A new ultrasensitive way to circumvent PCR-based allele distinction: Direct probing of unamplified genomic DNA by solution-phase hybridization using two-color fluorescence cross-correlation spectroscopy

Visualization of subdiffusive sites in a live single cell

We measured anomalous diffusion in human prostate cancer cells which were transfected with the Alexa633 fluorescent RNA probe and co-transfected with enhanced green fluorescent protein-labeled argonaute2 protein by laser scanning microscopy. The image analysis arose from diffusion based on a “two-level system”. A trap was an interaction site where the diffusive motion was slowed down. Anomalous subdiffusive spreading occurred at cellular traps. The cellular traps were not immobile. We showed how the novel analysis method of imaging data resulted in new information about the number of traps in the crowded and heterogeneous environment of a single human prostate cancer cell. The imaging data were consistent with and explained by our modern ideas of anomalous diffusion of mixed origins in live cells. Our original research presented in this study is significant as we obtained a complex diffusion mechanism in live single cells.

Comparative advantages and limitations of the basic metrology methods applied to the characterization of nanomaterials

Fabrication of modern nanomaterials and nanostructures with specific functional properties is both scientifically promising and commercially profitable. The preparation and use of nanomaterials require adequate methods for the control and characterization of their size, shape, chemical composition, crystalline structure, energy levels, pathways and dynamics of physical and chemical processes during their fabrication and further use. In this review, we discuss different instrumental methods for the analysis and metrology of materials and evaluate their advantages and limitations at the nanolevel.

Single molecule fluorescence under conditions of fast flow

We have experimentally determined the optimal flow velocities to characterize or count single molecules by using a simple microfluidic device to perform two-color coincidence detection (TCCD) and single pair Förster resonance energy transfer (spFRET) using confocal fluorescence spectroscopy on molecules traveling at speeds of up to 10 cm s(-1). We show that flowing single fluorophores at ≥0.5 cm s(-1) reduces the photophysical processes competing with fluorescence, enabling the use of high excitation irradiances to partially compensate for the short residence time within the confocal volume (10-200 μs). Under these conditions, the data acquisition rate can be increased by a maximum of 38-fold using TCCD at 5 cm s(-1) or 18-fold using spFRET at 2 cm s(-1), when compared with diffusion. While structural characterization requires more photons to be collected per event and so necessitates the use of slower speeds (2 cm s(-1) for TCCD and 1 cm s(-1) for spFRET), a considerable enhancement in the event rate could still be obtained (33-fold for TCCD and 16-fold for spFRET). Using flow under optimized conditions, analytes could be rapidly quantified over a dynamic range of up to 4 orders of magnitude by direct molecule counting; a 50 fM dual-labeled model sample can be detected with 99.5% statistical confidence in around 8 s using TCCD and a flow velocity of 5 cm s(-1).

PCR-free detection of genetically modified organisms using magnetic capture technology and fluorescence cross-correlation spectroscopy

The safety of genetically modified organisms (GMOs) has attracted much attention recently. Polymerase chain reaction (PCR) amplification is a common method used in the identification of GMOs. However, a major disadvantage of PCR is the potential amplification of non-target DNA, causing false-positive identification. Thus, there remains a need for a simple, reliable and ultrasensitive method to identify and quantify GMO in crops. This report is to introduce a magnetic bead-based PCR-free method for rapid detection of GMOs using dual-color fluorescence cross-correlation spectroscopy (FCCS). The cauliflower mosaic virus 35S (CaMV35S) promoter commonly used in transgenic products was targeted. CaMV35S target was captured by a biotin-labeled nucleic acid probe and then purified using streptavidin-coated magnetic beads through biotin-streptavidin linkage. The purified target DNA fragment was hybridized with two nucleic acid probes labeled respectively by Rhodamine Green and Cy5 dyes. Finally, FCCS was used to detect and quantify the target DNA fragment through simultaneously detecting the fluorescence emissions from the two dyes. In our study, GMOs in genetically engineered soybeans and tomatoes were detected, using the magnetic bead-based PCR-free FCCS method. A detection limit of 50 pM GMOs target was achieved and PCR-free detection of GMOs from 5 microg genomic DNA with magnetic capture technology was accomplished. Also, the accuracy of GMO determination by the FCCS method is verified by spectrophotometry at 260 nm using PCR amplified target DNA fragment from GM tomato. The new method is rapid and effective as demonstrated in our experiments and can be easily extended to high-throughput and automatic screening format. We believe that the new magnetic bead-assisted FCCS detection technique will be a useful tool for PCR-free GMOs identification and other specific nucleic acids.

Rapid homogenous detection of the Ibaraki virus NS3 cDNA at picomolar concentrations by magnetic modulation

Magnetic modulation biosensing (MMB) system is experimentally demonstrated for rapid and homogeneous detection of the Ibaraki virus NS3 cDNA. A novel fluorescent resonance energy transfer (FRET)-based probe discriminates the target DNA from the control. When detection is made, the FRET-based probe is cleaved using Taq-polymerase activity and fluorescent light is produced. The biotinylated probes are attached to streptavidin-coupled superparamagnetic beads and are maneuvered into oscillatory motion by applying an alternating magnetic field gradient through two electromagnetic poles. The beads are condensed into the detection area and their movement in and out the orthogonal laser beam produces a periodic fluorescent signal that is demodulated using synchronous detection. 1.9pM of the Ibaraki virus NS3 cDNA was detected in homogeneous solution within 18min without separation or washing steps.

Detection of prion protein immune complex for bovine spongiform encephalopathy diagnosis using fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) are powerful techniques to measure molecular interactions with high sensitivity in homogeneous solution and living cells. In this study, we developed methods for the detection of prion protein (PrP) using FCS and FCCS. A combination of a fluorescent-labeled Fab' fragment and another anti-PrP monoclonal antibody (mAb) enabled us to detect recombinant bovine PrP (rBoPrP) using FCS because there was a significant difference in the diffusion coefficients between the labeled Fab' fragment and the trimeric immune complex consisting of rBoPrP, labeled Fab' fragment, and another anti-PrP mAb. On the other hand, FCCS detected rBoPrP using two mAbs labeled with different fluorescence dyes. The detection limit for PrP in FCCS was approximately threefold higher than that in FCS. The sensitivity of FCCS in detection of abnormal isoform of PrP (PrP(Sc)) was comparable to that of enzyme-linked immunosorbent assay (ELISA). Because FCS and FCCS detect the PrP immune complex in homogeneous solution of only microliter samples with a single mixing step and without any washing steps, these features of measurement may facilitate automating bovine spongiform encephalopathy diagnosis.

Mobility and distribution of replication protein A in living cells using fluorescence correlation spectroscopy

Replication protein A (RPA), the eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for all pathways of DNA metabolism. To study the function of RPA in living cells the second largest RPA subunit and an N-terminal deletion mutant thereof were fused to green fluorescent protein (GFP; GFP-RPA2 and GFP-RPA2deltaN, respectively) in a controlled, molecular biological way. These proteins were expressed in HeLa cells under the control of the inducible tetracycline expression system. GFP-RPA2 and GFP-RPA2deltaN are predominately nuclear proteins as determined by confocal laser scanning microscopy. Low basal expression of GFP-RPA2deltaN allowed the measurement of kinetic parameters of RPA. Using fluorescence correlation spectroscopy (FCS) two populations--a fast and a slow moving species--were detected in the nucleus and the cytosol of human cells. The translational diffusion rates of these two RPA populations were approximately 15 microm2/s and 1.8 microm2/s. This new finding reveals the existence of different multiprotein and ssDNA-protein complexes of RPA in both cellular compartments and opens the possibility for their analyses.

Introduction: array technology - an overview

Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex situ synthesized biomacromolecules onto the substrate surface. The application of microarrays includes spatial addressing with target (macro) molecules and screening for interactions between immobilized probe and target. The screening is simplified by the microarray format, which features a known structure of every immobilized library element. The area of nucleic acid arrays is best developed, because such arrays are allowed to follow the biosynthetic pathway from genes to proteins, and because nucleic acid hybridization is a most straightforward screening tool. Applications to genomics, transcriptomics, proteomics, and glycomics are currently in the foreground of interest; in this postgenomic phase they are allowed to gain new insights into the molecular basis of cellular processes and the development of disease.

'True' single-molecule molecule observations by fluorescence correlation spectroscopy and two-color fluorescence cross-correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) and two-color fluorescence cross-correlation spectroscopy (FCCS) are a measure of fluctuations of detected light as a fluorescence molecule diffuses through a femtoliter detection volume caused by a tightly focused laser and confocal optics. Fluorescence from a single molecule can easily be distinguished from the slight background associated with a femtoliter of solvent. At a solution concentration of about 1 nM, the probability that there is an analyte molecule in the probe volume is less than one. Although fluorescence from individual molecules is collected, the data are analyzed by autocorrelation or two-color cross-correlation functions that are the average of thousands of molecules. Properties of single molecules are not obtained. I have been working on problems and opportunities associated with very dilute solutions. The molecule in the confocal probe volume is most probably the molecule that just diffused out, turned around, and diffused back in, i.e., reentered. For the first time, some theoretical results of the novel theory of the meaningful time are presented that enable study of just one single molecule over extended periods of times without immobilization or hydrodynamic focusing. Reentries that may also be called reoccurrences or encounters of a single molecule are significant because during measurement times they give rise to fluctuation phenomena such as molecule number fluctuations. Likewise, four criteria have been developed that can be used to verify that there is only one "selfsame" molecule in the laser probe volume during the experiment: (Földes-Papp, Z., 2006. What it means to measure a single molecule in a solution by fluorescence fluctuation spectroscopy. Exp. Mol. Pathol. 80 (3) 209-218).

What it means to measure a single molecule in a solution by fluorescence fluctuation spectroscopy

Traditional methodologies in micro- and nanofluidics measure biological mechanisms as an average of a population of molecules as only their combined effect can be detected. Fluorescence fluctuation spectroscopy methods such as fluorescence correlation spectroscopy (FCS) and two-color fluorescence cross-correlation spectroscopy (FCCS) are used as alternative experimental approaches in ultrasensitive analytics at the single-molecule level. However, what is the measurement time in which one is able to study just one single molecule in solution without immobilizing it? Existing theories are inadequate since they do not predict the meaningful time as a function of the concentration of other molecules of the same kind in bulk solution. This situation produces considerable concern, and experimental hypotheses differ according to which single-molecule detection methods are thought to have greater validity. This subject is clearly at the forefront of research and should be of great interest to experimental medical scientists. As will be seen in this article, it is worthwhile to obtain a correct form of the meaningful-time relationship through theoretical means. The new ideas are comprehensively presented, and this relationship is a new concept at this time. The meaningful time for studying just one molecule without immobilization specifies the time parameter in the selfsame molecule likelihood estimator. Possible users for this concept are those working in biotechnological applications dealing with gene technology. Furthermore, the concept is of interest for a great number of medical, pharmaceutical and chemical laboratories. It may serve as a foundation for further work in single-cell biology. It is suspected that heterogeneities play a much larger role inside the cell than in free solution--a perfect opportunity for single-molecule studies and, thus, a novel hypothesis regarding structure and dynamics of cellular networks is first presented for the minimal neurotrophin network model.