Concentration of dye-labeled nucleotides incorporated into DNA determined by surface plasmon resonance-surface plasmon fluorescence spectroscopy

Improved imaging and preservation of lysosome dynamics using silver nanoparticle-enhanced fluorescence

The dynamics of living cells can be studied by live-cell fluorescence microscopy. However, this requires the use of excessive light energy to obtain good signal-to-noise ratio, which can then photobleach fluorochromes, and more worrisomely, lead to phototoxicity. Upon light excitation, noble metal nanoparticles such as silver nanoparticles (AgNPs) generate plasmons, which can then amplify excitation in direct proximity of the nanoparticle's surface and couple to the oscillating dipole of nearby radiating fluorophores, modifying their rate of emission and thus, enhancing their fluorescence. Here, we show that AgNPs fed to cells to accumulate within lysosomes enhanced the fluorescence of lysosome-targeted Alexa488-conjugated dextran, BODIPY-cholesterol, and DQ-BSA. Moreover, AgNP increased the fluorescence of GFP fused to the cytosolic tail of LAMP1, showing that metal enhanced fluorescence can occur across the lysosomal membrane. The inclusion of AgNPs in lysosomes did not disturb lysosomal properties such as lysosomal pH, degradative capacity, autophagy and autophagic flux, and membrane integrity, though AgNP seemed to increase basal lysosome tubulation. Importantly, by using AgNP, we could track lysosome motility with reduced laser power without damaging and altering lysosome dynamics. Overall, AgNP-enhanced fluorescence may be a useful tool to study the dynamics of the endo-lysosomal pathway while minimizing phototoxicity.

Simple and sensitive detection of deoxyribonucleic acid using a RecA-GFP fusion protein-DNA filament as probe

A simple, rapid and highly sensitive method for detection of double-stranded DNA (dsDNA) was developed using a novel fluorescence probe composed of a RecA-GFP fusion protein that had specific recognition of ssDNA complexes (RecA-GFP-DNA filament). The RecA-GFP fusion protein not only had strong fluorescence, but could also occur by homologous recombination. In the presence of the target dsDNA, the complementary ssDNA of the RecA-GFP-DNA filaments invaded one end of the dsDNA chain. In addition, the other end of the ssDNA dissociated the RecA-GFP filaments. An assay of the probe showed a linear relationship with dsDNA concentration in the range 1-11 nM, with a correlation coefficient of 0.9923. The limit of detection for dsDNA was determined experimentally to be 0.3 nM (3δ). Compared with conventional methods, this method has the advantages of simple operation, high specificity, and high sensitivity.

Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand-Apoprotein Complex

In this work, the hybridization and dehybridization of ssDNA with 20 bases at gold coated sensor surfaces modified with complementary 20 bases capture probe ssDNA was investigated at 18 °C by quartz crystal microbalance measurements with dissipation monitoring (QCM-D). A sequence of 20 base pairs with a melting temperature of about 64 °C was chosen, since in many biosensor studies the target molecules are DNA or RNA oligomers of similar length. It turned out that at the applied experimental conditions the DNA hybridization was irreversible, and therefore the hybridization and dehybridization process could not be described by the Langmuir model of adsorption. Nevertheless, quantitative dehybridization could be achieved by rinsing the sensor surface thoroughly with pure water. When in contrast the hybridization of a target with only 10 bases complementary to the outermost 10 bases of the 20 bases capture probe was studied, binding and unbinding were reversible, and the hybridization/dehybridization process could be satisfactorily described by the Langmuir model. For the 10 base pair sequence, the melting temperature was about 36 °C. Apparently, for Langmuir behavior, it is important that the experiments are applied at a temperature sufficiently close to the melting temperature of the sequence under investigation to ensure that at least traces of the target molecules are unhybridized (i.e., there needs to be an equilibrium between hybridized and dehybridized target molecules). To validate the reliability of our experimental approach we also studied the reconstitution and disassembly of the flavoprotein dodecin at flavin-terminated DNA monolayers, as according to previous studies it is assumed that the apododecin-flavin system can be well described by the Langmuir model. As a result, this assumption could be verified. Using three different approaches, K_D values were obtained that differ not more than by a factor of 4.

Activatable QD-Based Near-Infrared Fluorescence Probe for Sensitive Detection and Imaging of DNA

Accurate detection of DNA is essential for the precise diagnosis of diseases. Here we report an activatable near-infrared (NIR) fluorescence nanoprobe (QD-Al-GFLX) composed of NIR quantum dots (QDs) and Al(III)-gatifloxacin (Al-GFLX) complexes for the sensitive detection of double-stranded DNA (dsDNA) both in aqueous solution and in living cells. We demonstrated that the initial strong NIR fluorescence of QDs in QD-Al-GFLX was quenched by the Al-GFLX complex via a photoinduced electron transfer (PET) mechanism. Upon interaction with dsDNA, the high binding affinity between dsDNA and Al-GFLX complex could trigger QD-Al-GFLX dissociation, which could eliminate the PET process, resulting in significant enhancement of NIR fluorescence. QD-Al-GFLX was sensitive and specific to detect dsDNA in aqueous solution, with a detection limit of 6.83 ng/mL. The subsequent fluorescence imaging revealed that QD-Al-GFLX holds a high ability to enter into live cells, generating strong NIR fluorescence capable of reporting on dsDNA levels. This study highlighted the potential of using QD-Al-GFLX nanoprobe for the real-time detection and imaging of dsDNA in living cells.

Detection of DNA using an “off-on” switch of a regenerating biosensor based on an electron transfer mechanism from glutathione-capped CdTe quantum dots to nile blue

A new DNA detection method, which relies on the “off-on” switch of a regenerated fluorescence biosensor based on an electron transfer mechanism from glutathione (GSH)-capped CdTe quantum dots (QDs) to nile blue (NB), is proposed.

FRET detection of DNA sequence via electrostatic interaction of polycationic phenyleneethynylene dendrimer with DNA/PNA hybrid

Interaction between a polycationic compound and DNA is a useful phenomenon for development of a new DNA sensing system. In this work, dendritic polycationic phenyleneethynylene fluorophores are investigated as a Förster resonance energy transfer (FRET) donor for the detection of DNA hybridization in conjunction with a fluorescein-labeled pyrrolidinyl peptide nucleic acid (Fl-acpcPNA) probe. The first generation dendrimer is an efficient energy donor for the fluorescein acceptor but also shows non-specific FRET signal with Fl-acpcPNA. The addition of N-methyl 2-pyrrolidone can virtually completely remove the non-specific interaction between Fl-acpcPNA and the dendrimer. Under the optimal condition, the complementary DNA gives a distinctively high FRET ratio (1.42) comparing with those of the non-complementary (0.26) and singly mismatched (0.51) DNAs. The FRET ratio responses linearly with the DNA concentration with the detection limit lower than 1nM. The FRET ratio is even higher for the complementary target DNAs with extra hanging nucleotide sequences, which is a more frequently encountered scenario in real applications.

Label free DNA detection based on gold nanoparticles quenching fluorescence of Rhodamine B

A novel and sensitive label free DNA detection method using gold nanoparticles (GNPs) and Rhodamine B (RB) has been developed. The assay is based on the following two properties. One is the different adsorption properties of single-stranded and double-stranded DNA on GNPs in colloidal solution. The other is the different quenching ability of aggregated GNPs and dispersed GNPs on RB. Un-aggregated GNPs could effectively quench the fluorescence of RB. However, the quenching ability greatly decreases after GNPs aggregated. The hybridization of probe DNA and target DNA is monitored by the fluorescence detection after the RB is added to the solution. Under the optimal experimental conditions, the detection limit of this assay is 2.9×10(-13) mol L(-1).

Electrochemical aptameric sensor based on the Klenow fragment polymerase reaction for cocaine detection

An electrochemical aptasensor based on Klenow fragment (KF) polymerase reaction that combines the aggregation of ferrocene-functionalized oligonucleotide has been developed successfully for cocaine detection. In the presence of cocaine, the recognition probe changed its hairpin conformation into the tripartite complex. The aptamer-cocaine complex gave a 3'-single-stranded tail sequence complementary to the surface-tethered capture probe. In KF polymerase reaction, the recognition probe served as a template for the extension of a capture probe. It requires a sample volume of 2 μL and is complete within 1 h. The ferrocene-appended oligonucleotide incorporated into the newly synthesized complementary probe leads to an electrochemical response. This sensitive detection of cocaine is due to a very low background signal and large signal enhancement up to 9-fold upon addition of analyte. It permits detection of as low as 200 μM cocaine. The simple and isothermal procedure does not require thermal cycling or special laboratory conditions, which makes it adaptable to low-cost and robust biosensing.

Fabrication of mixed self-assembled monolayers designed for avidin immobilization by irradiation promoted exchange reaction

An applicability of irradiation-promoted exchange reaction (IPER) to the fabrication of mixed self-assembled monolayers (SAMs) composed of the protein-repelling matrix and the moieties bearing binding sites for specific attachment of a target protein is demonstrated. As test systems, we took mixed films of oligoethylene glycol (OEG)-substituted alkanethiols (OEG-ATs) and biotin-substituted alkanethiols (BATs) on Au{111}. Such SAMs are suitable for the specific immobilization of avidin protein and its variants. The composition of the mixed OEG-AT/BAT SAMs could be precisely controlled by varying the irradiation dose, which is important prerequisite for the fabrication of the respective patterns by electron-beam lithography. While the general trend in the immobilization of avidin onto the mixed OEG-AT/BAT SAMs prepared by IPER was found to be consistent with the earlier reports regarding the analogous films fabricated by the coassembly method, the concentration of the BAT component in the mixed SAMs needed for the maximum surface coverage of the specific protein was found to be somewhat lower, and the maximum avidin coverage somewhat higher in the case of IPER as compared to the coassembly method. We ascribe these differences to the lack of phase segregation and better separation of the individual BAT species in the OEG-AT matrix in the case of IPER.

Fluorescence quantification for surface plasmon excitation

Surface plasmon resonance and surface plasmon fluorescence spectroscopy in combination have the potential to distinguish multicomponent surface processes. However, surface intensity variations from resonance angle shifts lead to a nonlinear response in the fluorescence intensity. We report a method to account for surface intensity variations using the experimentally measured relationship between fluorescence and reflectivity. We apply this method to monitor protease adsorption and proteolytic substrate degradation simultaneously. Multilayer protein substrates are prepared for these degradation studies using a layer-by-layer technique.

Microwave-accelerated surface plasmon-coupled directional luminescence 2: a platform technology for ultra fast and sensitive target DNA detection in whole blood

The application of Microwave-Accelerated Surface Plasmon-Coupled Luminescence (MA-SPCL) to fast and sensitive DNA hybridization assays in buffer and whole blood is presented. In this regard, a model DNA hybridization assay whereby a fluorophore-labeled target ssDNA specific to human immunodeficiency, Hepatitis C (Hep C), is probed by an anchor probe immobilized on thin gold films, is driven to completion within 1 min with microwave heating, as compared to an identical assay completed in approximately 4 h at room temperature. Finite-Difference Time-Domain calculations show that gold disks are preferentially heated around the edges creating a temperature gradient along the disks, which in turn results in the larger influx of complementary DNA towards anchor probe-modified surface. Thermal images of the assay platform during microwave heating also provide additional information on the microwave heating pattern in the microwave cavity. Finally, the effects of low power microwave heating on the ability of DNA to re-hybridize with the complimentary target on the surface gold films, which allows the multiple re-use of the gold films, is demonstrated. The MA-SPCL technique offers an alternative approach to current DNA based detection technologies, especially when speed and sensitivity are required, such as in the identification of DNA or even RNA-based diseases using whole blood samples that affect human health.

Plasmonic technology: novel approach to ultrasensitive immunoassays

At the Center for Fluorescence Spectroscopy, we have taken advantage of the favorable properties of surface plasmon-coupled emission (SPCE) to improve fluorescence-based immunoassays. SPCE occurs when excited fluorophores near conducting metallic structures efficiently couple to surface plasmons. These surface plasmons, appearing as free electron oscillations in the metallic layer, produce electromagnetic radiation that preserves the spectral properties of fluorophores but is highly polarized and directional. SPCE immunoassays provide several advantages over other fluorescence-based methods. This review explains new approaches to fluorescence immunoassays, including our own use of SPCE for simultaneous detection of more than one fluorescent marker and performance of immunoassays in the presence of an optically dense medium, such as whole blood.