Presence Of Nucleic Acids Research Articles

Synthesis of novel fluorescent styryl dyes based on the imidazo[1,2- a]pyridinium chromophore and their spectral-fluorescent properties in the presence of nucleic acids and proteins

The imidazo[1,2- a]pyridinium heterocyclic system was used to prepare styryl dyes. Improved synthetic methods were proposed for the parent imidazo[1,2- a]pyridines and their corresponding quaternary salts. The standard method for preparing styrylcyanines was modified for the synthesis of the target imidazo[1,2- a]pyridinium dyes. Spectral-luminescent properties of the obtained dyes in free state and in the presence of nucleic acids, BSA, and BSA/detergent system were studied. 7-[2-(4-Dihexylaminophenyl)-1-ethenyl]-2-(2,4-dimethoxyphenyl)-1-ethylimidazo[1,2- a]pyridin-1-ium iodide (SIP-8) containing C 6 aliphatic tails and 2,4-methoxy substituents in the 2-phenyl ring exhibited specificity to BSA.

Fluorescent homodimer styrylcyanines: synthesis and spectral-luminescent studies in nucleic acids and protein complexes

A series of homodimer styrylcyanine dyes based on ( p-dimethylaminostyryl)pyridinium, ( p-dimethylaminostyryl)benzoxazolium, ( p-dimethylaminostyryl)benzothiazolium, ( p-dimethylaminostyryl)-1,3,3-trimethyl-3 H-indolium residues were synthesized. Spectral-luminescent properties of the obtained homodimers in free state and in the presence of nucleic acids and BSA were studied. Homodimer styrylcyanines with the length of linkage group of 2 or more carbon atoms demonstrated a DNA-binding preference. Significant long-wave shifts of fluorescence and emission maxima of dyes with short linkage group could be explained by the interaction between chromophores due to the short distance between them, as it is the case for molecular aggregates. Homodimer dyes based on the ( p-dimethylaminostyryl)pyridinium residue having linkage group of 5 or more carbon atoms interact with dsDNA with significant emission increase and could be used as DNA specific fluorescent probes.

Photoadducts of Metallic Compounds with Nucleic Acids — Role Played by the Photoelectron Transfer Process and by the TAP and HAT Ligands in the RuII Complexes

AbstractFor Abstract see ChemInform Abstract in Full Text.

Photoadducts of Metallic Compounds with Nucleic Acids − Role Played by the Photoelectron Transfer Process and by the TAP and HAT Ligands in the RuII Complexes

AbstractThe properties that are characteristic of TAP (1,4,5,8‐tetraazaphenanthrene) and HAT (1,4,5,8,9,12‐hexaazatriphenylene) RuII complexes under illumination are highlighted and compared with those of other metallic complexes. In particular, the photo‐oxidizing power of their 3MLCT states leads to a quenching of luminescence accompanied by a photoreaction when they are in presence of nucleic acids. The proton‐coupled photoinduced electron transfer with the guanine nucleobases produces metallic adducts on DNA guanine units. The mechanism of formation, structure, and possible applications of these photoadducts are discussed and compared with other DNA metallic adducts currently in the literature. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Homodimeric monomethine cyanine dyes SOSO-1 and TOTO-1-6C—synthesis and fluorescence properties in the presence of nucleic acids

Two new homodimeric asymmetric monomethine cyanine dyes SOSO-1 and TOTO-1- 6C bearing four and six positive charges respectively have been synthesized. The longest wavelength absorption maxima of both dyes lie between 495 and 520 nm; the molar absorptivities are between 110,000 and 150,000 l mol −1 cm −1. SOSO-1 and TOTO-1-6C do not fluoresce in TE buffer and bidistilled water but become strongly fluorescent upon binding to dsDNA. The fluorescence maxima are at 540.4 and 534.4 nm and the fluorescence quantum yields are 0.25 and 0.35, respectively.

Simple and Sensitive Assay for Nucleic Acids Using their Quenching Effect on the Chemiluminescence Reaction Between Luminol and Hydrogen Peroxide with Manganese-Tetrasulfonatophthalocyanine as a New Catalyst

The manganese-tetrasulfonatophthalo-cyanine (MnTSPc) catalyzed luminol-hydrogen peroxide chemiluminescence (CL) system can be quenched in the presence of nucleic acids. A new and highly sensitive CL quenching method for determining nucleic acids in aqueous solutions has been developed. Under optimum conditions, linear relationships were found between the quenched intensity of CL and the concentration of nucleic acids in the range 0.10–2.0 µg mL−1 for calf thymus DNA and 0–1.6 µg mL−1 for fish sperm DNA. The limits of detection were 14.8 ng mL−1 for calf thymus DNA and 21.7 ng mL−1 for fish sperm DNA. The relative standard deviation (RSD) of nine replicate measurements is 1.4% for 1.0 µg mL−1 calf thymus DNA. The method was applied to the analysis of nucleic acids in synthetic samples and the results are satisfactory.

Novel fluorescent colloids as a DNA fluorescence probe.

Fluorescent perylene colloids in the 80-90 nm size range have been prepared by the reprecipitation method. These nanoparticles were modified by cetyltrimethylammonium bromide (CTAB) which inhibited their growth. The nanoparticles also readily interacted with DNA. The fluorescence emission was measured at lambda(ex)/ lambda(em)=400/565 nm. The fluorescence decrease of colloid-CTAB in aqueous solution was measured in the presence of nucleic acids. Under the optimum conditions, the ratio of fluorescence intensity in the absence and presence of nucleic acids was proportional to the concentration of nucleic acids over the range 0.02-5.1 micro g mL(-1) for FS (fish sperm) DNA or CT (calf thymus) DNA. The detection limits were 0.01 micro g mL(-1) for FS DNA and 0.012 micro g mL(-1) for CT DNA, respectively. Based on this approach, a new quantitative method for DNA assay is presented in this paper.

Luminescence spectroscopic studies of trimethinecyanines substituted in polymethine chain with nucleic acids and proteins

The series of symmetrical β-substituted and α,γ-substituted trimethinecyanine dyes were studied for their absorption and fluorescent characteristics in unbound state and in the presence of nucleic acids and proteins. It was shown that β-substituted and α,γ-bridged trimethinecyanines containing extended heterocyclic systems or N-phenyl as well as N-cyclohexyl substituents demonstrate increased affinity to proteins. At the same time the presence of both N-phenyl and N-cyclohexyl substituents leads to the decrease of the dye fluorescence intensity in complexes with nucleic acids. For trimethinecyanines similarly to unsymmetrical monomethines the presence of N-ω-hydroxy alkyl substituents results in the increase of fluorescence intensity of dye–DNA complex and the emission decrease of dye–RNA complex.

Tuff life: Bioalteration in volcaniclastic rocks from the Ontong Java Plateau

We report microscopic textural, geochemical, isotopic, and biomolecular evidence for microbial alteration of glass shards in a 337.7 m thick sequence of poorly sorted vitric and lithic tuffs recovered during Leg 192 of the Ocean Drilling Program on the Ontong Java Plateau. Petrographic analysis has revealed the highest density and variety of exceptionally preserved microbial alteration textures in the glass shards, when compared to previous studies of glassy pillow basalt margins from ocean crust and ophiolites. Two textural types of microbial alteration are commonly observed: tubular and granular. Tubular textures are characterized by well‐preserved, micron‐scale, tubular to vermicular, channel‐like features with both smooth and scalloped walls that commonly extend from a granular alteration interface rimmed by clay into unaltered glass. These channels are highly convoluted or twisted and in some instances bifurcate. Detailed scanning electron microscopy (SEM) images reveal the presence of delicate filaments and desiccated thin films with morphologies suggestive of a biogenic origin within the channels. Granular textures appear as solid bands, semicircles, or irregular patches of individual and/or coalesced spherical bodies with irregular protrusions into fresh glass. Microprobe X‐ray element maps show elevated levels of carbon, nitrogen, phosphorous, and potassium associated with the microbial alteration features. Bulk‐rock carbon isotope ratios of disseminated carbonates in tuffs preserving fresh glass are depleted (<−9‰), suggesting biologic fractionation. The presence of nucleic acids within the microbial alteration features has been confirmed though staining with ethidium bromide, a stain that specifically binds to double‐stranded DNA and RNA. The presence of DNA/RNA suggests that the biogenic features may be relatively recent and that microbes may be currently active.

Determination of Nucleic Acids on the Basis of Enhancement Effect of Resonance Light Scattering of Toluidine Blue

Based on a detailed study of the interaction of toluidine blue (TB) with nucleic acids, a novel resonance light scattering (RLS) method was developed for the determination of nucleic acids. The RLS intensity of TB at 400 nm was greatly enhanced in the presence of nucleic acids at pH 3.17. Linear relationships between the enhanced RLS intensity and the concentration of nucleic acids were observed in the range of 0.0–2.7 µg cm−3 for calf thymus DNA (ctDNA), 0.0–2.2 µg cm−3 for fish sperm DNA (fsDNA), and 0.0–0.5 µg cm−3 for yeast RNA (yRNA), respectively. The limits of detection (3σ) were determined to be 24.0 ng cm−3 for ctDNA, 22.7 ng cm−3 for fsDNA and 5.1 ng cm−3 for yRNA. The binding constants were evaluated to be 1.1 × 104 dm3 mol−1 for ctDNA, 1.8 × 104 dm3 mol−1 for fsDNA, and 1.7 × 104 dm3 mol−1 for yRNA. The maximum binding numbers (n) were 2.7, 5.5, and 15.0 for ctDNA, fsDNA and yRNA, respectively. The proposed method was applied for determination of the nucleic acids in chicken blood. The analytical results obtained by the present method were in good with that from a UV method.

A monomethine cyanine dye Cyan 40 for two-photon-excited fluorescence detection of nucleic acids and their visualization in live cells.

Monomethine cyanine dye 4-((1-methylbenzothiazolyliliden-2)methyl)-1,2,6-trimethylpyridinium perchlorate (Cyan 40) was investigated as a two-photon-excited fluorescence probe for nucleic acids (NA). Cyan 40 has been shown to demonstrate efficient two-photon-excited fluorescence in the presence of NA in vitro in contrast to solutions without NA. Two-photon confocal laser scanning microscopy (TPCLSM) and two-photon laser scanning microspectrofluorometry were used to check the possibility of using Cyan 40 as two-photon-excited fluorescence label for NA in living cells. Study of dye effect on viability of cells was also carried out. We ascertained that Cyan 40 is a cell-permeant dye, manifesting efficient two-photon-excited fluorescence when bound to NA in living cells, without any significant influence on viability of cells. TPCLSM images obtained from stained cells indicate preferential RNA staining by Cyan 40 compared with DNA.

Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development.

The LIM-domain-binding protein Ldb1 is a key factor in the assembly of transcriptional complexes involving LIM-homeodomain proteins and other transcription factors that regulate animal development. We identified Ssdp proteins (previously described as sequence-specific, single-stranded-DNA-binding proteins) as components of Ldb1-associated nuclear complexes in HeLa cells. Ssdp proteins are associated with Ldb1 in a variety of additional mammalian cell types. This association is specific, does not depend on the presence of nucleic acids, and is functionally significant. Genes encoding Ssdp proteins are well conserved in evolution from Drosophila to humans. Whereas the vertebrate Ssdp gene family has several closely related members, the Drosophila Ssdp gene is unique. In Xenopus, Ssdp encoded by Drosophila Ssdp or mouse Ssdp1 mRNA enhances axis induction by Ldb1 in conjunction with the LIM-homeobox gene Xlim1. Furthermore, we were able to demonstrate an interaction between Ssdp and Chip (the fly homolog of Ldb1) in Drosophila wing development. These findings indicate functional conservation of Ssdp as a cofactor of Ldb1 during invertebrate and vertebrate development.

Fluorescence Characteristics of Variously Charged Asymmetric Monomethine Cyanine Dyes in the Presence of Nucleic Acids

Three asymmetric monomethine cyanine dyes bearing one, two, and three positive charges have been synthesized, and their absorption and fluorescence characteristics in the presence of nucleic acids were studied. The maxima of their longest wavelength absorption band lie between 500 and 520 nm. The dyes do not show fluorescence of their own in TE buffer (pH 5 7.5), but become strongly fluorescent (QF 5 0.2‐0.6) on binding to double-stranded DNA. The fluorescence maxima of the investigated dye-dsDNA complexes are in the region of 530‐550 nm. The influence of the dye/DNA ratio on both the position and intensity of the fluorescence maxima of the complexes is investigated.

Spectral properties of symmetrical threemethine cyanines with α-, γ-substituted polymethine chain in the presence of nucleic acids

Spectral properties of symmetrical threemethine cyanines with α-, γ-substituted polymethine chain in the presence of nucleic acids

An Investigation of Tricarbocyanines “Stains-All” and “iso-Stains-All” as Fluorescent Nucleic Acids Probes

Luminescent properties of carbocyanine dyes Stains-All and its isomer iso-Stains-All were studied in the presence of nucleic acids. Both dyes show sufficient fluorescent intensity increase in the presence of DNA and RNA and may be used as fluorescent probes for nucleic acids (NA) detection in homogeneous assays. It was supposed that Stains-All and iso-Stains-All bind with nucleic acids through different interaction modes.

Interaction of cyanine dyes with nucleic acids. XXV. Influence of affinity-modifying groups in the structure of benzothiazol-4-[2,6-dimethylpyridinium] dyes on the spectral properties of the dyes in the presence of nucleic acids

Novel monomethine pyridinium cyanine dyes of similar structure and containing ‘affinity-modifying’ groups of different chemical nature were studied by spectral-luminescent methods as possible fluorescent probes for the nucleic acids detection. It was shown that the nature of the functional groups in the dye linker influences the fluorescent properties of the dye–nucleic acids complexes. Incorporation of a hydroxyl group into the linker structure leads to a significant increase in the fluorescence intensity of the dye — double-stranded DNA complexes relative to the parent dye Cyan 40.

Interaction of morin-cetyltrimethylammonium bromide with nucleic acids and determination of nucleic acids at nanograms per milliliter levels based on the enhancement of preresonance light scattering.

A new preresonance light scattering (PRLS) assay of nucleic acids is presented. At pH 7.30, the weak PRLS of morin-cetyltrimethylammonium bromide (CTMAB) can be greatly enhanced by the addition of nucleic acids, owing to the interaction between the nucleic acid and morin-CTMAB. After the addition of morin and CTMAB to DNA, the zeta potential of DNA decreases and changes from negative to positive, which is due to the formation of an associate, the aggregation of morin on nucleic acids and the electric neutralization between DNA and the cationic surfactant CTMAB. Mechanism studies showed that the enhanced PRLS comes from the aggregation of morin in the presence of nucleic acids and CTMAB. The enhanced intensity of PRLS is in proportion to the concentration of nucleic acids in the range 7.5 x 10(-9)-1.0 x 10(-5) g ml(-1) for calf thymus DNA, 7.5 x 10(-9)-1.0 x 10(-6) g ml(-1) for salmon sperm DNA and 1.0 x 10(-8)-1.0 x 10(-6) g ml(-1) for yeast RNA. The detection limits are 3.4, 6.2 and 4.1 ng ml(-1) for calf thymus DNA, salmon sperm DNA and yeast RNA, respectively. Synthetic samples were analyzed satisfactorily.

Exploring the frontier between life and death in Escherichia coli: evaluation of different viability markers in liveand heat- or UV-killed cells

A number of methods have been proposed to assess the viability of cells without culture. Each method is based on criteria that reflect different levels of cellular integrity or functionality. As a consequence, the interpretation of viability is often ambiguous. The purposes of this work were to evaluate the capacity of current viability markers to distinguish between live and dead Escherichia coli K-12 cells. Methods that assess ‘viability’ by the demonstration of metabolic activities (esterase activity, active electron transport chain, transport of glucose), cellular integrity (membrane integrity, presence of nucleic acids) or the building up of cellular material (cell elongation) have been evaluated in live and UV- or heat-killed cells. With live cells, viability markers detected cells in counts similar to the colony count. However, these so-called viability markers could stain dead cells for some time after the lethal treatment. For the UV-killed cells, residual activities were detected even after 48 h of storage at 20 °C. However, for heat-treated cells, these activities disappeared within hours after heat treatment. Only a combination of fluorescence in situ hybridization with rRNA probes and cell elongation in response to nutrients (in the presence of an inhibitor of cell division) had the ability to differentiate live from dead cells. Problems in the definition of a viable but nonculturable state are in part due to the lack of a clear definition of bacterial death. We consider death as an irreversible state where no growth, cell elongation or protein synthesis may occur.

Cationic cyanine as a near-infrared fluorescent probe for the determination of nucleic acids.

A new method with a cationic near-IR cyanine as fluorescent probe was developed for the determination of nucleic acids. The near-IR cyanine shows maximum excitation and emission wavelengths at 765 and 790 nm, respectively, in aqueous solution. The method is based on the fluorescence decrease of near-IR cyanine in the presence of nucleic acids. Under optimal conditions, the ratio of fluorescence intensity in the absence and presence of nucleic acids was proportional to the concentration of nucleic acids over the range 0.10-1.2 microg/mL for CT (calf thymus) DNA or SM (salmon sperm) DNA, and 0.10-1.6 microg/mL for yeast RNA. The detection limits were 30 ng/mL for CT DNA, 25 ng/mL for SM DNA and 70 ng/mL for yeast RNA. The relative standard deviation (n = 6) was 2.1% for 500 ng/mL CT DNA, 2.4% for 500 ng/mL SM DNA and 2.7% for 500 ng/mL yeast RNA, respectively.

A role for the GSG domain in localizing Sam68 to novel nuclear structures in cancer cell lines.

The GSG (GRP33, Sam68, GLD-1) domain is a protein module found in an expanding family of RNA-binding proteins. The numerous missense mutations identified genetically in the GSG domain support its physiological role. Although the exact function of the GSG domain is not known, it has been shown to be required for RNA binding and oligomerization. Here it is shown that the Sam68 GSG domain plays a role in protein localization. We show that Sam68 concentrates into novel nuclear structures that are predominantly found in transformed cells. These Sam68 nuclear bodies (SNBs) are distinct from coiled bodies, gems, and promyelocytic nuclear bodies. Electron microscopic studies show that SNBs are distinct structures that are enriched in phosphorus and nitrogen, indicating the presence of nucleic acids. A GFP-Sam68 fusion protein had a similar localization as endogenous Sam68 in HeLa cells, diffusely nuclear with two to five SNBs. Two other GSG proteins, the Sam68-like mammalian proteins SLM-1 and SLM-2, colocalized with endogenous Sam68 in SNBs. Different GSG domain missense mutations were investigated for Sam68 protein localization. Six separate classes of cellular patterns were obtained, including exclusive SNB localization and association with microtubules. These findings demonstrate that the GSG domain is involved in protein localization and define a new compartment for Sam68, SLM-1, and SLM-2 in cancer cell lines.