Label-free and enzyme-free detection of transcription factors with graphene oxide fluorescence switch-based multifunctional G-quadruplex-hairpin probe

A CRISPR-Cas12a-based electrochemical biosensor for the detection of microphthalmia-associated transcription factor

A novel electrochemical biosensor that combines the CRISPR-Cas12a system with a gold electrode is reported for the rapid and sensitive detection of microphthalmia-associated transcription factor (MITF). The biosensor consists of a gold electrode modified with DNA1, which contains the target sequence of MITF and is labeled with ferrocene, an electroactive molecule. The biosensor also includes hairpin DNA, which has a binding site for MITF and can hybridize with helper DNA to form a double-stranded complex that activates CRISPR-Cas12a. When MITF is present, it binds to hairpin DNA and prevents its hybridization with helper DNA, thus inhibiting CRISPR-Cas12a activity and preserving the DPV signal of ferrocene. When MITF is absent, hairpin DNA hybridizes with helper DNA and activates CRISPR-Cas12a, which cleaves DNA1 and releases ferrocene, thus reducing the DPV signal. The biosensor can detect MITF with high sensitivity (with an LOD of 8.14 fM), specificity, and accuracy in various samples, such as cell nuclear extracts and human serum. The biosensor can also diagnose and monitor melanocyte-related diseases and melanin production. This work provides a simple, fast, sensitive, and cost-effective biosensor for MITF detection and a valuable tool for applications in genetic testing, disease diagnosis, and drug screening.

A Bioluminescent Protein-Graphene Oxide Donor-Quencher Pair in DNA Hybridization Assays

Despite fluorescent quenching with graphene oxide (GO) having shown great success in various applications - bioluminescent quenching has not yet been demonstrated using GO as a quencher. To explore the ability of GO to quench bioluminescence, we used Gaussia luciferase (Gluc) as a donor and GO as a quencher and demonstrated its application in sensing of two target analytes, HIV-1 DNA and IFN-γ. We demonstrated that the incubation of Gluc conjugated HIV-1 and IFN-γ oligonucleotide probes with GO provided for monitoring of probe-target interactions based on bioluminescence measurement in a solution phase sensing system. The limits of detection obtained for IFN-γ and HIV-1 DNA detection were 17 nM and 7.59 nM, respectively. Both sensing systems showed selectivity toward the target analyte. The detection of IFN-γ in saliva matrix was demonstrated. The use of GO as a quencher provides for high sensitivity while maintaining the selectivity of designed probes to their respective targets. The use of GO as a quencher provides for an easy assay design and low cost, environmentally friendly reporter.

An exonuclease protection and CRISPR/Cas12a integrated biosensor for the turn-on detection of transcription factors in cancer cells

Transcription factors (TFs) are critical proteins that regulate the expression of genes, and the abnormal change of TFs levels is directly related to physical dysfunctions. Herein, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensor for the measurement of TFs level with the assistance of exonuclease protection assay. A dsDNA (activator) with the ability to activate Cas12a was engineered to contain TFs binding domain, and the binding between TFs and the activator can protect the dsDNA from being digested by exonuclease III (Exo III). The reserved activator then triggered a CRISPR/Cas12a reporting reaction to produce fluorescent signal for detection. In the detection of nuclear factor-kappa B (NF-κB) p50 subunit, the limit of detection of 0.2 pM and limit of quantification of 0.6 pM were obtained respectively, and the performance of this biosensor has been challenged by cell nucleoprotein extracts. Additionally, this method can be applied in the screening and evaluation of TFs inhibitors, calculating the IC50 of oridonin. Integrating merits including high sensitivity, low cost, and good portability, this method may enrich the arsenal for TFs-related applications.

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.

A low-background fluorescent aptasensor for acetamiprid detection based on DNA three-way junction-formed G-quadruplexes and graphene oxide

A simple fluorescence detection platform has been established for acetamiprid assay based on DNA three-way junctions (TWJs), which can triple the fluorescence signal without any other amplification. It is designed with three single-stranded DNAs (ssDNA), each of which contains one-third or two-thirds of the G-quadruplex sequence at each end. Upon the addition of acetamiprid, the conformation of the aptamer-containing double-stranded DNA (dsDNA) changes from its original conformation and releases a strand of ssDNA. This ssDNA, with the other two ssDNAs, can assemble into DNA TWJs, and the three pairs of the branched ends of the DNA TWJs are adjacent to each other, allowing them to form three units of G-quadruplexes. Hence, the fluorescence of N-methyl mesoporphyrin IX (NMM) is lighted by the nascent G-quadruplexes. Graphene oxide (GO) is then added to minimize the detection background by absorbing the free NMM and non-target-induced ssDNA. The proposed strategy can assay acetamiprid in a wide linear range of 0-500 nM with a detection limit of 5.73 nM. More importantly, this assay platform demonstrates high potential for acetamiprid assay in food control and environmental monitoring.

Equipment-free and visualized biosensor for transcription factor rapid assay based on dopamine-functionalized cellulose paper

A cellulose paper-based biosensor was developed for the equipment-free and naked-eye detection of a transcription factor (TF) using dopamine as the signal-responsive material based on exonuclease III-assisted cycling amplification. Compared with other TF biosensors, the proposed biosensor demonstrates low-cost, portable, disposable, and naked-eye detection features.

Silver ion-stabilized DNA triplexes for completely enzyme-free and sensitive fluorescence detection of transcription factors via catalytic hairpin assembly amplification

A new silver ion-stabilized DNA triplex enables enzyme-free and amplified sensitive fluorescence detection of transcription factors.

Detecting transcription factors with allosteric DNA-Silver nanocluster switches

Sensitive and efficient detection of protein markers, such as transcription factors (TFs), is an important issue in postgenomic era. In this paper, we report a DNA nanodevice, allosteric DNA-silver nanocluster switches (AgSwitches), for TFs detection. The mechanism of this nanodevice is based on the binding-induced allostery whereby the binding between AgSwitches and TFs alters the conformation of AgSwitches. This alteration brings DNA-silver nanocluster (DNA-AgNCs) and guanine-rich enhancer sequences (GRS) into close proximity, generating fluorescent enhancement for quantifications. Our results revealed that the sequence design of AgSwitches can be rationally optimized according to stimulated free energy, and we demonstrated that this method can not only be used for detecting TFs in nuclear extracts of cells, but also be developed as a tool for screening inhibitors of TFs. Overall, this work expanded the category allosteric DNA nanodevices by first introducing DNA-AgNCs into this area, and the obtained method was efficient for TFs-related investigations.

Target binding protection mediated rolling circle amplification for sensitive detection of transcription factors

Transcription factors (TFs) play central roles in the regulation of gene expression by binding with specific DNA sequences. As a potential diagnostic marker, sensitive detection of TFs is essential for pharmacological research development and clinical disease diagnosis. Here, a new fluorescent method based on target binding protection mediated rolling circle amplification (RCA) was developed for TFs detection. A hairpin probe with recognition site for target binding, cleavage site for Nt.BbvCI digestion and two hanging DNA strands with part of G-quadruplex complementary sequences for signal output was designed. Moreover, the hairpin probe could serve as template of RCA after being ligated. Firstly, TFs bound with hairpin probes and protected signal complementary sequences against cleavage by Nt.BbvCI due to space hindrance effect, while the excess hairpin probes were effectively digested to avoid false positive signal. Then, TFs and Nt.BbvCI were dissociated from hairpin probes by heating, complete hairpin probes being preserved. Next, protected hairpin probes were specifically connected to dumbbell templates under the action of T4 DNA ligase. Subsequently, dumbbell templates hybridized with primer to initiate the RCA reaction, obtaining numerous G-quadruplex sequences. Finally, N-methyl-mesoporphyrin IX (NMM) bound with G-quadruplex to generate enhanced fluorescence signal. The proposed assay system achieved excellent specificity and sensitivity toward TATA-binding protein (TBP) with a detection limit as low as 88pM, and with a linear range from 100pM to 40nM. The strategy proposed here was looking forward to offer a powerful tool for TFs related bioanalysis and disease diagnostics.

Fluorescent "on-off-on" switching sensor based on CdTe quantum dots coupled with multiwalled carbon nanotubes@graphene oxide nanoribbons for simultaneous monitoring of dual foreign DNAs in transgenic soybean

With the increasing concern of potential health and environmental risk, it is essential to develop reliable methods for transgenic soybean detection. Herein, a simple, sensitive and selective assay was constructed based on homogeneous fluorescence resonance energy transfer (FRET) between CdTe quantum dots (QDs) and multiwalled carbon nanotubes@graphene oxide nanoribbons (MWCNTs@GONRs) to form the fluorescent "on-off-on" switching for simultaneous monitoring dual target DNAs of promoter cauliflower mosaic virus 35s (P35s) and terminator nopaline synthase (TNOS) from transgenic soybean. The capture DNAs were immobilized with corresponding QDs to obtain strong fluorescent signals (turning on). The strong π-π stacking interaction between single-stranded DNA (ssDNA) probes and MWCNTs@GONRs led to minimal background fluorescence due to the FRET process (turning off). The targets of P35s and TNOS were recognized by dual fluorescent probes to form double-stranded DNA (dsDNA) through the specific hybridization between target DNAs and ssDNA probes. And the dsDNA were released from the surface of MWCNTs@GONRs, which leaded the dual fluorescent probes to generate the strong fluorescent emissions (turning on). Therefore, this proposed homogeneous assay can be achieved to detect P35s and TNOS simultaneously by monitoring the relevant fluorescent emissions. Moreover, this assay can distinguish complementary and mismatched nucleic acid sequences with high sensitivity. The constructed approach has the potential to be a tool for daily detection of genetically modified organism with the merits of feasibility and reliability.

Silver-functionalized g-C3N4 nanohybrids as signal-transduction tags for electrochemical immunoassay of human carbohydrate antigen 19-9

A simple and feasible electrochemical immunosensing platform was developed for highly efficient screening of a disease-related protein (human carbohydrate antigen 19-9, CA 19-9 used in this case) using silver-functionalized g-C3N4 nanosheets (Ag/g-C3N4) as signal-transduction tags. Initially, Ag/g-C3N4 nanohybrids were synthesized by combining thermal polymerization of the melamine precursor with the photo-assisted reduction method. Thereafter, the as-synthesized Ag/g-C3N4 nanohybrids were utilized for the labeling of the anti-CA 19-9 detection antibody by using a typical carbodiimide coupling method. The assay was carried out on a capture antibody-modified glassy carbon electrode in a sandwich-type detection mode. The detectable signal mainly derived from the voltammetric characteristics of the immobilized nanosilver particles on the g-C3N4 nanosheets within the applied potentials. Under the optimal conditions, the voltammetric peak currents increased with the increasing amount of target CA 19-9, and exhibited a wide linear range from 5.0 mU mL(-1) to 50 U mL(-1) with a detection limit of 1.2 mU mL(-1). Our strategy also displayed good reproducibility, precision and specificity. The results of the analysis of clinical serum specimens were in good accordance with the results obtained by an enzyme-linked immunosorbent assay (ELISA) method. The newly developed immunosensing system is promising for enzyme-free and cost-effective analysis of low-abundance proteins.

Nitrogen and Sulfur Codoped Reduced Graphene Oxide as a General Platform for Rapid and Sensitive Fluorescent Detection of Biological Species

Nitrogen (N) and sulfur (S) codoped reduced graphene oxide (N,S-rGO) was synthesized through a facile solvothermal process. The introduction of N and S heteroatoms into GO effectively activated the sp(2)-hybridized carbon lattice and made the material an ideal electron/energy acceptor. Such unique properties enable this material to perform as a general platform for rapid and sensitive detection of various biological species through simple fluorescence quenching and recovering. When quantum dot (QD)-labeled HBV (human being disease-related gene hepatitis B virus DNA) and HIV (human being disease-related gene human immunodeficiency virus DNA) molecular beacon probes were mixed with N,S-rGO, QD fluorescence was quenched; when target HBV and HIV DNA were added, QD fluorescence was recovered. By the recovered fluorescence intensity, the target virus DNA detection limits were reduced to 2.4 nM for HBV and 3.0 nM for HIV with detection time of less than 5 min. It must be stressed out that different viruses in the same homogeneous aqueous media could be discriminated and quantified simultaneously through choosing diverse QD probes with different colors. Moreover, even one mismatched target DNA could be distinguished using this method. When altering the molecular beacon loop domain to protein aptamers, this sensing strategy was also able to detect thrombin and IgE in 5 min with detection limits of 0.17 ng mL(-1) and 0.19 ng mL(-1), respectively, which was far more rapid and sensitive than bare GO-based fluorescence detection strategy.

A versatile fluorescent biosensor based on target-responsive graphene oxide hydrogel for antibiotic detection

A fluorescent sensing platform based on graphene oxide (GO) hydrogel was developed through a fast and facile gelation, immersion and fluorescence determination process, in which the adenosine and aptamer worked as the co-crosslinkers to connect the GO sheets and then form the three-dimensional (3D) macrostructures. The as-prepared hydrogel showed high mechanical strength and thermal stability. The optimal hydrogel had a linear response for oxytetracycline (OTC) of 25-1000μg/L and a limit of quantitation (LOQ) of 25μg/L. Moreover, together with the high affinity of the aptamer for its target, this assay exhibited excellent sensitivity and selectivity. According to its design principle, the as-designed hydrogel was also tested to possess the generic detection function for other molecules by simply replacing its recognition element, which is expected to lay a foundation to realize the assembly of functionalized hierarchical graphene-based materials for practical applications in analytical field.

A novel dinuclear iridium(III) complex as a G-quadruplex-selective probe for the luminescent switch-on detection of transcription factor HIF-1α

A novel dinuclear Ir(III) complex 5 was discovered to be specific to G-quadruplex DNA, and was utilized in a label-free G-quadruplex-based detection platform for transcription factor activity. The principle of this assay was demonstrated by using HIF-1α as a model protein. Moreover, this HIF-1α detection assay exhibited potential use for biological sample analysis.

Label-free electrochemiluminescent detection of transcription factors with hybridization chain reaction amplification

Label-free and efficient ECL strategy for detection of NF-κB based on the HCR signal amplification.

Protein binding-protected DNA three-way junction-mediated rolling circle amplification for sensitive and specific detection of transcription factors

A novel fluorescent strategy for transcription factors assay was developed based on protein binding-protected DNA three-way junction-mediated rolling circle amplification.