Sensitive Detection of Transcription Factor in Nuclear Extracts by Target-Actuated Isothermal Amplification-Mediated Fluorescence Enhancement

Thermodynamic Allosteric Switch-Actuated 3D DNA Nanomachine for Ultrasensitive Electrochemical/Fluorescent Dual-Mode Biosensing of a Transcription Factor

Herein, we reported an innovative thermodynamic allosteric switch-actuated 3D DNA nanomachine for selective, sensitive, and accurate electrochemical (EC)/fluorescent (FL) dual-mode biosensing of a microphthalmia-associated transcription factor (MITF). The thermodynamic allosteric switch was ingeniously customized as a hairpin probe (HP) that was in dynamic equilibrium but rapidly interconverting conformations. At the "inactive state", the MITF-binding region and the switch part were "sequestered". Upon the introduction of MITF, an MITF-HP complex promptly formed, and the equilibrium of HP thermodynamically inclined from the "inactive state" toward the "active state" conformation. Immediately, the exposed switch on HP effectively actuated the 3D DNA nanomachine and synchronously produced the restriction site for Nb.BbvCI nicking endonuclease. After the autonomous conveying of the 3D DNA nanomachine by means of the high-efficiency circularly nicking endonuclease signal amplification (NESA), not only was MB-S1 in the supernatant used for FL measurements but also MB-SP/MNs/S2 in the precipitate was adapted for EC analysis, significantly improving the utilization of output products derived from the 3D DNA nanomachine. Accordingly, benefiting from the efficient DNA nanomachine signal amplification manner and the self-calibration function of a dual-mode bioassay, the constructed biosensor exhibits superior sensitivity and accuracy for MITF determination.

2-Aminopurine-based quencher-free DNA tweezers with fluorescence properties well tuned by surrounding bases

Reversible structural changes in DNA nanomachines have great potential in the field of bioanalysis. Here, we demonstrate an assembly strategy for quencher-free and tunable DNA tweezers based on 2-aminopurine (2-AP), avoiding the tedious fluorescence labelling step. The conformational state of the tweezers could be controlled by specific oligonucleotides (fuel or anti-fuel). Taking advantage of the local environmental sensitivity of 2-AP, the structural changes of the tweezers were easily tracked, and multiple cyclic switching of the tweezers between the open and closed states was achieved. In addition, the influence of oligonucleotide structure on the fluorescence properties of 2-AP was deeply explored. We figured out that the fluorescence of 2-AP was highly quenched by the base-stacking of natural bases in DNA oligonucleotides. Moreover, by comprehensively regulating the type of bases surrounding the inserted 2-AP site, a sensitive fluorescence response towards dynamic change can be obtained. This principle of quencher-free nanodevices based on 2-AP provides a convenient method for monitoring the structural changes of DNA nanomachines.

Paper-Based Progesterone Sensor Using an Allosteric Transcription Factor

Progesterone monitoring is an essential component of in vitro fertilization treatments and reproductive management of dairy cows. Gold-standard biosensors for progesterone monitoring rely on antibodies, which are expensive and difficult to procure. We have developed an alternative transcription factor-based sensor that is superior to conventional progesterone biosensors. Here, we incorporate this transcription factor-based progesterone sensor into an affordable, portable paperfluidic format to facilitate widespread implementation of progesterone monitoring at the point of care. Oligonucleotides labeled with a fluorescent dye are immobilized onto nitrocellulose via a biotin-streptavidin interaction. In the absence of progesterone, these oligonucleotides form a complex with a transcription factor that is fluorescently labeled with tdTomato. In the presence of progesterone, the fluorescent transcription factor unbinds from the immobilized DNA, resulting in a decrease in tdTomato fluorescence. The limit of detection of our system is 27 nm, which is a clinically relevant level of progesterone. We demonstrate that transcription factor-based sensors can be incorporated into paperfluidic devices, thereby making them accessible to a broader population due to the portability and affordability of paper-based devices.

Full liberation of 2-Aminopurine with nucleases digestion for highly sensitive biosensing

2-Aminopurine (2-AP), a fluorescent isomer of adenine, is a popular fluorescent tag for DNA-based biosensors. The fluorescence of 2-AP is highly dependent on its microenvironment, i.e., almost non-fluorescent and merely fluorescent in dsDNA and ssDNA, respectively, but can be greatly brightened as mononucleotide. In most 2-AP-based biosensors, DNA transformation from dsDNA to ssDNA was employed, while selective digestion of 2-AP-labeled DNA with nucleases represents an appealing approach for improving the biosensor sensitivity. However, some detailed fundamental information, such as the reason for nuclease digestion, the influence of the labeling site, neighboring bases, or the label number of 2-AP for final signal output, are still largely unknown, which greatly limits the utility of 2-AP-based biosensors. In this work, using both steady- and excited-state fluorescence (lifetime), we demonstrated that nuclease digestion resulted in almost full liberation of 2-AP mononucleotides, and was free from labeling site and neighboring bases. Furthermore, we also found that nuclease digestion could lead to multiplexed sensitivity from increasing number of 2-AP labelling, but was not achievable for the conventional biosensors without full liberation of 2-AP. Considering the popularity of 2-AP in biosensing and other related applications, the above obtained information in sensitivity boosting is fundamentally important for future design of 2-AP-based biosensors.

Fluorescence nucleobase analogue-based strategy with high signal-to-noise ratio for ultrasensitive detection of food poisoning bacteria

We developed a simple and ultrasensitive strategy for the identification of foodborne pathogens utilizing a fluorescent nucleobase analogue [2-aminopurine (2-AP)]-containing split G-quadruplex that binds blocker DNA. Compared to a previous strategy that did not use blocker DNA, this strategy showed a significant increase in the signal-to-noise ratio-by approximately 300%-owing to the displacement of the blocker DNA by the target DNA that induces the formation of an active G-quadruplex structure, thereby leading to a substantial increase in the 2-AP fluorescence signal. The proposed strategy was rationally combined with polymerase chain reaction, which resulted in the successful determination of genomic DNA (within the range of 10-106 copies) derived from the food poisoning bacterium Escherichia coli, with a limit of detection of 5.2 copies and high selectivity. In addition, the practical applicability of this method was demonstrated by analyzing E. coli-spiked lettuce samples.

Binding mediated MNAzyme signal amplification strategy for enzyme-free and label-free detection of DNA-binding proteins

A novel MNAzyme signal amplification strategy was developed for enzyme-free and label-free detection of DNA-binding proteins. This strategy relied on the binding-mediated MNAzyme cleavage and G-quadruplex-based light-up fluorescence switch. Three DNA sequences were designed to construct the MNAzyme in which DNA1 (including half binding site of the target protein and a toehold sequence) and DNA2 (including another half binding site of the target protein and one MNAzyme partzyme) firstly hybridized. The target protein recognized the binding sites on DNA1-DNA2 hybrid to form a stable protein-DNA1-DNA2 conjugates. Then, the MNAzyme was assembled with the presence of DNA3 which contained another MNAzyme partzyme and the complementary sequence of DNA1. The active MNAzyme cleaved DNA4 to release the G-quadruplex that was locked in the stem of DNA4. Finally, N-methyl mesoporphyrin IX (NMM) was inserted into the released G-quadruplex structure and the fluorescence signal was turned on. Taking nuclear factor-κB p50 (NF-κB p50) as the model, the limit of detection was low to 0.14 nM. Furthermore, the sequence-specific recognition of NF-κB p50 with DNA displayed excellent selectivity and specificity. The results in present work showed that this strategy will be a promising tool for DNA-binding proteins analysis in biomedical exploration and clinical diagnosis.

Sensitive detection of transcription factor by coupled fluorescence-encoded microsphere with exonuclease protection

Aberrant transcription factors (TFs) activities are closely related to the occurrence and development of various diseases. Herein, we presented a fluorescence-encoded microsphere-based approach for TFs detection coupling with common DNA footprinting assay. Target TFs specifically bound the binding sites of double-stranded DNA (dsDNA) probes which were conjugated to microspheres. Thus, the probes were protected from being hydrolyzed by exonuclease III (Exo III). Afterwards, biotins labeled on the probes reacted with streptavidin-phycoerythrin (SA-PE) to produce fluorescent signal; however, in the absence of target TFs, the dsDNA probes would be hydrolyzed by Exo III resulting in biotins falling off and thus fluorescence signal was not generated. This strategy can be used to detect nuclear factor-kappa B p50 (NF-κB p50) with a detection limit of 0.2 nM. The steric hindrance of microspheres overcome the disadvantage of Exo III that can nibble into the protein-bound DNA region. Meanwhile, the fluorescent label of microsphere was specific to each TF, enabling multiplex detection could be achieved by changing specific protein binding site of corresponding dsDNA probe. This method has been successfully applied for simultaneous detection of NF-κB p50, AP-1 and CREB in nuclear extract isolated from HeLa cells stimulated or unstimulated by TNF-α, showing great potential for biomedical researches and precise disease diagnosis.

Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification

Flap endonuclease 1 (FEN1), an endogenous nuclease with the ability to cleave the 5' overhang of branched dsDNA, is of significance in DNA replication and repair. The overexpression of FEN1 is common in cancer because of the ubiquitous upregulation of DNA replication; thus, FEN1 has been recognized as a potential biomarker in oncological investigations. However, few analytical methods targeting FEN1 with high sensitivity and simplicity have been developed. This work developed a signal-amplified detection of FEN1 based on the cleavage-induced ligation of a dumbbell DNA probe and rolling circle amplification (RCA). A flapped dumbbell DNA probe (FDP) was rationally designed with a FEN1 cleavable flap at the 5' end. The cleavage generated a nick site with juxtaposed 5' phosphate and 3' hydroxyl ends, which were linkable by T4 DNA ligase to form a closed dumbbell DNA probe (CDP) with a circular conformation. The CDP functioned as a template for RCA, which produced abundant DNA that could be probed using SYBR Green I. The highly sensitive detection of FEN1 with a limit of detection of 15 fM was achieved, and this method showed high specificity, which enabled the quantification of FEN1 in real samples. The inhibitory effects of chemicals on FEN1 were also evaluated. This study represents the first attempt to develop an FEN1 assay that involves signal amplification, and the novel biosensor method enriches the tools for FEN1-based diagnostics.

A CRISPR-derived biosensor for the sensitive detection of transcription factors based on the target-induced inhibition of Cas12a activation

Transcription factors (TFs) are the key proteins for the decision of cell fates, and they have been recognized as potent markers for diagnostic and treatment of diseases. Herein, we report on a highly sensitive biosensor for the detection of TFs based on the CRISPR/Cas12a system. This biosensor was accomplished based on the competitive binding of the Cas12a-crRNA and TFs towards a dsDNA referred to as activator. Without TFs, the activator can be recognized by Cas12a-crRNA and cause the activation of the DNase activity of Cas12a. When TFs were added, the TFs can bind with the activator because the activator was designed to contain the specific binding sites of target TFs. We find that this binding can inhibit the association between Cas12a-crRNA and the activator, which hinders the activation of Cas12a. As a proof-of-concept, the rapid detection of five kinds of TFs was presented, and the detection was extended to the analysis of TFs expression in xenograft solid tumors from mice. This investigation is the first attempt to apply CRISPR technology in the sensing of TFs, and it discloses that the blocking of activator can be applied as a new sensing mechanism for the development of CRISPR-based biosensor.

A signal transduction approach for multiplexed detection of transcription factors by integrating DNA nanotechnology, multi-channeled isothermal amplification, and chromatography

The variation patterns of transcription factors (TFs) provide direct information for the states of cell populations, which is of significance for biomedical research and clinical diagnostics. Herein, we show that through multi-channeled isothermal amplification, it is feasible to connect DNA-based signal transduction with chromatography for multiplexed detection of TFs. The described system is referred to as "PAC" which includes three major steps: (i) Protection, which uses DNA-modified magnetic beads to capture TFs and converts the capturing event into triggering signal; (ii) Amplification, which receives the triggering signal and generate DNA reporters through multi-channeled extension and nicking of oligonucleotides; and (iii) Chromatography, which separates and detects the DNA reporters in liquid chromatography. The quantitative detection of five essential TFs includes p50, p53, AP-1, MITF, and c-Myc is realized in a multiplexed manner, with the lowest detection limit of 0.5 pM. PAC can also provide effective means to measure the above five TFs in real samples, including cultured cells, xenograft tumors, and blood-based liquid biopsy. This study not only established a solution for multiplexed measurement of TFs for molecular diagnostics, but also paved avenue for bridging the gap between DNA nanotechnology and chromatography.

Development of a bidirectional isothermal amplification strategy for the sensitive detection of transcription factors in cancer cells

We develop a bidirectional isothermal amplification strategy for the sensitive detection of transcription factors in cancer cells.

Antibody free ELISA-like assay for the detection of transcription factors based on double-stranded DNA thermostability

Transcription factors (TFs) play critical roles in gene expression regulation and disease development. Herein we report a chemiluminescence assay for the detection of transcription factor based on double-stranded DNA thermostability.

Generation of unconventional Fano-comb resonances in multilayered core-shell nanoparticles

We theoretically propose a design of core-shell nanoparticles consisting of a dielectric core coated by several alternating plasmonic and dielectric shell layers for the generation of comb-like scattering resonances. We demonstrate that the obtained scattering resonances are independent of the polarization, observation angle and background medium, since they originate from the unconventional Fano interference between Mie modes with the same multipole moment inside each plasmonic shell layer. Furthermore, we also demonstrate that controlling either the core or the shell parameters can precisely tune the spectral positions of the comb-like resonances. At last, we show that the comb-like resonances can be well maintained even for the non-perfect spherical core-shell nanoparticles. All these features make the proposed multilayered core-shell nanoparticles attractive candidates for multichannel and ultrasensitive optical tags.

A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules

We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10^-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10^-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.

A label-free fluorescence method for detection of ureC gene and diagnosis of Helicobacter pylori infection

The feasibility of using a polymerase chain reaction (PCR)-based label-free DNA sensor for the detection of Helicobacter pylori is investigated. In particular, H. pylori ureC gene, a specific H. pylori nucleic acid sequence, was selected as the target sequence. In the presence of ureC gene, the target DNA could be amplified to dsDNA with much higher detectable levels. After added the SYBR green I (SGI), the sensing system could show high fluorescence. Thus, the target DNA can be detected by monitoring the change of fluorescence intensity of sensing system. The clinical performance of this method was determined by comparing it with another conventional technique urea breath test (UBT). The result also showed good distinguishing ability between negative and positive patient, which was in good agreement with that obtained by the UBT. It suggests that the label-free fluorescence-based method is more suitable for infection confirmation test of H. pylori. This approach offers great potential for simple, sensitive and cost-effective identification of H. pylori infection.

Amplified probing of protein/DNA interactions for sensitive fluorescence detection of transcription factors

Coupling the enzyme protection strategy with metal-ion dependent DNAzyme amplification leads to sensitive monitoring of protein/DNA interactions.

A one-step structure-switching electrochemical sensor for transcription factor detection enhanced with synergistic catalysis of PtNi@MIL-101 and Exo III-assisted cycling amplification

We present a new type of PtNi@MIL-101 electrocatalyst and Exo III-assisted cycling amplification for one-step electrochemical detection of NF-κB p50.