Fluorescence Resonance Energy Transfer Constructs Research Articles

FRET-Based Single-Molecule Detection of Pathogen Protein IsdA Using Computationally Selected Aptamers.

Iron-regulated surface determinant protein A (IsdA) is a key surface protein found in the foodborne bacteria─Staphylococcus aureus (S. aureus)─which is known to be critical for bacterial survival and colonization. S. aureus is pathogenic and has been linked to foodborne diseases; thus, early detection is critical to prevent diseases caused by this bacterium. Despite IsdA being a specific marker for S. aureus and several detection methods have been developed for sensitive detection of this bacteria such as cell culture, nucleic acids amplification, and other colorimetric and electrochemical methods, the detection of S. aureus through IsdA is underdeveloped. Here, by combining computational generation of target-guided aptamers and fluorescence resonance energy transfer (FRET)-based single-molecule analysis, we presented a widely applicable and robust detection method for IsdA. Three different RNA aptamers specific to the IsdA protein were identified and their ability to switch a FRET construct to a high-FRET state in the presence of protein was verified. The presented approach demonstrated the detection of IsdA down to picomolar levels (×10-12 M, equivalent to ∼1.1 femtomoles IsdA) with a dynamic range extending to ∼40 nM. The FRET-based single-molecule technique that we reported here is capable of detecting the foodborne pathogen protein IsdA with high sensitivity and specificity and has a broader application in the food industry and aptamer-based sensing field by enabling quantitative detection of a wide range of pathogen proteins.

Measuring System Calibration Factors by Unmixing the Excitation–Emission Spectra of One Dish of Cells

Abstract Accurate predetermination of the quantum yield ratio (QA/QD) and the extinction coefficient ratio (KA/KD) between acceptor and donor is a prerequisite for quantitative fluorescence resonance energy transfer (FRET) imaging. We here propose a method to measure KA/KD and QA/QD by measuring the excitation–emission spectra (ExEm-spectra) of one dish of cells expressing m (≥3) kinds of FRET constructs. The ExEm-spectra images are unmixed to obtain the weight maps of donor (WD), acceptor (WA), and acceptor sensitization (WS). For each cell, the frequency distribution plots of the WS/WD and WS/WA images are fitted by using a single-Gaussian function to obtain the peak values of WS/WD (SD) and WS/WA (SA). The statistical frequency-SD/SA plots from all cells are fitted by using a multi-Gaussian function to obtain the peak values of both SD and SA, and then the ranges of WS/WD (RSD) and WS/WA (RSA) for each FRET construct are predetermined. Based on the predetermined RSD and RSA values of FRET constructs, our method is capable of automatically classifying cells expressing different FRET constructs. Finally, the WS/WD–WA/WD plot from different kinds of cells is linearly fitted to obtain KA/KD and QA/QD values.

Linear Behavior of the Phase Lifetime in Frequency-Domain Fluorescence Lifetime Imaging of FRET Constructs

We utilize a cost-effective frequency-domain fluorescence lifetime imaging microscope to measure the phase lifetime of mTFP1 in mTFP1-mVenus fluorescence resonance energy transfer (FRET) constructs relevant to the VinTS molecular tension probe. Our data were collected at 15 modulation frequencies ω/2π selected between 14 and 70 MHz. The lifetime of mTFP1 was τD = 3.11 ± 0.02 ns in the absence of acceptor. For modulation frequencies, ω, such that (ω · τD) < 1.1, the phase lifetime of mTFP1in the presence of acceptor (mVenus), τϕDA, was directly related to the amplitude-weighted lifetime τaveDA inferred from the known FRET efficiency (EFRETtrue) of the constructs. A linear fit to a plot of (ω·τϕDA) vs. (ω·τaveDA) yielded a slope of 0.79 ± 0.05 and intercept of 0.095 ± 0.029 (R2 = 0.952). Thus, our results suggest that a linear relationship exists between the apparent EFRETapp based on the measured phase lifetime and EFRETtrue for frequencies such that (ω · τD) < 1.1. We had previously reported a similar relationship between EFRETapp and EFRETtrue at 42 MHz. Our current results provide additional evidence in support of this observation, but further investigation is still required to fully characterize these results. A direct relationship between τϕDAand τaveDA has the potential to simplify significantly data acquisition and interpretation in fluorescence lifetime measurements of FRET constructs.

Mitochondria specific oxidative injury by near-infrared energy transfer nanoclusters for amplified photodynamic potency

To promote practical applications of photodynamic therapy, near-infrared (NIR) photosensitizers are manufactured based on fluorescence resonance energy transfer (FRET) between donors of anti-stoke NIR upconversion nanoparticles and acceptors of photodynamic chlorin e6. The manufactured FRET constructs displayed deep tissue penetration and FRET activation under 980 nm irradiation. Furthermore, surface decoration with mitochondria-targeting (4-marboxybutyl) triphenyl phosphonium bromide (TPP) led to mitochondrion-targeted accumulation of singlet oxygen resulting in potent cell apoptosis. Notably, in vivo anti-tumor test validates the complete ablation of intractable solid tumors based on single-dose treatment of our proposed photodynamic constructs. Therefore, the obtained results herald the tempting perspective of our carefully engineered photodynamic constructs, which could have broad utilities in clinical treatment of intractable premalignancies.

Improved spectrometer-microscope for quantitative fluorescence resonance energy transfer measurement based on simultaneous spectral unmixing of excitation and emission spectra.

Based on our recently developed quantitative fluorescence resonance energy transfer (FRET) measurement method using simultaneous spectral unmixing of excitation and emission spectra (ExEm-spFRET), we here set up an improved spectrometer-microscope (SM) for implementing modified ExEm-spFRET (mExEm-spFRET), in which a system correction factor (fsc) is introduced. Our SM system is very stable for at least six months. Implementation of mExEm-spFRET with four or two excitation wavelengths on SM for single living cells expressing different FRET constructs obtained consistent FRET efficiency (E) and acceptor-donor concentration ratio (Rc) values. We also performed mExEm-spFRET measurement for single living cells coexpressing cyan fluorescent protein (CFP)-Bax and yellow fluorescent protein (YFP)-Bax and found that the E values between CFP-Bax and YFP-Bax were very low (2.2%) and independent of Rc for control cells, indicating that Bax did not exist as homooligomer in healthy cells, but positively proportional to Rc in the case of Rc<1 and kept constant value (25%) when Rc>1 for staurosporine (STS)-treated cells, demonstrating that all Bax formed homooligomer after STS treatment for 6h.

Wide-field microscopic FRET imaging using simultaneous spectral unmixing of excitation and emission spectra.

Simultaneous spectral unmixing of excitation and emission spectra (ExEm unmixing) has the inherent ability to resolve donor emission, fluorescence resonance energy transfer (FRET)-sensitized acceptor emission and directly excited acceptor emission. We here develop an ExEm unmixing-based quantitative FRET measurement method (EES-FRET) independent of excitation intensity and detector parameter setting. The ratio factor (rK), predetermined using a donor-acceptor tandem construct, of total acceptor absorption to total donor absorption in excitation wavelengths used is introduced for determining the concentration ratio of acceptor to donor. We implemented EES-FRET method on a wide-field microscope to image living cells expressing tandem FRET constructs with different donor-acceptor stoichiometry.

Miniature fiber optic spectrometer-based quantitative fluorescence resonance energy transfer measurement in single living cells.

Spectral measurement of fluorescence resonance energy transfer (FRET), spFRET, is a widely used FRET quantification method in living cells today. We set up a spectrometer-microscope platform that consists of a miniature fiber optic spectrometer and a widefield fluorescence microscope for the spectral measurement of absolute FRET efficiency (E) and acceptor-to-donor concentration ratio (R(C)) in single living cells. The microscope was used for guiding cells and the spectra were simultaneously detected by the miniature fiber optic spectrometer. Moreover, our platform has independent excitation and emission controllers, so different excitations can share the same emission channel. In addition, we developed a modified spectral FRET quantification method (mlux-FRET) for the multiple donors and multiple acceptors FRET construct (mD∼nA) sample, and we also developed a spectra-based 2-channel acceptor-sensitized FRET quantification method (spE-FRET). We implemented these modified FRET quantification methods on our platform to measure the absolute E and R(C) values of tandem constructs with different acceptor/donor stoichiometries in single living Huh-7 cells.

Optimizing the Roche LightCycler(R) for Single-Tube Multiplexed RT-PCR Assays.

The Roche Diagnostics LightCycler® (LC) Carousel-Based Systems are a single-source thermocycler capable of detecting light emissions from fluorescing molecules released during RT-PCR. This technology utilizes a single light source at 470 nm to excite fluorophores for read-out in one of three channels (530, 640 and 705 nm) for older 1.5 models and up to six channels (530, 560, 610, 640, 670, and 705nm) for the 2.0 model. The persistent challenge of LC technology is multiplexing, the ability to discriminate more than one target with different fluorophores in a single capillary tube that can be excited at the same 470-nm wavelength and read on 3 or 6 different channels without cross-talk or “bleed-over”. The most commonly employed fluorescent probe is 6-carboxyfluorescein (FAM), fluorescing in channel 1 (530 nm), with bleed-over into the other channels, which is currently compensated for by surrendering valuable carousel space for extraction controls, amplification controls, and duplicate sample runs to assure the generated answer is correct. Using the 705 nm channel requires resonance transfer probes, as few fluorescent molecules exist with Stokes’ shifts wide enough to achieve detection in this channel. In 2009, a fluorescence resonance energy transfer (FRET)-based method was developed which, when combined with TaqMan style probes, provides a linker that emits a signal that can be read in the unused third channel of the LC 1.5 [1]. This “FRET-MAN” technology works well; however, designing assays with dual probes and quenchers can be challenging. To address this challenge, Biosearch Technologies designed a probe called the Pulsar® 650, which is a fluorescent reporter dye based on a Ru (bpy)3 complex with a large Stokes shift, (λex = 460 nm, λem = 650 nm) that can be used in place of a two-dye FRET construct. Importantly, this dye is stable under oligonucleotidesynthesis conditions, strong acids, and strong bases (Biosearch Technologies, http://www.biosearchtech.com). We present here an extension of a duplexed assay originally developed for the LC 1.2 [2] to an RNA-based viral target with the inclusion of an internal control for robust quantitation. Here, the primary target was one of two strains of influenza A, chosen due to the increase of awareness of public health in recent years. The third-channel duplex probe was designed based on the human RNase P (hRP), GAPDH, 18S ribosomal RNA, β-actin, cyclophilin or gyrase [3–8]. To demonstrate the ability of duplexed detection, inclusion of the internal controls (ICs) is shown herein to function in both laboratory buffered samples and in clinical matrices. Theoretically, the second probe could instead be used as a detector for a second target organism.

Binomial distribution-based quantitative measurement of multiple-acceptors fluorescence resonance energy transfer by partially photobleaching acceptor

We report that binomial distribution depending on acceptor photobleaching degree can be used to characterize the proportions of various kinds of FRET (Fluorescence Resonance Energy Transfer) constructs resulted from partial acceptor photobleaching of multiple-acceptors FRET system. On this basis, we set up a rigorous quantitation theory for multiple-acceptors FRET construct named as Mb-PbFRET which is not affected by the imaging conditions and fluorophore properties. We experimentally validate Mb-PbFRET with FRET constructs consisted of one donor and two or three acceptors inside living cells on confocal and wide-field microscopes.

Effects of Redox State on the Efficient Uptake of Cell Permeable Peptide in Mammalian Cells

We investigated whether a cell-penetrating peptide linked via a disulfide bond to a fluorophore-labeled cargo peptide can be used to interrogate changes in cellular redox state. A fluorescence resonance energy transfer (FRET) pair was constructed so that the cargo peptide was labeled with fluorescein amidite (FAM) and the cell-penetrating peptide was attached to a quencher. Incubation of cells in culture with the FRET construct was visualized using live-cell, time-lapse imaging, which demonstrated earlier cellular uptake of the construct when cells were treated with the reducing agent n-acetylcysteine (NAC). The FRET peptide construct was easily detected in cells cultured in 96-well plates using a plate-reader. Treatment of cells with various classes of reducing or oxidizing agents resulted in an increase or decrease in FAM fluorescence, respectively. Changes in FAM fluorescence correlated significantly with redox-sensitive green fluorescent protein ratios in cells treated with hydrogen peroxide but not NAC. Detection of relative changes in cellular redox state was enhanced by the fact that uptake of the cell-penetrating peptide occurred more quickly in relatively reduced compared with oxidized cells. We conclude that cell-penetrating peptides coupled via disulfide bonds to detectable cargo is a novel and specific approach for assessment of relative changes in cellular thiol redox state.

Cleft Closure Mechanism in Gating of Acid Sensing Ion Channel 1A

Acid sensing ion channels (ASICs) are trimeric proton activated channels which share sequence similarities with Degenerin/Epithelial sodium channels. They are responsible for proton evoked currents in central nervous system of most vertebrates. Their physiological functions include synaptic transmission, sensory perception, learning, and pathophysiology of stroke. Crystal structure of the low pH state of chicken ASIC shows thumb and palm like domains in the extracellular part of each subunit connected through hydrogen bonds between carboxylate residue pairs, thought to be part of proton sensors in ASIC. Based on the low pH structure it's been hypothesized that these domains would be further apart at high pH due to negative charges and protonation would allow the two domains to move closer, which in turn could trigger changes in the transmembrane segments, causing channel opening. We have used Fluorescence Resonance Energy Transfer(FRET) to study the high pH resting structure of ASIC and determined conformational changes between the thumb and palm domains. Cysteine residues were introduced on these domains and tagged with thiol reactive donor and acceptor fluorophores. The recognition site for protease Xa was introduced on either side of the cysteine on the palm domain. This allowed us to perform the FRET measurements in oocytes and HEK-293 cells without purification, as addition of the protease allowed us to quantitively characterize the background FRET. The FRET constructs were characterized using electrophysiology to establish that they were functional. The FRET based distances showed 3A decrease in distance between thumb domain residue 340 and palm domain residues 130 and 139 upon changing the pH from 8 to 6. This decrease in distance provides evidence for the hypothesized movement in the extracellular domain of ASIC and also supports the protonation of the carboxylate pairs across these domains.

Fluorescence Resonance Energy Transfer Glucose Sensor from Site-Specific Dual Labeling of Glucose/Galactose Binding Protein Using Ligand Protection

Site-selective modification of proteins at two separate locations using two different reagents is highly desirable for biosensor applications employing fluorescence resonance energy transfer (FRET), but few strategies are available for such modification. To address this challenge, sequential selective modification of two cysteines in glucose/galactose binding protein (GGBP) was demonstrated using a technique we call "ligand protection." In this technique, two cysteines were introduced in GGBP and one cysteine is rendered inaccessible by the presence of glucose, thus allowing sequential attachment of two different thiol-reactive reagents. The mutant E149C/A213C/L238S was first labeled at E149C in the presence of the ligand glucose. Following dialysis and removal of glucose, the protein was labeled with a second dye, either Texas Red (TR) C5 bromoacetamide or TR C2 maleimide, at the second site, A213C. Changes in glucose-dependent fluorescence were observed that were consistent with FRET between the nitrobenzoxadiazole and TR fluorophores. Comparison of models and spectroscopic properties of the C2 and C5 TR FRET constructs suggests the greater rigidity of the C2 linker provides more efficient FRET. The ligand protection strategy provides a simple method for labeling GGBP with two different fluorophores to construct FRET-based glucose sensors with glucose affinity within the human physiological glucose range (1-30 mM). This general strategy may also have broad utility for other protein-labeling applications.

QUANTITATIVE FRET MEASUREMENT BASED ON CONFOCAL MICROSCOPY IMAGING AND PARTIAL ACCEPTOR PHOTOBLEACHING

Fluorescence resonance energy transfer (FRET) technology had been widely used to study protein–protein interactions in living cells. In this study, we developed a ROI-PbFRET method to real-time quantitate the FRET efficiency of FRET construct in living cells by combining the region of interest (ROI) function of confocal microscope and partial acceptor photobleaching. We validated the ROI-PbFRET method using GFPs-based FRET constructs including 18AA and SCAT3, and used it to quantitatively monitor the dynamics of caspase-3 activation in single live cells stably expressing SCAT3 during staurosporine (STS)-induced apoptosis. Our results for the first demonstrate that ROI-PbFRET method is a powerful potential tool for detecting the dynamics of molecular interactions in live cells.

Development of Probes for Cellular Functions Using Fluorescent Proteins and Fluorescence Resonance Energy Transfer

Many genetically encoded probes that employ fluorescent proteins and fluorescence resonance energy transfer (FRET) have been developed to better understand the spatiotemporal regulation of various cellular processes. The different types of FRET and measurement techniques necessitate characterization of their specific features. Here I provide theoretical and practical comparisons of bimolecular and unimolecular FRET constructs, intensity-based and lifetime-based FRET measurements, FRET imaging using live- and fixed-cell samples, green fluorescent protein-based and chemical fluorophore-based FRET, and FRET efficiency and indices. The potential benefits and limitations of a variety of features in the technologies using fluorescent proteins and FRET are discussed.

Cross-talk between Carboxypeptidase M and the Kinin B1 Receptor Mediates a New Mode of G Protein-coupled Receptor Signaling

G protein-coupled receptor (GPCR) signaling is affected by formation of GPCR homo- or heterodimers, but GPCR regulation by other cell surface proteins is not well understood. We reported that the kinin B1 receptor (B1R) heterodimerizes with membrane carboxypeptidase M (CPM), facilitating receptor signaling via CPM-mediated conversion of bradykinin or kallidin to des-Arg kinin B1R agonists. Here, we found that a catalytically inactive CPM mutant that still binds substrate (CPM-E264Q) also facilitates efficient B1R signaling by B2 receptor agonists bradykinin or kallidin. This response required co-expression of B1R and CPM-E264Q in the same cell, was disrupted by antibody that dissociates CPM from B1R, and was not found with a CPM-E264Q-B1R fusion protein. An additional mutation that reduced the affinity of CPM for C-terminal Arg and increased the affinity for C-terminal Lys inhibited the B1R response to bradykinin (with C-terminal Arg) but generated a response to Lys(9)-bradykinin. CPM-E264Q-mediated activation of B1Rs by bradykinin resulted in increased intramolecular fluorescence resonance energy transfer (FRET) in a B1R FRET construct, similar to that generated directly by a B1R agonist. In cytokine-treated human lung microvascular endothelial cells, disruption of B1R-CPM heterodimers inhibited B1R-dependent NO production stimulated by bradykinin and blocked the increased endothelial permeability caused by treatment with bradykinin and pyrogallol (a superoxide generator). Thus, CPM and B1Rs on cell membranes form a critical complex that potentiates B1R signaling. Kinin peptide binding to CPM causes a conformational change in the B1R leading to intracellular signaling and reveals a new mode of GPCR activation by a cell surface peptidase.

ATP Changes the Fluorescence Lifetime of Cyan Fluorescent Protein via an Interaction with His148

Recently, we described that ATP induces changes in YFP/CFP fluorescence intensities of Fluorescence Resonance Energy Transfer (FRET) sensors based on CFP-YFP. To get insight into this phenomenon, we employed fluorescence lifetime spectroscopy to analyze the influence of ATP on these fluorescent proteins in more detail. Using different donor and acceptor pairs we found that ATP only affected the CFP-YFP based versions. Subsequent analysis of purified monomers of the used proteins showed that ATP has a direct effect on the fluorescence lifetime properties of CFP. Since the fluorescence lifetime analysis of CFP is rather complicated by the existence of different lifetimes, we tested a variant of CFP, i.e. Cerulean, as a monomer and in our FRET constructs. Surprisingly, this CFP variant shows no ATP concentration dependent changes in the fluorescence lifetime. The most important difference between CFP and Cerulean is a histidine residue at position 148. Indeed, changing this histidine in CFP into an aspartic acid results in identical fluorescence properties as observed for the Cerulean fluorescent based FRET sensor. We therefore conclude that the changes in fluorescence lifetime of CFP are affected specifically by possible electrostatic interactions of the negative charge of ATP with the positively charged histidine at position 148. Clearly, further physicochemical characterization is needed to explain the sensitivity of CFP fluorescence properties to changes in environmental (i.e. ATP concentrations) conditions.

An allosteric mechanism to displace nuclear export cargo from CRM1 and RanGTP by RanBP1

The karyopherin CRM1 mediates nuclear export of proteins and ribonucleoproteins bearing a leucine-rich nuclear export signal (NES). To elucidate the precise mechanism by which NES-cargos are dissociated from CRM1 in the cytoplasm, which is important for transport directionality, we determined a 2.0-A resolution crystal structure of yeast CRM1:RanBP1:RanGTP complex, an intermediate in the disassembly of the CRM1 nuclear export complex. The structure shows that on association of Ran-binding domain (RanBD) of RanBP1 with CRM1:NES-cargo:RanGTP complex, RanBD and the C-terminal acidic tail of Ran induce a large movement of the intra-HEAT9 loop of CRM1. The loop moves to the CRM1 inner surface immediately behind the NES-binding site and causes conformational rearrangements in HEAT repeats 11 and 12 so that the hydrophobic NES-binding cleft on the CRM1 outer surface closes, squeezing out the NES-cargo. This allosteric mechanism accelerates dissociation of NES by over two orders of magnitude. Structure-based mutagenesis indicated that the HEAT9 loop also functions as an allosteric autoinhibitor to stabilize CRM1 in a conformation that is unable to bind NES-cargo in the absence of RanGTP.

Live Cell Fluorescence Resonance Energy Transfer Predicts an Altered Molecular Association of Heterologous PrPSc with PrPC

Prion diseases result from the accumulation of a misfolded isoform (PrP(Sc)) of the normal host prion protein (PrP(C)). PrP(Sc) propagates by templating its conformation onto resident PrP(C) to generate new PrP(Sc). Although the nature of the PrP(Sc)-PrP(C) complex is unresolved, certain segments or specific residues are thought to feature critically in its formation. The polymorphic residue 129 is one such site under considerable study. We combined transmission studies with a novel live cell yeast-based fluorescence resonance energy transfer (FRET) system that models the molecular association of PrP in a PrP(Sc)-like state, as a way to explore the role of residue 129 in this process. We show that a reduction in efficiency of prion transmission between donor PrP(Sc) and recipient PrP(C) that are mismatched at residue 129 correlates with a reduction in FRET between PrP-129M and PrP-129V in our yeast model. We further show that this effect depends on the different secondary structure propensities of Met and Val, rather than the specific amino acids. Finally, introduction of the disease-associated P101L mutation (mouse- equivalent) abolished FRET with wild-type mouse PrP, whereas mutant PrP-P101L displayed high FRET with homologous PrP-P101L, as long as residue 129 matched. These studies provide the first evidence for a physical alteration in the molecular association of PrP molecules differing in one or more residues, and they further predict that the different secondary structure propensities of Met and Val define the impaired association observed between PrP(Sc) and PrP(C) mismatched at residue 129.

Abstract A170: High-content screening for inhibitors of oncogenic transcription by c-Myc

Abstract There is evidence that Myc partners with another molecule called TRRAP to regulate genes required for transformation. Our hypothesis is that blocking the interaction of Myc with TRRAP will selectively kill breast cancer cells. Traditional drug screening approaches to identify compounds that will break apart two interacting proteins have rarely been successful. However, our approach is to screen compounds in live breast cancer cells for those that prevent Myc and TRRAP from binding to each other. Since the cell is constantly replacing Myc, a compound that prevents it from binding TRRAP should kill even established tumors. Importantly, we previously mapped the places on Myc and TRRAP that bind them together and showed they don't involve the parts of the protein involved in other important functions. Therefore, compounds we find that prevent Myc-TRRAP binding should not be toxic to normal cells. Methods: We have established a new assay in which Myc and TRRAP are expressed as fusion proteins to Cerulean and Citrine fluorescence proteins, respectively. We are developing two different but related assays for the interaction between the two proteins. In one we rely on proximity resulting in complementation between non-fluorescent fragments of the Cerulean fluorescence protein. In this assay heterodimerization results in increased fluorescence. In the other assay proximity results in fluorescence resonance energy transfer (FRET) between the Cerulean and Citrine fluorescence proteins. We detect FRET by fluorescence lifetime imaging (FLIM). Results: A novel robotic microscope that can automatically perform high speed FLIM and thereby detect Myc-TRRAP binding quickly and accurately has been assembled and tested. Our automated microscope has had an environmental stage for live cell imaging fitted and tested. Both FRET standards and constructs based on the Cerulean-Myc / TRRAP-Citrine pair have been measured to validate the assay. Cell lines are being optimized for use for screening. Conclusions: High speed FLIM can be used to detect FRET between Cerulean-Myc and TRRAP-Citrine in live cells. Using our automated microscope we can test individually the effect of large numbers of small molecules in live breast cancer cells. This will let us identify compounds that are not only effective but that get into breast cancer cells and are not toxic to normal cells. Relevance/Impact: To stimulate the development of new drugs effective against a wide spectrum of cancers, we are identifying small drug like molecules that disrupt the function of a particularly potent cell growth gene called Myc, which is often misregulated in breast cancer. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A170.

FRET-Based Optical Assay for Monitoring Riboswitch Activation

Riboswitches are regulatory RNAs located in the 5'-untranslated region of mRNA sequences that recognize and bind to small molecules and regulate the expression of downstream genes. Creation of synthetic riboswitches to novel ligands depends on the ability to monitor riboswitch activation in the presence of analyte. In our work, we have coupled a synthetic riboswitch to an optical reporter assay based on fluorescence resonance energy transfer (FRET) between two genetically encoded fluorescent proteins. The theophylline-sensitive riboswitch was placed upstream of the Tobacco Etch Virus (TEV) protease coding sequence. Our FRET construct was composed of eGFP and a nonfluorescent yellow fluorescent protein mutant called REACh (for resonance energy-accepting chromoprotein) connected with a peptide linker containing a TEV protease cleavage site. Addition of theophylline to the E. coli cells activates the riboswitch and initiates the translation of mRNA. Synthesized protease cleaves the linker in the FRET-based fusion protein causing a change in the fluorescence signal. By this method, we observed an 11-fold increase in cellular extract fluorescence in the presence of theophylline. The advantage of using an eGFP-REACh pair is the elimination of acceptor fluorescence. This leads to an improved detection of FRET via better signal-to-noise ratio, allowing us to monitor riboswitch activation in a wide range of analyte concentrations from 0.01 to 2.5 mM.