriers. In spite of that, fluorescent quantum yields are high in both cases. Conformations in solution are discussed.     

Selection of a DNA aptamer for the development of fluorescent aptasensor for carbaryl detection

An improved ssDNA library immobilized systematic evolution of ligands by enrichment(SELEX) was applied to select aptamers against carbaryl.After nine selection rounds,a highly enriched ssDNA pool was obtained.The Apta3 was demonstrated as the optimal aptame r.In order to facilitate the modification of aptamer,the Apta3 was further truncated with the dissociation constant(K_d) of 0.3 64 ± 0.055 μmol/L and a fluorescent aptasensor was developed.The linear range for carbaryl was from 100 nmol/L to1500 nmol/L,with the limit of detection was as low as 15.23 nmol/L.Besides,the biosensor was validated for the carbaryl spiked real samples,and the recoveries were between 97.7% and 107.3%.     

Spectrophotometric investigation on the aggregation in water of some benzothiazole cationic dyes

The aggregation ability in water of some practically important benzothiazole diazahemicyanine dyes in the range, where only the monomer-dimer equilibrium exist, is investigated. The equilibrium constants K_D and thermodynamic parameters of dimerization are determined and their influence on the dye aggregation is discussed. The “sandwich” structure of the dimer is suggested from the pure monomer and dimer absorption spectra. The distance R between the molecules in the dimer and the angle α between the two transition dipole moments are determined.