Current Pharmaceutical Biotechnology - Volume 5, Issue 2, 2004

Fluorescence Correlation Spectroscopy (FCS) has developed into a routine method to quantitatively study diffusion of molecules and kinetic processes. FCS has recently become popular to complement live cell imaging with biophysical information. The enabling technology has been commercially realised by combining laser scanning microscopes and fluorescence correlation spectrometers in one integrated platform. This article provides an overview of the Zeiss solution of such a combined instrument, the LSM 510 META / ConfoCor 2 system. We focus on the instrumental set up as well as technical advances and improvements in the software that controls FCS data acquisition and evaluation. In addition, we outline the calibration of the instrument and the work flow for data analysis with emphasis on in vivo pharmacological applications.

Fluorescence correlation spectroscopy (FCS) is an important technique for studying low concentrations of analyte molecules in solution. The core molecular characteristic that can be addressed by FCS is the translational diffusion coefficient of the analyte molecules, which can be used for i.e. studying molecular binding and reactions, or conformational changes of macromolecules. The present paper discusses several possible optical and photophysical effects that can influence the outcome of a FCS measurement and thus can bias the value of the derived diffusion coefficient.

Many theoretical models of molecular interactions, biochemical and chemical reactions are described on the single-molecule level, although our knowledge about the biochemical/chemical structure and dynamics primarily originates from the investigation of many-molecule systems. At present, there are four experimental platforms to observe the movement and the behavior of single fluorescent molecules: wide-field epi-illumination, near-field optical scanning, and laser scanning confocal and multiphoton microscopy. The platforms are combined with analytical methods such as fluorescence resonance energy transfer (FRET), fluorescence auto-or two-color cross-correlation spectroscopy (FCS), fluorescence polarizing anisotropy, fluorescence quenching and fluorescence lifetime measurements. The original contribution focuses on counting and characterization of freely diffusing single molecules in a single-phase like a solution or a membrane without hydrodynamic flow, immobilization or burst size analysis of intensity traces. This can be achieved, for example, by Fluorescence auto- or two-color cross-Correlation Spectroscopy as demonstrated in this original article. Three criteria (Foldes-Papp (2002) Pteridines, 13, 73-82; Foldes-Papp et al. (2004a) J. Immunol. Meth., in press; Földes-Papp et al. (2004b) J. Immunol. Meth., in press) are discussed for performing continuous measurements with one and the same single (individual) molecule, freely diffusing in a solution or a membrane, from sub-milliseconds up to severals hours. The 'algorithms' developed for single-molecule fluorescence detection are called the 'selfsame singlefluorescent- molecule regime'. An interesting application of the results found is in the field of immunology. The application of the theory to experimental results shows that the theory is consistent with the experiments. The exposition of the novel ideas on Single (Solution)-Phase Single-Molecule Fluorescence auto- or two-color cross-Correlation Spectroscopy (SPSM-FCS) are comprehensively presented. As technology continues to improve, the limits of what FCS/FCCS is being asked to do are concomitantly pushed.

The selection of specific binding molecules like peptides and proteins from biolibraries using, for instance, phage display methods can be quite time-consuming. It is therefore desirable to develop a strategy that is much faster in selection and sorting of potential binders out of a biolibrary. In this contribution we separately discuss the current achievements in generation of biolibraries, single-molecule detection techniques and microfluidic devices. A highthroughput microfluidic platform is then proposed that combines the propulsion of liquid containing fluorescent components of the biolibrary through microchannels, single-molecule fluorescence photon burst detection and real-time sorting of positive hits.

Compounds can be screened for pharmaceutical activity either by detecting interactions with specified target molecules such as receptors or enzymes (molecular screening) or observing effects on the structure or physiological activities of cells or tissues (phenotypic screening). Screening at the molecular level has been greatly enhanced by fluorescence methods. Especially the combination of confocal detection with measurements of the amplitudes and time courses of fluorescence fluctuations have reduced sample volumes to 100,000 compounds per day. Screening at the molecular level, however, does not provide information about the effects of test compounds on cellular functions. Phenotypic screening, although much slower than molecular screening, does provide information about effects on cell or tissue structure or function and therefore can be used to eliminate at an early stage compounds that are toxic or do not produce the desired cellular response. Tissue constructs reconstituted using cells of specified types and defined extracellular matrix components provide test systems for detecting the effects of test compounds on cellular mechanical functions such as the development of contractile force and on cell and matrix structure and stiffness. For example, constructs based on vascular smooth muscle cells provide information about effects on cellular contractile force that can be used to identify agents that control blood pressure. Tissue constructs that mimic skeletal, smooth and heart muscles and connective tissues have been produced and can be used to study mechanical and structural responses to active compounds.

The direct analysis of single biological molecules is getting increasingly important in basic as well as pharmaceutical research (e.g. for gene expression analysis). In particular single-molecule fluorescence detection provides exciting new opportunities to probe biochemical processes in unprecedented detail. Currently several academic and industrial research groups work on the development of single molecule detection based technologies in order to directly detect and analyze RNA and DNA molecules. As these developed methods are characterized as homogenous assays and obviate any amplification of the target or the signal, they provide clear advantages compared to methods like real-time PCR or DNA- arrays. In the following we describe a recently developed approach based on fluorescence correlation spectroscopy (FCS). This expression assay is based on gene-specific hybridization of two dye-labeled DNA probes to a selected target molecule (either DNA or RNA) in solution. The subsequent dual color cross-correlation analysis allows the quantification of the bio-molecule of interest in absolute numbers. Target concentrations of less than 10-12 M can be easily monitored, covering the direct analysis of the expression levels of high, medium and low abundant genes.

FCS and FCCS measurements provide two important analytical parameters, the average number of molecules in the detection area and the translational diffusion constant of the molecules at the single molecule level. Considering these properties, FCS and FCCS have been applied to analysis of the cellular environment and dynamic processes of molecules in the living cell. More recently, a systematic approach for the analysis of macromolecule complex formation has focused on the new field of single molecule detection in the post-genome era. In this work, we tested the sensitivities of FCS and FCCS based on the distance between fluorophores in DNA as a model macromolecule complex. The results show that FCCS is not limited by the size of the macromolecular complex even in a very small detection area.

Receptor binding studies most often require the use of radioactively labeled ligands. In certain cases, the numbers of receptors are few per cell and no specific binding is detected because of a high background. Specific interactions between certain ligands (e.g. peptides, hormones, natural products) and their receptors are, therefore, often overlooked by the conventional binding technique. Fluorescence correlation spectroscopy (FCS) allows detection of the interaction of ligands with receptors in their native environment in live cells in a tiny confocal volume element (0.2 fl) at single-molecule detection sensitivity. This technique permits the identification of receptors which were not possible before to detect by isotope labeling. The beauty of the FCS technique is that there is no need for separating an unbound ligand from a bound one to calculate the receptor bound and free ligand fractions. This review will show FCS as a sensitive and a rapid technique to study ligand-receptor interaction in live cells and will demonstrate that the FCS-analysis of ligand-receptor interactions in live cells fulfils all the criteria of a ligand binding to its receptor i.e. it is able to provide information on the affinity and specificity of a ligand, binding constant, association and dissociation rate constants as well as the number and mobility of receptors carrying a fluorescently labeled ligand. This review is of pharmaceutical significance since it will provide insights on how FCS can be used as a rapid technique for studying ligand-receptor interactions in cell cultures, which is one step forward towards a high throughput drug screening in cell cultures.

Cell-to-cell communication is mediated by molecular interactions at the surface of the cell by soluble ligands released from distant cells or by cell surface molecules on adjacent cells. These interactions lead to activation of intracellular signaling pathways that subsequently can lead to activation of specific genes. This signal transduction process controls cellular activities as diverse as proliferation, differentiation and apoptosis, so we must understand the underlying molecular events in detail in order to understand broader questions related to development, uncontrolled growth in tumors, tissue regeneration and use of stem cells to name a few. Binding of a ligand in the extracellular space to a transmembrane receptor constitutes the first crucial step for activation of a signaling pathway within the cell. This binding can either lead to oligomerization of individual receptors, to reorganization of existing clusters of receptors or to changes in the protein conformations, which in turn results in recruitment of signaling molecules in the cytoplasm. While different membrane receptors activate different downstream signaling pathways, some receptors can activate more than one pathway and a particular pathway can be activated by different receptors. It appears that these processes are regulated either by agonists and antagonists in the extracellular medium, by receptor-receptor interactions in the membrane or by a number of signaling mediators in the cytoplasm of the cell. Our work has focused on understanding how the intermolecular interactions in the membrane can control the signal transduction process: Are there specialized structures on the surface that facilitate receptor-receptor interactions? Do the receptors exist as monomers or pre-existing complexes that enhance the probability of activation? Do different receptors associate in the same domains or are there distinct organizational principles for each receptor type. In order to address these questions, we seek to develop tools that allow us to examine intermolecular interactions and reactions directly on the cell surface, particularly on live cells in culture or in tissue. This review discusses some of the approaches that are currently available and highlights some of the key advantages and disadvantages they represent with particular focus on image cross correlation spectroscopy as a relatively new quantitative tool developed by us to address some of these issues.

During the last years confocal techniques have become increasingly popular for probing biological enzymatic reactions. In this paper we will summarize some of these methods, mainly focusing on measurement techniques suitable for analysis of freely diffusing molecules, where either the substrates or the enzymes are fluorescently labeled. The different approaches are classified according to their basic principles and algorithms. Several examples of enzymatic studies involving correlation strategies for data processing, like auto- and cross correlation analysis, will be presented. In addition, other evaluation schemes like coincidence analysis and fluorescence intensity distribution analysis are introduced and discussed. With respect to assay development, the fluorescence energy transfer principle is addressed as far as it is has been applied for investigating biocatalysis in solution. Finally, one part of this review addresses the aspects of bioconjugation and the basic requirements for proper labeling dyes in order to be compatible with single molecule fluorescent spectroscopy.

The past few years we have witnessed a tremendous surge of interest in so-called array-based miniaturised analytical systems due to their value as extremely powerful tools for high-throughput sequence analysis, drug discovery and development, and diagnostic tests in medicine (see articles in Issue I). Terminologies that have been used to describe these array-based bioscience systems include (but are not limited to): DNA-chip, microarrays, microchip, biochip, DNAmicroarrays and genome chip. Potential technological benefits of introducing these miniaturised analytical systems include improved accuracy, multiplexing, lower sample and reagent consumption, disposability, and decreased analysis times, just to mention a few examples. Among the many alternative principles of detection-analysis (e.g. chemiluminescence, electroluminescence and conductivity), fluorescence-based techniques are widely used, examples being fluorescence resonance energy transfer, fluorescence quenching, fluorescence polarisation, time-resolved fluorescence, and fluorescence fluctuation spectroscopy (see articles in Issue II). Time-dependent fluctuations of fluorescent biomolecules with different molecular properties, like molecular weight, translational and rotational diffusion time, colour and lifetime, potentially provide all the kinetic and thermodynamic information required in analysing complex interactions. In this mini-review article, we present recent extensions aimed to implement parallel laser excitation and parallel fluorescence detection that can lead to even further increase in throughput in miniaturised array-based analytical systems. We also report on developments and characterisations of multiplexing extension that allow multifocal laser excitation together with matched parallel fluorescence detection for parallel confocal dynamical fluorescence fluctuation studies at the single biomolecule level.