DNA damage detection technique applying time-resolved fluorescence measurements

Quantifying Heme-Protein Maturation from Ratiometric Fluorescence Lifetime Measurements on the Single Fluorophore in Its GFP Fusion

Protein maturation by heme insertion is a common post-translation modification of key biological importance. Nonetheless, where and when this maturation occurs in eukaryotic cells remain unknown for most heme proteins. Here, we demonstrate for the first time that the maturation of a chromosomally expressed, endogenous heme protein fused to a green fluorescent protein (GFP) can be tracked in live cells. Selecting yeast cytochrome c peroxidase (Ccp1) as our model heme-binding protein, we first characterized the emission in vitro of recombinant Ccp1-GFP with GFP fused C-terminally to Ccp1 by the linker GRRIPGLIN. Time-correlated single-photon counting reveals a single fluorescence lifetime for heme-free apoCcp1-GFP, τ₀ = 2.84 ± 0.01 ns. Heme bound to Ccp1 only partially quenches GFP fluorescence since holoCcp1-GFP exhibits two lifetimes, τ₁ = 0.95 ± 0.02 and τ₂ = 2.46 ± 0.03 ns with fractional amplitudes a₁ = 38 ± 1.5% and a₂ = 62 ± 1.5%. Also, τ and a are independent of Ccp1-GFP concentration and solution pH between 5.5 and 8.0, and a standard plot of a₁ vs % holoCcp1-GFP in mixtures with apoCcp1-GFP is linear, establishing that the fraction of Ccp1-GFP with heme bound can be determined from a₁. Fluorescence lifetime imaging microscopy (FLIM) of live yeast cells chromosomally expressing the same Ccp1-GFP fusion revealed 30% holoCcp1-GFP (i.e., mature Ccp1) and 70% apoCcp1-GFP in agreement with biochemical measurements on cell lysates. Thus, ratiometric fluorescence lifetime measurements offer promise for probing heme-protein maturation in live cells, and we can dispense with the reference fluorophore required for ratiometric intensity-based measurements.

Carbon dots based FRET for the detection of DNA damage

Here, we aimed our attention at the synthesis of carbon dots (C-dots) with the ability to interact with DNA to suggest an approach for the detection of DNA damage. Primarily, C-dots modified with amine moieties were synthesized using the one-step microwave pyrolysis of citric acid in the presence of diethylenetriamine. The C-dots showed strong photoluminescence with a quantum yield of 4%. In addition, the C-dots (2.8±0.8nm) possessed a good colloidal stability and exhibited a positive surface charge (ζ=36mV) at a neutral pH. An interaction study of the C-dots and the DNA fragment of λ bacteriophage was performed, and the DNA binding resulted in changes to the photoluminescent and absorption properties of the C-dots. A binding of the C-dots to DNA was also observed as a change to DNA electrophoretic mobility and a decreased ability to intercalate ethidium bromide (EtBr). Moreover, the Förster (or fluorescence) resonance energy transfer (FRET) between the C-dots and EtBr was studied, in which the C-dots serve as an excitation energy donor and the EtBr serves as an acceptor. When DNA was damaged using ultraviolet (UV) radiation (λ=254nm) and hydroxyl radicals, the intensity of the emitted photoluminescence at 612nm significantly decreased. The concept was proved on analysis of the genomic DNA from PC-3 cells and DNA isolated from melanoma tissues.

Fluorescence Detection and Discrimination of ss- and ds-DNA with a Water Soluble Oligopyrene Derivative

A novel water-soluble cationic conjugated oligopyrene derivative, oligo(N(1),N(1),N(1),N(4),N(4),N(4)-hexamethyl-2-(4-(pyren-1-yl) butane-1,4-diaminium bromide) (OHPBDB), was synthesized by a combination of chemical and electrochemical synthesis techniques. Each oligomer chain has five pyrene derivative repeating units and brings 10 positive charges. OHPBDB showed high and rapid fluorescence quenching in aqueous media upon addition of trace amounts of single-stranded (ss) and double-stranded (ds) DNA. The Stern-Volmer constants for ss- and ds-DNA were measured to be as high as 1.3 × 10(8) mol(-1)·L and 1.2 × 10(8) mol(-1)·L, respectively. On the other hand, distinct fluorescence enhancement of OHPBDB upon addition of large amount of ss-DNA or ds-DNA was observed. Furthermore, ss-DNA showed much stronger fluorescence enhancement than that of ds-DNA, thus yielding a clear and simple signal useful for the discrimination between ss- and ds-DNA in aqueous media.

Effect of UVC-Induced Damage to DNA on the Intercalation of Thiazole Orange: A Convenient Reporter for DNA Damage†

We report a novel method of identifying damage to DNA leading to the loss of intercalation sites. Thiazole orange (TO), an intercalating cyanine dye, fluoresces strongly when intercalated in DNA, but not free in solution. Upon UVC-induced damage to DNA, the change in TO fluorescence is greater than the change in any of the other spectral or biochemical indicators (absorbance, circular dichroism and agarose gel electrophoresis), thus providing a fast screening method to identify damage to DNA. The method is geared toward high levels of damage, such as those that may result during radiation treatment of food products.

Recent advances in biosensor techniques for environmental monitoring

Biosensors for environmental applications continue to show advances and improvements in areas such as sensitivity, selectivity and simplicity. In addition to detecting and measuring specific compounds or compound classes such as pesticides, hazardous industrial chemicals, toxic metals, and pathogenic bacteria, biosensors and bioanalytical assays have been designed to measure biological effects such as cytotoxicity, genotoxicity, biological oxygen demand, pathogenic bacteria, and endocrine disruption effects. This article is intended to discuss recent advances in the area of biosensors for environmental applications.

Use of a capillary electrophoresis instrument with laser-induced fluorescence detection for DNA quantitation

Highly selective and sensitive assays are required for detection and quantitation of the small masses of DNA typically encountered in clinical and forensic settings. High detection sensitivity is achieved using fluorescent labeling dyes and detection techniques such as spectrofluorometers, microplate readers and cytometers. This work describes the use of a laser-induced fluorescence (LIF) detector in conjunction with a commercial capillary electrophoresis instrument for DNA quantitation. PicoGreen and YO-PRO-1, two fluorescent DNA labeling dyes, were used to assess the potential of the system for routine DNA analysis. Linearity, reproducibility, sensitivity, limits of detection and quantitation, and sample stability were examined for the two assays. The LIF detector response was found to be linear (R2 > 0.999) and reproducible (RSD < 9%) in both cases. The PicoGreen assay displayed lower limits of detection and quantitation (20 pg and 60 pg, respectively) than the YO-PRO-1 assay (60 pg and 260 pg, respectively). Although a small variation in fluorescence was observed for the DNA/dye complexes over time, quantitation was not significantly affected and the solutions were found to be relatively stable for 80 min. The advantages of the technique include a 4- to 40-fold reduction in the volume of sample required compared to traditional assays, a 2- to 20-fold reduction in the volume of reagents consumed, fast and automated analysis, and low cost (no specific instrumentation required).

Experimental and theoretical study of the interaction of single-stranded DNA homopolymers and a monomethine cyanine dye: nature of specific binding

The photophysical properties of an intercalating unsymmetrical monomethine cyanine dye and single-stranded DNA homopolymers show strong association for poly(dA) and poly(dG), but not for poly(dC) and poly(dT), as determined by several spectroscopic techniques and molecular dynamics calculations. While poly(dA) and poly(dG) appear to bind the dye as a monomer (with dramatic increase in fluorescence), poly(dC) and poly(dT) bind only very weakly, and seem to promote dye aggregation. Only in the case of poly(dA) there seems to be a unique, well defined form of intercalation, that molecular dynamics calculations suggest involve the quinoline ring between two bases, in an arrangement that should favor pi-stacking; consistently with this, the decay of the fluorescence shows a single exponential, the absorption spectrum shows a shift in the dye maximum, the fluorescence is strong, and the induced circular dichroism follows a simple pattern.

Role of the Spacer in the Singlet−Singlet Energy Transfer Mechanism (Förster vs Dexter) in Cofacial Bisporphyrins

The cofacial bisporphyrins H4DPS (DPS = 4,6-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]dibenzothiophene), H4DPO (DPO = 4,6-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]dibenzofuran), H4DPX (DPX = 4,5-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]-9,9-dimethylxanthene), H4DPA (DPA = 1,8-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]anthracene), and H4DPB (DPB = 1,8-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]biphenylene) have been monometalated by Zn(OAc)2.2H2O and by GaCl3 to explore the singlet-singlet energy transfer from the photoexcited metal porphyrin center to the linked free base porphyrin. The spectroscopic (UV-vis and fluorescence) and photophysical properties (fluorescence lifetimes, tauF, and quantum yields, phiF) have been investigated at 298 and 77 K in degassed 2-MeTHF for the donor-acceptor systems, (Zn)H2DPS, (Zn)H2DPO, (Zn)H2DPA, (Zn)H2DPX, and (Zn)H2DPB, as well as for the bis-zinc complexes, (Zn)2DPS, (Zn)2DPO, (Zn)2DPX, and (Zn)2DPB, respectively, and the monoporphyrin derivatives, H2P, (Zn)P, and (Ga-OMe)P (P2- = 5-phenyl-2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrin-dianion). The singlet-singlet energy transfer rate constants (KET) were obtained using KET = (1/tauF -1/tauFo), where tauFo is the fluorescence lifetime of the corresponding bis-zinc(II) systems (or (Zn)P and (Ga-OMe)P) where no energy transfer occurs. The tauF value for three bis-zinc(II) compounds varies from 1.69 to 2.01 ns and is 1.84 (at 298 K) and 3.20 ns (at 77 K) for (Ga-OMe)P. In the donor-acceptor bismacrocycles, depending on the spacer and the temperature, the fluorescence lifetimes decrease down to 50-240 ps. The KET values range from approximately 4 to approximately 21 (ns(-1)) and have been analyzed considering both the Förster and the Dexter mechanisms. Using the C(meso)-C(meso) distance parameters in the calculations, the Förster and Dexter mechanisms operate for DPS and DPO, and for DPA, DPX, and DPB spacer systems, respectively. The limit distance where one mechanism dominates over the other is estimated to be around 5-6 A.