Fluorescence Resonance Energy Transfer Technology Research Articles

Rapid detection and differentiation of human pathogenic orthopox viruses by a fluorescence resonance energy transfer real-time PCR assay.

The orthopox viruses that are pathogenic for humans include variola major virus (VAR), monkeypox virus (MPV), cowpox virus (CPV), and to a lesser extent, camelpox virus (CML) and vaccinia virus (VAC). PCR is a powerful tool to detect and differentiate orthopox viruses, and real-time PCR has the further advantages of rapid turnaround time, low risk of contamination, capability of strain differentiation, and use of multiplexed probes. We used real-time PCR with fluorescence resonance energy transfer technology to simultaneously detect and differentiate VAR, MPV, CPV/VAC, and CML. An internal control generated by cloning and mutating the PCR target gene facilitated monitoring of PCR inhibition in each individual test reaction. Strain differentiation results showed little interassay variability (CV, 0.4-0.6%), and the test was 100-fold more sensitive than virus culture on Vero cells. Low copy numbers of DNA could be detected with > or =95% probability (235-849 genome copies/mL of plasma). The real-time PCR assay can detect and differentiate human pathogenic orthopox viruses. The use of an internal control qualifies the assay for high sample throughput, as is likely to be needed in situations of suspected acts of biological terrorism, e.g., use of VAR.

Fluorescence resonance energy transfer to study receptor dimerization in living cells.

The versatility, sensitivity, and feasibility of fluorescence methods are very attractive to study protein-protein interaction at low levels of protein expression. However, one of the most severe limits in protein chemistry has been the difficulty of introducing site-specific fluorescent labels. The development of genetically encoded fluorescent probes, that is, green fluorescent protein (GFP) and its variants therefore opened up a broad field of novel applications. To characterize protein-protein interactions and determine detailed spatio-temporal dynamics of partners that are molecularly well characterized, fluorescence energy transfer methods are excellent nondestructive tools in living cells. Cellular responses to external factors are extensively based on direct molecular interaction and especially G-protein-coupled receptors (GPCRs) have been shown to interact with an unexpected level of complexity. Classical models of signal transduction describe GPCRs as monomeric proteins, while recent studies using fluorescence resonance energy transfer (FRET) and other methods show that GPCRs can also function as homo- or heterodimers. Theoretical background information on FRET technology and its diverse applications are summarized here. A detailed description of a spectroscopic method for FRET studies in the field of GPCR interaction is presented to facilitate and propagate studies to increase our understanding of protein-protein interactions involving GPCRs.

Proteolysis in prokaryotes: protein quality control and regulatory principles.

Proteolysis in prokaryotes: protein quality control and regulatory principles.

Evaluation of germline sequence variants within the promoter region of RANTES gene in a cohort of women with endometriosis from Spain.

The RANTES (regulated upon activation normal T cells expressed and secreted) chemokine, is known to be expressed in endometriotic lesions in a concentration correlating with the severity of endometriosis. Since it has been widely demonstrated that endometriosis has a genetic basis, we postulated that the gene encoding RANTES could be a good candidate gene for the disease. We have used fluorescence resonance energy transfer (FRET) technology to genotype and evaluate the role of the variants -403G-->A and -28C-->G, located within the promoter region of the gene, as susceptibility factors in a cohort of Spanish women with endometriosis. No differences have been found in the allelic frequencies of both variants nor in the haplotype/ genotype distribution between patients and controls. These data are consistent with the lack of association between these polymorphisms and endometriosis in our population. They do not exclude completely a possible role of other variants within RANTES gene in this pathology.

Detection of infectious bronchitis virus by real-time reverse transcriptase-polymerase chain reaction and identification of a quasispecies in the Beaudette strain.

In this report, we describe a real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) diagnostic test for infectious bronchitis virus (IBV) with the use of fluorescence resonance energy transfer (FRET) technology. Two primers that amplify a 383-base pair product between nucleotide positions 703 and 1086 relative to the start codon for the S1 gene of the Massachusetts 41 virus were designed and used to amplify the Beaudette, Massachusetts 41, Florida 18288, Connecticut, Iowa 97, Arkansas DPI, CA/NE95/99, DE/072/ 92, and GA/0470/98 strains of IBV. The primers were specific and did not amplify New Castle disease virus, Mycoplasma spp., or infectious laryngotracheitis virus. For RRT-PCR by FRET, an anchor probe conjugated to fluorescein and a detection probe conjugated to a red fluorophore were designed to anneal to a hypervariable region within the 383-base pair product. The level of sensitivity was 1 x 10(4) RNA molecules used as starting template. After amplification, a melting curve analysis was conducted to specifically identify IBV types. Because of sequence differences in the annealing position of the detection probe, the Arkansas, Connecticut, Beaudette, and Massachusetts 41 strains could be differentiated. No fluorescence was observed for the DE/072/ 92 and GA/0470/98 viruses with the anchor and detection probes. When the Beaudette strain was examined, two melting peaks were observed at 44 C and 51 C, indicating a quasispecies in that laboratory strain of IBV. Routine typing of vaccine strains of IBV was possible with this technology, but high standard deviations associated with the melting curve analysis of the FRET probes described herein made it difficult to use this test reliably for routine typing of IBV field isolates.

Synthesis and evaluation of fluorescent probes for the detection of calpain activity

Two new probes for the detection of calpain I activity based on fluorescence resonance energy transfer technology have been synthesized and evaluated. The probes incorporated the cleavage site present in α-spectrin, a naturally occurring substrate of calpain I. The design of the internally quenched substrates is such that the calpain-sensitive bond of the peptides (between the Tyr-Gly residues) is located centrally between the donor and the quencher chromophores. The calpain assay protocol is capable of detecting enzymatic activity in the nanomolar region.

FRET-based analysis of TRPC subunit stoichiometry

By analogy to other cation channel subunits with six transmembrane-spanning domains, the seven members of the “classical” or “canonical” transient receptor potential channels (TRPC) family are believed to assemble into homo- or heterotetrameric complexes. These complexes have been verified by classical methods such as coimmunoprecipitation, crosslinking analysis or functional assays applying dominant negative pore mutants. More recently, fluorescence resonance energy transfer (FRET)—a measure for the close proximity of fluorescent molecules—has become instrumental in monitoring protein assembly in living cells. Here we demonstrate further possibilities and verification procedures of the FRET technology to test the assembly of ion channel subunits. Temporally and spatially resolved FRET imaging demonstrates an early assembly of TRPC subunits in the endoplasmic reticulum and the Golgi apparatus. Confocal FRET imaging verifies FRET signals over the plasma membrane at high spatial resolution. Taking advantage of the quantitative analysis of digital video imaging, we demonstrate that FRET between TRPC subunits is only poorly concentration-dependent. Moreover, a correlation between the efficiency of energy transfer and the molar ratio of the FRET donor to the acceptor was exploited to verify the tetrameric stoichiometry of TRPC complexes. Finally, we introduce a competition-FRET assay to test the ability of wild-type TRPC subunits to recruit fluorescent TRPC subunits into separate channel complexes.

Rapid and accurate detection of point mutations conferring resistance to clarithromycin in Helicobacter pylori by real-time PCR

The main cause of failure of Hclicobacter pylori eradication therapy is resistance to clarithromycin. The resistance is due to point mutations in 2 positions on the 23S rRNA. Our aim was to develop a rapid and accurate method to detect these mutations directly on biopsy specimens. We developed a real-time PCR assay including a simultaneous detection of the amplicons by hybridization of two probes labelled with LC-Red and flurorescein using the Fluorescence Resonance Energy Transfer technology. The assay was first apphed successfully on reference strains, reference plasmids, and H. pylori negative biopsies. Then biopsies from 200 patients having failed a first eradication attempt and for whom the Helicobacter pylori strain was available were tested with the new assay. A result was obtained in 199 cases, a single genotype was detected in 157 cases, two genotypes in 41 cases, and three genotypes in one case. There were in total 7 discrepancies between the real-time PCR assay and the phenotypic methods of determination of clarithromycin susceptibility, and in an additional 4 eases the 2 phenotypie methods were in disagreement. PCR-RFLP was applied to a sampling of biopsies including all of the cases with multiple genotypes and all with discrepant results. Finally, in 4 cases with discrepant results, the real-time PCR assay detected the resistant population at a concentration so low that it could not be detected by the phenotyptc method, while in 3 cases other mutations could be involved. This assay had an accuracy at least as satisfactory as the phenotypic tests and could he performed within 2 hours, allowing it to be used before the administration of therapy in the case of a first H. pyiori eradication.

Real-time PCR assay for rapid and accurate detection of point mutations conferring resistance to clarithromycin in Helicobacter pylori.

The main cause of failure of Helicobacter pylori eradication therapy is resistance to clarithromycin. The resistance is due to three point mutations in two positions on the 23S rRNA (A2142C, A2142G, and A2143G). Our aim was to develop a rapid and accurate method to detect these mutations directly on biopsy specimens. We developed a real-time PCR that included a simultaneous detection of the amplicons by hybridization of two probes labeled with LC-Red and fluorescein by using the fluorescence resonance energy transfer (FRET) technology and melting curve analysis with the LightCycler thermocycler. The assay was first applied successfully on reference strains, reference plasmids, and H. pylori-negative biopsies. Biopsies from 200 patients having failed a first eradication attempt and for whom the H. pylori strain was available were then tested with the new assay. A result was obtained in 199 cases; a single genotype was detected in 157 cases, two genotypes were detected in 41 cases, and three genotypes were detected in one case. There were, in total, seven discrepancies between the real-time PCR and the phenotypic method of determination of clarithromycin susceptibility, and in an additional four cases the two phenotypic methods were in disagreement. PCR-restriction fragment length polymorphism was applied to a sampling of biopsies, including all of the cases with multiple genotypes and all the cases with discrepant results. Finally, in four cases with discrepant results, the real-time PCR detected the resistant population at a concentration so low that it could not be detected by the phenotypic method, while in three cases other mutations could be involved. This assay had an accuracy at least as satisfactory as that of the phenotypic tests and could be performed within 2 h, allowing it to be used before the administration of therapy in the case of a first H. pylori eradication.

Rapid detection of influenza A and B viruses in clinical specimens by Light Cycler real time RT-PCR.

the influenza viruses cause morbidity and mortality annually among children and elderly. Surveillance and rapid diagnosis is imperative in the reference laboratory, as clinical symptoms are insufficient for proper diagnosis. this study involved the design of a rapid detection method for influenza A and B viruses using real time RT-PCR from clinical specimens. Methods were specifically designed for use on the Light Cycler. The sensitivity and specificity were also to be determined. the identification and discrimination of influenza A and B viruses employs two dual probe systems based on fluorescence resonance energy transfer (FRET) technology. Following submission by physicians participating in the Florida sentinel influenza network, 58 specimens were chosen for testing using both tissue culture and Light Cycler methods. of the 35 identified positive for influenza virus via tissue culture isolation, the Light Cycler results matched identification and typing with 100% agreement. However, the Light Cycler recognized 16 additional specimens that were positive for the presence of the virus. RT-PCR and nucleotide sequencing confirmed the presence of influenza A virus in these specimens. Using tenfold serial dilutions, the sensitivity of the Light Cycler method was determined to be 0.01 TCID50. The lower limit of RNA detection was determined as 1.6 x 10(-7) microg for influenza A virus, and 1.2 x 10(-7) microg for influenza B virus. Specificity of the Light Cycler method was determined by testing specimens containing adenovirus, parainfluenza virus and echovirus, all of which yielded negative results with no discernible background. overall, this newly developed method of simultaneous detection and typing of influenza types A and B using the Light Cycler proves to be more sensitive than tissue culture isolation, with corresponding specificity. This technique may be valuable for surveillance and rapid identification of influenza for early diagnosis.

Glutathione S-transferase P1–1 (GSTP1–1) Inhibits c-Jun N-terminal Kinase (JNK1) Signaling through Interaction with the C Terminus

c-Jun N-terminal kinase (JNK)-mediated cell signaling pathways are regulated endogenously in part by protein-protein interactions with glutathione S-transferase P1-1 (GSTP1-1) (). Using purified recombinant proteins, combined with fluorescence resonance energy transfer technology, we have found that the C terminus of JNK is critical to the interaction with GSTP1-1. The apparent K(d) for full-length JNK was 188 nm and for a C-terminal fragment (residues 200-424) 217 nm. An N-terminal fragment (residues 1-206) did not bind to GSTP1-1. Increased expression of the C-terminal JNK fragment in a tetracycline-inducible transfected NIH3T3 cell line produced a concentration-dependent increase in the kinase activity of JNK under normal, unstressed growth conditions indicating a dominant-negative effect. This suggests that the fragment can compete with endogenous full-length functional JNK resulting in dissociation of the GSTP1-1-JNK interaction and concomitant JNK enzyme activation. By using an antibody to hemagglutinin-tagged C-JNK, a concentration-dependent co-immunoprecipitation of GSTP1-1 was achieved. These data provide evidence for direct interactions between the C-terminal of JNK and GSTP1-1 and a rationale for considering GSTP1-1 as a critical ligand-binding protein with a role in regulating kinase pathways.

Quantification of bacterial transcripts during infection using competitive reverse transcription-PCR (RT-PCR) and LightCycler RT-PCR.

Bacteria have evolved sophisticated regulatory circuits to modulate their gene expression in response to disparate environments. In order to monitor bacterial gene expression and regulation in the host, methods for direct transcript analysis from clinical specimens are needed. For most bacterial infections, amplification of the mRNAs of interest is necessary due to the low numbers of cells present and the low levels of specific transcripts. Here we compare two methods of quantitative reverse transcription-PCR (RT-PCR)-competitive RT-PCR using a one-tube system followed by standard gel analysis and the real-time detection of PCR product formation by fluorescence resonance energy transfer technology using the LightCycler unit. We isolated Staphylococcus aureus RNA directly from clinical specimens obtained from cystic fibrosis patients with chronic S. aureus lung infection and from an animal model of foreign-body infection with no further cultivation of the bacteria. Competitive RT-PCR and LightCycler RT-PCR were tested for their ability to quantify the transcription of a constitutively expressed gyrase gene (gyr) and a highly regulated alpha-toxin gene (hla) of S. aureus. Reproducible results were obtained with both methods. A sensitivity of 10(4) (gyr) and 10(3) (hla) copies, respectively, was reached, which was sufficient for the quantification of transcripts during bacterial infection. Overall, the competitive RT-PCR is a robust technique which does not need special RNA purification. On the negative side, it is labor intensive and time consuming, thus limiting the numbers of samples which can be analyzed at a given time. LightCycler RT-PCR is very susceptible to even traces of inhibitors, but it allows high-throughput processing of samples.

Efficient Syntheses of a Flavin and an 8-Hydroxy-5-deazaflavin Amino Acid and Their Incorporation into Oligopeptides

We report a convenient synthesis for the cofactor amino acids (S)-3 and (S)-4 in which the C5-ribose chain of the original riboflavin and ribo-5-deazaflavin cofactors is replaced by a C5-amino acid side chain. Both cofactor amino acids are available in enantiomerically pure form in gram quantities and can be incorporated into oligopeptides using a standard Fmoc-based solid-phase peptide synthesis protocol. The benzyl-protecting group of the 8-hydroxy-5-deazaflavin can be cleaved by hydrogenolysis directly on the peptide. This allows the investigation of the properties of the peptide bound redox active OH- and the deprotonated O--form of the deazaflavin. Due to the electron- and energy-transfer properties of both cofactors, applications of both amino acid in the preparation of peptide- and protein-based biosensors, of catalytically active peptides, or as chemical rulers for distance measurements in biopolymers based on the fluorescence resonance energy-transfer technology can be envisaged.

Application of fluorescence resonance energy transfer in the clinical laboratory: Routine and research

Fluorescence resonance energy transfer (FRET) phenomenon has been applied to a variety of scientific challenges in the past. The potential utility of this biophysical tool will be revisited in the 21st century. The rapid digital signal processing in conjunction with personal computers and the wide use of multicolor laser technology in clinical flow cytometry opened an opportunity for multiplexed assay systems. The concept is very simple. Color-coded microspheres are used as solid-phase matrix for the detection of fluorescent labeled molecules. It is the homogeneous assay methodology in which solid-phase particles behave similarly to the dynamics of a liquid environment. This approach offers a rapid cost-effective technology that harnesses a wide variety of fluorochromes and lasers. With this microsphere technology, the potential applications for clinical flow cytometry in the future are enormous. This new approach of well-established clinically proven methods sets the stage to briefly review the theoretical and practical aspects of FRET technology. The review shows various applications of FRET in research and clinical laboratories. Combination of FRET with monoclonal antibodies resulted in a boom of structural analysis of proteins in solutions and also in biological membranes. Cell surface mapping of cluster of differentiation molecules on immunocompetent cells has gained more and more interest in the last decade. Several examples for biological applications are discussed in detail. FRET can also be used to improve the spectral characteristics of fluorescent dyes and dye combinations, such as the tandem dyes in flow and image cytometry and the FRET primers in DNA sequencing and polymerase chain reactions. The advantages and disadvantages of donor-acceptor dye combinations are evaluated. In addition, the sensitivity of FRET provides the basis for establishing fast, robust, and accurate enzyme assays and immunoassays. Benefits and limitations of FRET-based assays are thoroughly scrutinized. At the end of the paper we review the future of FRET methodology.