MASH-FRET: A Simplified Approach for Single-Molecule Multiplexing Using FRET

Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels

Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.

An in-situ blocking strategy for improved anti-interference inspection of AFB1 based on hollow covalent organic framework capsules with commodious and undisturbed microenvironment

This work proposed an in-situ blocking strategy for improved anti-interference and signal-amplified inspection of hazards via constructing hollow covalent organic framework (HCOF) capsules. An aptamer-FRET nanoprobe integrated with carbon dots and CuS was introduced into the micro-capsule as signal indicator to demonstrate the proof-of-concept. The HCOF was successfully prepared by removing the metal-organic frameworks (MOF) core from the MOF@COF that had been preloaded with the nanoprobes under mild conditions. Meanwhile, the hydrophobic surface of HCOF enhanced the adsorption and penetration of aflatoxin B1 (AFB1) into the capsule to interact with the nanoprobes. This strategy was applied to detect AFB1 in food samples, achieving a linear response of 1-300 nM along with a detection limit of 0.3 nM. Selectivity test verified that the prepared sensing platform could specifically recognize AFB1 without complex sample pretreatment. This study provides new ideas for improved anti-interference inspection of hazards against complex sample matrix.

Deep-LASI: deep-learning assisted, single-molecule imaging analysis of multi-color DNA origami structures

Single-molecule experiments have changed the way we explore the physical world, yet data analysis remains time-consuming and prone to human bias. Here, we introduce Deep-LASI (Deep-Learning Assisted Single-molecule Imaging analysis), a software suite powered by deep neural networks to rapidly analyze single-, two- and three-color single-molecule data, especially from single-molecule Förster Resonance Energy Transfer (smFRET) experiments. Deep-LASI automatically sorts recorded traces, determines FRET correction factors and classifies the state transitions of dynamic traces all in ~20-100 ms per trajectory. We benchmarked Deep-LASI using ground truth simulations as well as experimental data analyzed manually by an expert user and compared the results with a conventional Hidden Markov Model analysis. We illustrate the capabilities of the technique using a highly tunable L-shaped DNA origami structure and use Deep-LASI to perform titrations, analyze protein conformational dynamics and demonstrate its versatility for analyzing both total internal reflection fluorescence microscopy and confocal smFRET data.

Ensemble Force Spectroscopy of a G-Quadruplex Cluster on a Single-Molecule Platform

Single-molecule methods offer high sensitivities with precisions superior to bulk assays. However, these methods are low in throughput and cannot repetitively interrogate the same cluster of molecular units. In this work, we investigate a tandem array of G-quadruplexes on a single-molecule DNA template with a throughput of at least two orders of magnitude higher than single-molecule force spectroscopy. During mechanical unfolding by optical tweezers, the array of G-quadruplexes experiences identical force, temperature, and ionic conditions, which not only reduce environmental noise but also render unfolding transitions indistinguishable among individual G-quadruplexes. The resultant ensemble behaviors are analyzed by scanning force diagrams, which reveals accurate F1/2 values, where 50% of G-quadruplexes are unfolded. Independent of the number of G-quadruplexes (n > 15) contained in a cluster, F1/2 can effectively evaluate G-quadruplex ligands in a new method called differential scanning forcemetry. When the same G-quadruplex cluster is subject to a series of constant forces in force-jump experiments, unfolding rate constants of G-quadruplexes can be effectively evaluated as a function of force. The high precision demonstrated in all of these measurements reflects the power of repetitive sampling on the same cluster of single-molecule entities under identical conditions. Since biomolecules such as DNA, RNA, and proteins can be conveniently incorporated in a tandem array, we anticipate that this ensemble assay on single-molecule entities (EASE) provides a generic means of ensemble force spectroscopy to amalgamate the accuracy of ensemble measurements with the precision of single-molecule methods.

Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex

Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes.

Single-Molecule Mechanochemical Sensing

Single-molecule mechanochemical sensing (SMMS) is a novel biosensing technique using mechanical force as a signal transduction mechanism. In the mechanochemical sensing, the chemical binding of an analyte molecule to a sensing template is converted to mechanical signals, such as tensile force, of the template. Since mechanical force can be conveniently monitored by single-molecule tools, such as optical tweezers, magnetic tweezers, or Atomic Force Microscopy, mechanochemical sensing is often carried out at the single molecule level. In traditional format of ensemble sensing, sensitivity can be achieved via chemical or electrical amplifications, which are materials intensive and time-consuming. To address these problems, in 2011, we used the principle of mechanochemical coupling in a single molecular template to detect single nucleotide polymorphism (SNP) in DNA fragments. The single-molecule sensitivity in such SMMS strategy allows to removing complex amplification steps, drastically conserving materials and increasing temporal resolution in the sensing. By placing many probing units throughout a single-molecule sensing template, SMMS can have orders of magnitude better efficiency in the materials usage (i.e., high Atom Economy) with respect to the ensemble biosensing. The SMMS sensing probes also enable topochemical arrangement of different sensing units. By placing these units in a spatiotemporally addressable fashion, single-molecule topochemical sensors have been demonstrated in our lab to detect an expandable set of microRNA targets. Because of the stochastic behavior of single-molecule binding, however, it is challenging for the SMMS to accurately report analyte concentrations in a fixed time window. While multivariate analysis has been shown to rectify background noise due to stochastic nature of single-molecule probes, a template containing an array of sensing units has shown ensemble average behaviors to address the same problem. In this so-called ensemble single-molecule sensing, collective mechanical transitions of many sensing units occur in the SMMS sensing probes, which allows accurate quantification of analytes. For the SMMS to function as a viable sensing approach readily adopted by biosensing communities, the future of the SMMS technique relies on the reduction in the complexity and cost of instrumentation to report mechanical signals. In this account, we first explain the mechanism and main features of the SMMS. We then specify basic elements employed in SMMS. Using DNA as an exemplary SMMS template, we further summarize different types of SMMS which present multiplexing capability and increased throughput. Finally, recent efforts to develop simple and affordable high throughput methods for force generation and measurement are discussed in this Account for potential usage in the mechanochemical sensing.

Single-Molecule Sensor for High-Confidence Detection of miRNA

MicroRNAs (miRNAs) play a crucial role in regulating gene expression and have been linked to many diseases. Therefore, sensitive and accurate detection of disease-linked miRNAs is vital to the emerging revolution in early diagnosis of diseases. While the detection of miRNAs is a challenge due to their intrinsic properties such as small size, high sequence similarity among miRNAs and low abundance in biological fluids, the majority of miRNA-detection strategies involve either target/signal amplification or involve complex sensing designs. In this study, we have developed and tested a DNA-based fluorescence resonance energy transfer (FRET) sensor that enables ultrasensitive detection of a miRNA biomarker (miRNA-342-3p) expressed by triple-negative breast cancer (TNBC) cells. The sensor shows a relatively low FRET state in the absence of a target but it undergoes continuous FRET transitions between low- and high-FRET states in the presence of the target. The sensor is highly specific, has a detection limit down to low femtomolar (fM) without having to amplify the target, and has a large dynamic range (3 orders of magnitude) extending to 300 000 fM. Using this strategy, we demonstrated that the sensor allows detection of miRNA-342-3p in the miRNA-extracts from cancer cell lines and TNBC patient-derived xenografts. Given the simple-to-design hybridization-based detection, the sensing platform developed here can be used to detect a wide range of miRNAs enabling early diagnosis and screening of other genetic disorders.