Fluorescence Readout Research Articles

Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors.

RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.

Synergistic Combinatorial effect of L-asparaginase and Trastuzumab against HER2+ breast cancer cells

Multi-targeted drug combinations which selectively inhibit the proliferation of cancer cells are required for effective anticancer treatment. The current anti-HER2 positive breast cancer therapy involves Trastuzumab and doxorubicin drug combination which produces toxic side effects in clinical settings including high cardiotoxicity. In this study, anticancer activity of single drug as well as the drug combination effect of L-asparaginase (Celginase) and Trastuzumab (Herceptin) was studied on HER2 positive breast cancer (SKBR3) cells. Inhibition of cell proliferation assay based on fluorescence readout was studied to estimate the anticancer effect of the drugs. HUVEC cells were used as negative control cells. Individually as a single drug, Trastuzumab (Herceptin) and L-asparaginase (Celginase) showed anticancer activity against SKBR3 cells with IC50 value of 0.031ng/ml and 1.168µg/ml respectively. The drug combination interaction of Trastuzumab and L-asparaginase resulted in combination index of less than 1(CI < 1) showing their synergistic effect against SKBR3 cells. No cytotoxic effect was observed in control HUVEC cells. The results suggested that the antitumor activity of Trastuzumab and L-asparaginase against HER2 positive breast cancer was found specific to HER2 positive cancer (SKBR3) cells. This synergistic drug interaction of L-asparaginase and Trastuzumab could be further explored to as an alternative to current drug combination therapy against the HER2 positive breast cancer.

Sensitive Detection of Salmonella Based on CRISPR-Cas12a and the Tetrahedral DNA Nanostructure-Mediated Hyperbranched Hybridization Chain Reaction.

Salmonella severely threatens global human health and causes financial burden. The ability to sensitively detect Salmonella in food samples is highly valuable but remains a challenge. Herein, a sensitive detection method for Salmonella was developed by coupling immunomagnetic separation with the CRISPR-Cas12a system and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction (TDN-hHCR). In the detection system, the target Salmonella was immunomagnetically separated and labeled with bio-barcode DNA-modified gold nanoparticles (AuNPs), which could transfer and magnify the signal of a bacterial cell into numerous bio-barcode DNA molecules. Afterward, the bio-barcode DNA can trigger the trans-cleavage activity of CRISPR-Cas12a to inhibit the process of the TDN-hHCR to generate a fluorescence readout. Due to the high immunomagnetic separation efficiency and the effective signal amplification of CRISPR-Cas12a and the TDN-hHCR, Salmonella as low as 8 CFU/mL could be easily detected. Meanwhile, this has been applied for practical use and showed the capability to detect 17 and 25 CFU/mL in spiked milk and egg white, respectively, indicating its potential application in real samples.

Strategies for Monitoring "Ubiquitin C-Terminal Hydrolase 1" (Yuh1) Activity.

The family of ubiquitin C-terminal hydrolases (UCHs(releases ε-linked amide bonds positioned at the C-terminus of ubiquitin. UCHL3 is a highly conserved and dual functional member of this family, recognizing C-terminal extensions of two paralogous modifiers: ubiquitin and NEDD8. The Saccharomyces cerevisiae orthologue of UCHL3, namely, Yuh1, is the only UCH family member in this organism. Like UCHL3, Yuh1 recognizes ubiquitin as well as Rub1, the direct orthologue of NEDD8 in S. cerevisiae. We describe here a method for examining the activity of bacteria and yeast expressed Yuh1 by monitoring the C-terminal trimming of UBB+1 and Rub1+1 through immunoblotting and the increased AMC fluorescence readout detected through a plate reader.

Strip-based lateral flow-type indicator displacement assay for γ-hydroxybutyric acid (GHB) detection in beverages

The use of gamma-hydroxybutyric acid (GHB) in drug-facilitated sexual assault has increased due to its availability and high solubility in aqueous solutions and alcoholic beverages, necessitating the development of rapid methods for GHB detection. In this respect, portable testing methods for use in the field, based on lateral flow assays (LFAs) and capable of detecting trace concentrations of target analytes, are particularly attractive and hold enormous potential for the detection of illicit drugs. Using this strategy, here we report a rapid, low cost, easy-to-handle strip-based LFA for GHB analysis employing a smartphone for fluorescence readout. At molecular signalling level, the ensemble is based on a Cu2+ complex with a tetradentate ligand and the fluorescent dye coumarin 343, which indicate GHB through an indicator displacement assay (IDA) in aqueous solution. When incorporated in a LFA-based strip test this system shows a detection limit as low as 0.03 µM for GHB in MES buffer solution and is able to detect GHB at concentrations of 0.1 µM in soft drinks and alcoholic beverages in only 1 min.

Harnessing enhanced CRISPR/Cas12a trans-cleavage activity with extended reporters and reductants for early diagnosis of Helicobacter pylori, the causative agent of peptic ulcers and stomach cancer

Developing rapid and non-invasive diagnostics for Helicobacter pylori (HP) is imperative to prevent associated diseases such as stomach gastritis, ulcers, and cancers. Owing to HP strain heterogeneity, not all HP-infected individuals incur side effects. Cytotoxin-associated gene A (CagA), and vacuolating cytotoxin A (VacA) genes predominantly drive HP pathogenicity. Therefore, diagnosing CagA and VacA genotypes could alert active infection and decide suitable therapeutics. We report an enhanced LbCas12a trans-cleavage activity with extended reporters and reductants (CEXTRAR) for early detection of HP. We demonstrate that extended ssDNA reporter acts as an excellent signal amplifier, making it a potential alternative substrate for LbCas12a collateral activity. Through a systematic investigation of various buffer components, we demonstrate that reductants improve LbCas12a trans-cleavage activity. Overall, our novel reporter and optimal buffer increased the trans-cleavage activity to an order of 16-fold, achieving picomolar sensitivity (171 pM) without target pre-amplification. Integrated with loop-mediated isothermal amplification (LAMP), CEXTRAR successfully attained attomolar sensitivity for HP detection using real-time fluorescence (43 and 96 aM), in-tube fluorescence readouts (430 and 960 aM), and lateral flow (4.3 and 9.6 aM) for CagA and VacA, respectively. We also demonstrate a rapid 2-min Triton X-100 lysis for clinical sample analysis, which could provide clinicians with actionable information for rapid diagnosis. CEXTRAR could potentially spot the 13C urea breath test false-negatives. For the first time, our study unveils an experimental outlook to manipulate reporters and reconsider precise cysteine substitution via protein engineering for Cas variants with enhanced catalytic activities for use in diagnostics and genetic engineering.

Tracking Mechanical Stress and Cell Migration with Inexpensive Polymer Thin-Film Sensors.

Polydiacetylene (PDA) Langmuir films are well known for their blue to red chromatic transitions in response to a variety of stimuli, including UV light, heat, bio-molecule bindings and mechanical stress. In this work, we detail the ability to tune PDA Langmuir films to exhibit discrete chromatic transitions in response to applied mechanical stress. Normal and shear-induced transitions were quantified using the Surface Forces Apparatus and established to be binary and tunable as a function of film formation conditions. Both monomer alkyl tail length and metal cations were used to manipulate the chromatic transition force threshold to enable discrete force sensing from ~50 to ~500 nN μm-2 for normal loading and ~2 to ~40 nN μm-2 for shear-induced transitions, which are appropriate for biological cells. The utility of PDA thin-film sensors was demonstrated with the slime mold Physarum polycephalum. The fluorescence readout of the films enabled: the area explored by Physarum to be visualized, the forces involved in locomotion to be quantified, and revealed novel puncta formation potentially associated with Physarum sampling its environment.

Nondestructive All-Optical Readout through Photoswitching of Intramolecular Excimer Emission.

We report the first intramolecular excimer photoswitching induced by molecular motion within a dithienylethene (DTE) molecule without destructive readout. The photochromic compound DTE bears two pyrene chromophores, judiciously positioned to face each other in the DTE's open form. The close proximity of the pyrenes in the open form is confirmed by NMR experiments and geometry optimization. Intense pyrene excimer luminescence is recorded, upon both one- and two-photon excitation (OPE and TPE). The photocyclization reaction of the DTE core induces a molecular motion of one pyrene moiety which thus prevents the possibility of formation of an excimer. Our DTE-based pyrene is stable upon TPE irradiation and shows a high photocyclization quantum yield. Such property specifications allow us to report the original nondestructive readout fluorescence by alternating exposure to OPE and TPE.

Rapid and Visual Detection of Type 2 Porcine Reproductive and Respiratory Syndrome Virus by Real-Time Fluorescence-Based Reverse Transcription Recombinase-Aided Amplification.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important diseases that has brought significant economic losses to the swine industry worldwide. Rapid and accurate PRRS virus (PRRSV) detection is one of the key factors for PRRS prevention and control. This study developed a real-time fluorescence-based reverse transcription recombinase-aided amplification (RF-RT-RAA) method for type 2 PRRSV (PRRSV-2) detection. The RF-RT-RAA assay could be performed at 42 °C for 20 min with the optimal primers and a probe. RF-RT-RAA results could be monitored using real-time fluorescence read-out or visually observed with the naked eye using a portable blue light transilluminator. The method had a strong specificity; no cross-reaction was identified with the detected common swine viruses. Moreover, the technique yielded high sensitivity with the lowest detection limit of 101 copies/μL and exhibited good repeatability and reproductively with the coefficients of variation (CV) less than 10%. Eighty-seven clinical samples were tested using RF-RT-RAA and a commercial PRRSV-2 RT-qPCR detection kit. The coincidence rate was 100% between RF-RT-RAA (real-time fluorescence read-out) and RT-qPCR, and 97.7% between RF-RT-RAA (visually observed) and RT-qPCR. The RF-RT-RAA assay provides a new method for rapid and visual detection of PRRSV-2.

Abstract 14660: Truncating Variants in MYBPC3 Cause Ubiquitin Proteasome System Dysfunction Related to Hypertrophic Cardiomyopathy in Human Induced Pluripotent Stem Cell Model

Introduction: Hypertrophic cardiomyopathy (HCM) is the most common inherited monogenic cardiomyopathy. Cardiac myosin binding protein C ( MYBPC3 ) is the most frequently mutated gene in this disease, and most pathogenic variants in MYBPC3 are truncating variants including splice site variants. The ubiquitin proteasome system (UPS), a major intracellular protein degradation system, plays an important role in the heart. Although impairment of UPS is reportedly caused by truncated cMyBP-C, the underlying molecular mechanism causing HCM is largely unknown. Hypothesis: Truncating variants in MYBPC3 lead to impaired UPS activity in human iPS cell-derived cardiomyocytes (hiPSC-CMs) and are associated with HCM phenotypes. Methods: Patient derived iPSC clones were generated from HCM patients with MYBPC3 variants (IVS11-9G>A and IVS27+1G>A). Corrected isogenic control of IVS27+1G>A was generated by base editing. To evaluate UPS activity, we employed ubiquitin fusion degradation reporter, Ub-G76V-GFP, which provides fluorescence readout of UPS activity. BNP expression of hiPSC-CMs were evaluated by antibody labeling and fluorescence-activated cell sorting (FACS). Contractility and Ca 2+ transient were measured from single biopatterned hiPSC-CMs. Results: Both MYBPC3 variant lines exhibited UPS impairment as reflected by increased GFP fluorescence compared to isogenic and healthy controls (Fig. A). IVS27+1G>A showed higher expression of BNP (Fig. B and C). Enhanced contractility and Ca 2+ handling abnormalities were observed in MYBPC3 variant iPSC-CM lines as compared to control (Fig. D and E). Conclusions: Impairment of UPS activity may be associated with a marker of cellular hypertrophy, and contractility and Ca 2+ handling abnormalities in hiPSC-CMs with MYBPC3 truncating variants. These findings support prior reports suggesting that decreased UPS activity contribute to the pathophysiological mechanism of HCM caused by truncating MYBPC3 variants.

Technological and computational advances driving high-throughput oncology.

Engineering and computational advances have opened many new avenues in cancer research, particularly when being exploited in interdisciplinary approaches. For example, the combination of microfluidics, novel sequencing technologies, and computational analyses has been crucial to enable single-cell assays, giving a detailed picture of tumor heterogeneity for the very first time. In a similar way, these 'tech' disciplines have been elementary for generating large data sets in multidimensional cancer 'omics' approaches, cell-cell interaction screens, 3D tumor models, and tissue level analyses. In this review we summarize the most important technology and computational developments that have been or will be instrumental for transitioning classical cancer research to a large data-driven, high-throughput, high-content discipline across all biological scales.

"Three-in-one" Zr-MOF Multifunctional Carrier-mediated Fluorescent and Colorimetric Dual-signal Readout Biosensing Platform to Enhance Analytical Performance.

To address the urgent demand for sensitive and stable detection applications, significant efforts have been made in the development of dual-signal readout assays for precise target detection and timely health risk control. Here, a new nanomaterial, Pt@PCN-224-HRP-initiator DNA (PP-HRP-iDNA), was exploited to construct a dual-signal readout biosensing platform. Zr-MOF (PCN-224) was loaded with as many Pt nanoparticles (NPs) and as much horseradish peroxidase (HRP) as possible to enhance the brightness of the colorimetric signal recognizable to the naked eye while also acting as a gatekeeper to protect the enzyme activity and ensuring the stability of the assay process. Moreover, the Pt NPs and HRP displayed a synergistic catalytic effect, which promoted the sensitivity of detection. Further, the formation of the Zr-O-P bond eliminated the instability of the interactions between PCN-224 and iDNA in a controllable manner. After the immunoreaction, iDNA stimulated a hybridization chain reaction, resulting in a significant reduction of the fluorescent DNA in the supernatant and a fluorescent signal change. Subsequently, the PP-HRP-iDNA probe implemented UV-light response (450 nm) where 3,3',5,5'-tetramethylbenzidine was used as a substrate for the colorimetric signal readout. By virtue of the nanomaterial-modulated transduction mechanism and the antigen-antibody interactions, this dual-signal biosensor displays high sensitivity, with a limit of detection of 0.65 pg/mL for aflatoxin B1 and 4 CFU/mL for Salmonella enteritidis, suggesting the detection potential of the biosensing platform for analyzing various targets.

A Single Fluorescent Protein-Based Indicator with a Time-Resolved Fluorescence Readout for Precise pH Measurements in the Alkaline Range.

The real-time monitoring of the intracellular pH in live cells with high precision represents an important methodological challenge. Although genetically encoded fluorescent indicators can be considered as a probe of choice for such measurements, they are hindered mostly by the inability to determine an absolute pH value and/or a narrow dynamic range of the signal, making them inefficient for recording the small pH changes that typically occur within cellular organelles. Here, we study the pH sensitivity of a green-fluorescence-protein (GFP)-based emitter (EGFP-Y145L/S205V) with the alkaline-shifted chromophore's pKa and demonstrate that, in the pH range of 7.5-9.0, its fluorescence lifetime changes by a factor of ~3.5 in a quasi-linear manner in mammalian cells. Considering the relatively strong lifetime response in a narrow pH range, we proposed the mitochondria, which are known to have a weakly alkaline milieu, as a target for live-cell pH measurements. Using fluorescence lifetime imaging microscopy (FLIM) to visualize the HEK293T cells expressing mitochondrially targeted EGFP-Y145L/S205V, we succeeded in determining the absolute pH value of the mitochondria and recorded the ETC-uncoupler-stimulated pH shift with a precision of 0.1 unit. We thus show that a single GFP with alkaline-shifted pKa can act as a high-precision indicator that can be used in a specific pH range.

Optimization of Ultrahigh-Throughput Screening Assay for Protein Engineering of d-Allulose 3-Epimerase

d-Allulose is the corresponding epimer of d-fructose at the C-3 position, which exhibits a similar taste and sweetness to sucrose. As a low-calorie sweetener, d-allulose has broad application prospects in the fields of medicine, food, and so on. Currently, the production method of d-allulose is mainly the enzymatic conversion of d-fructose by d-allulose 3-epimerase (DAEase). However, the limited specific activity and thermal stability of DAEase restrict its industrial application. Herein, an ultrahigh-throughput screening assay based on the transcription factor PsiR was extensively optimized from the aspects of culture medium components, screening plasmid, and expression host, which enhanced the correction between the fluorescent readout and the enzyme activity. Then, the error-prone PCR (epPCR) library of Clostridium cellulolyticum H10 DAEase (CcDAEase) was screened through the above optimized method, and the variant I228V with improved specific activity and thermal stability was obtained. Moreover, after combining two beneficial substitutions, D281G and C289R, which were previously obtained by this optimized assay, the specific activity of the triple-mutation variant I228V/D281G/C289R reached up to 1.42-fold of the wild type (WT), while its half-life (T1/2) at 60 °C was prolonged by 62.97-fold. The results confirmed the feasibility of the optimized screening assay as a powerful tool for the directed evolution of DAEase.

Construction of a Stimuli-Responsive DNAzyme-Braked DNA Nanomachine for the Amplified Imaging of miRNAs in Living Cells and Mice

Construction of a Stimuli-Responsive DNAzyme-Braked DNA Nanomachine for the Amplified Imaging of miRNAs in Living Cells and Mice

Magnetic relaxation switch and fluorescence dual-mode biosensor for rapid and sensitive detection of ricin B toxin in edible oil and tap water

The ultrasensitive and rapid detection of ricin B toxin (RTB) is essential for food safety and environmental monitoring. Herein, a dual-mode magnetic relaxation switch (MRS) and fluorescence (FL) biosensing strategy was developed to efficiently detect RTB using fluorescent magnetic nanoparticles (MNP300@SiO2(FITC)). Meanwhile, the as-prepared composite MNP300@SiO2(FITC) exhibited superior biocompatibility and increased FL readout and was coupled with aptamer (Apt) to form a captured probe. Magnetic nanoparticles, 30 nm in diameter (MNP30), were coupled to a Blocker to form a paired probe to compete with RTB for Apt binding. The presence of the RTB triggered the dual-mode detection switch, thus, weakening the magnetic and fluorescent signals. Compared with the single-mode detection method, the Δ T2 and Δ FL intensity here exhibited an excellent linear relationship with logarithm of RTB concentrations at 0.001–500 ng/mL and 0.005–500 ng/mL, and obtained ultrahigh sensitivities of 0.8 pg/mL and 3 pg/mL, respectively. In addition, the dual-mode biosensor gained satisfactory spiked recoveries and relative standard deviations for quantitative detection of spiked RTB in edible oil and tap water samples. To our knowledge, this is the first study to describe the accurate quantification of RTB using a sensitive MRS-FL biosensor. We anticipate that this strategy will provide novel avenues for the development of dual-mode sensing assays.

Systematically investigating the fluorescent signal readout of CRISPR-Cas12a for highly sensitive SARS-CoV-2 detection

The CRISPR/Cas system is widely used for molecular diagnostics after the discovery of trans-cleavage activity, especially now with the COVID-19 outbreak. However, the majority of contemporary trans-cleavage activity-based CRISPR/Cas biosensors exploited standard single-strand DNA (ssDNA) reporters, which were based on the FRET principle from pioneering research. An in-depth comparison and understanding of various fluorescent readout types are essential to facilitate the outstanding analytical performance of CRISPR probes. We investigated various types of fluorescent reporters of Cas12a comprehensively. Results show that trans-cleavage of Cas12a is not limited to ssDNA and dsDNA reporters, but can be extended to molecular beacons (MB). And MB reporters can achieve superior analytical performance compared with ssDNA and ds DNA reporters at the same conditions. Accordingly, we developed a highly-sensitive SARS-CoV-2 detection with the sensitivity as low as 100 fM were successfully achieved without amplification strategy. The model target of ORF1a could robustly identify the current widespread emerging SARS-CoV-2 variants. A real coronavirus GX/P2V instead of SARS-CoV-2 were chosen for practical application validation. And a minimum of 27 copies/mL was achieved successfully. This inspiration can also be applied to other Cas proteins with trans-cleavage activity, which provides new perspectives for simple, highly-sensitive and universal molecular diagnosis in various applications.

Reprogramming the Cleavage Specificity of Botulinum Neurotoxin Serotype B1.

Proteases with reprogrammed specificity for nonnative substrates are highly desired in synthetic biology and biomedicine. However, generating reprogrammed proteases that are orthogonal and highly specific for a new target has been a major challenge. In this work, we sought to expand the versatility of protease systems by engineering an orthogonal botulinum neurotoxin serotype B (BoNT/B) protease that recognizes an orthogonal substrate. We designed and validated an orthogonal BoNT/B protease system in mammalian cells, combining mutations in the protease with compensatory mutations in the protease substrate and incorporating a truncated target sequence and then demonstrated use of this orthogonal BoNT/B protease-substrate combination to regulate complex transcriptional circuitry in mammalian cells. Transposing this platform into yeast, we demonstrated utility of this approach for in vivo protease evolution. We tested this platform with the newly designed orthogonal protease and then used it in a high-throughput screen to identify novel orthogonal protease/protease substrate combinations. While carrying out this work, we also generated new cleavage reporters that could be used to report botulinum toxin protease activity in mammalian cells using simple fluorescent readouts. We envision that these approaches will expand the applications of botulinum protease in new directions and aid in the development of new reprogrammed proteases.

Fluorescent Detection of Two Pesticides Based on CRISPR-Cas12a and Its Application for the Construction of Four Molecular Logic Gates.

An intelligent detection platform was developed through molecular logic gate operation based on CRISPR-Cas12a and signal amplification circuits using two kinds of pesticides [acetamiprid (ACE) and atrazine (ATR)] as inputs. The pesticide-aptamer bindings activate the signal amplification process to produce numerous double-stranded DNA, which can be identified by CRISPR-Cas12a. Under the optimal assay conditions, the sensor exhibits excellent analytical performance, with the detection limits for ACE and ATR of 2.5 and 0.2 pM, respectively. The practicality of the platform was verified by testing pesticide concentrations in food samples. Several molecular logic gates (OR, AND, XOR, and INHIBIT) were constructed using "0" and "1" to encode the target pesticides and the fluorescence readout. The logic detection platform with simple operation, high sensitivity, and multiple logic functions is promising to become a powerful sensing system for the intelligent assay of different pesticides in food samples.

Kill three birds with one stone: Zr-MOF-mediated composite multi-functional materials to enhance the efficiency for fluorescent and colorimetric dual-signal readout bioassay

In this work, we report a fluorescent and colorimetric dual readout bioassay for deoxynivalenol detection to ensure public food safety. A multifunctional fluorescent and colorimetric signal probe was constructed to develop the bioassay for deoxynivalenol detection based on the characteristics of Zr-MOF (PCN-224; i.e., high porosity, a large surface area, and excellent fluorescence quenching performance). Platinum nanoparticles (Pt NPs) were grown in situ outside, while glucose oxidase was stored inside (PPG). Glucose oxidase and Pt NPs are both enriched by Zr-MOF, achieving the first signal amplification, and cascade catalysis by the glucose-TMB system for colorimetric signal readout leads to the second signal amplification. PPG was quenched through the spontaneous formation of ZrOP bonds with fluorescent DNA to achieve a highly sensitive fluorescent readout. The self-supplied H2O2 in the colorimetric detection further improved the self-accuracy of the dual-mode analysis strategy (the accuracy of independent signal readout modes from two different signal transduction mechanisms). This multifunctional PPG probe avoids the time-consuming assembly of different probes and reduces error accumulation from uncontrollable factors in complex experimental procedures. It allows for the sensitive and accurate detection of deoxynivalenol with excellent limits of detection (5.3 pg/mL for the fluorescent assay and 34 pg/mL for the colorimetric method). Overall, this work demonstrates a viable approach for the construction of a dual-signal biosensing platform based on multifunctional MOF probes for biological analysis.