Sensitive and Visual Detection of Sequence-Specific DNA-Binding Protein via a Gold Nanoparticle-Based Colorimetric Biosensor

A dual-mode strategy based on β-galactosidase and target-induced DNA polymerase protection for transcription factor detection using colorimetry and a glucose meter

In this work, we report a novel dual-mode method for the highly specific and sensitive detection of transcription factors (TFs) via the integration of Klenow polymerase protection induced by target-specific recognition, cascade-signal amplification using the hybridization chain reaction (HCR) and CRISPR/Cas12a system, and dual-signal transduction mediated by β-galactosidase (β-gal) and two substrates. A dual-mode signal-sensing interface was constructed by immobilizing the oligo DNA probe (P1) tethered β-gal in a 96-well plate. A hairpin H1 with the ability to initiate HCRs was designed to contain the TF binding site. The binding between the TF and H1 protected the H1 from being extended by the Klenow fragment. After thermal denaturation, the reserved H1 launched the HCR and the HCR products activated CRISPR/Cas12a to cleave P1 and reduce the β-gal on the sensing interface, and thus the contents of the TFs and the corresponding signals mediated by the catalysis of β-gal showed a correlation. This work was the first attempt at utilizing β-gal for dual-signal transduction. It is a pioneering study to utilize the HCR-CRISPR/Cas12a system for dual-mode TF sensors. It revealed that DNA polymerase protection through the binding of TF and DNA could be applied as a new pattern to develop TF sensors.

Response of HPRT Gene Fragment Functionalized Gold Nanoparticles to Gamma Ray Irradiation

Radiation-sensitive biomolecules are highly significant for studying biological effects of radiation and developing ionizing radiation detectors based on biomolecules. In this work, we selected hypoxanthine phosphoribosyl transferase gene fragments sensitive to gamma-ray irradiation as a sensing element for radiation detection. The end was modified with thiol groups. The thiol-modified oligonucleotide sequences were coupled to the surface of gold nanoparticles by Au-S covalent bonds. The DNA attached to the surface of gold nanoparticles forms a DNA-AuNPs assembly through base pairing. The assembly was irradiated by gamma rays. And its response to radiation was studied with ultraviolet-visible spectroscopy and surface-enhanced Raman scattering (SERS) spectroscopy techniques. SERS spectroscopy and ultraviolet spectroscopy can detect the response of the DNA-AuNPs assembly to gamma-ray irradiation below 100 and 100 - 250 Gy, respectively. The results indicated that it was feasible to develop a new approach of gamma-ray detectors using biomolecular assemblies of gold nanoparticles.

Determination of the concentration of transcription factor by using exonuclease III-aided amplification and gold nanoparticle mediated fluorescence intensity: A new method for gene transcription related enzyme detection

Herein, we report a new probe for the determination of the concentration of NF-κB p50, one kind of DNA-binding transcription factors (TFs), by using Exonuclease III (Exo III)-aided amplification and gold nanoparticle mediated fluorescence intensity. Since TFs play critical roles in various biological processes, the detection of TFs can provide a lot of useful biological information for studding gene expression regulation related disease. In our system, in the presence of transcription factor, Exo III based amplification reaction was trigged. This enzymatic digestion results in the release of intermediate DNA and ultimately liberating the fluorophore (which, separated from the quencher of AuNP and BHQ2, now fluoresces). The released intermediate DNA then hybridizes with another strand3, whence the cycle starts anew. So, the fluorescence intensity reflects the NF-κB p50 concentration with a detection limit of 1.32 pM. Importantly, this method might be further extended to selectively detect various dsDNA-binding proteins by simply changing the binding-site sequences of strand1/strand2 duplex probes.

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.

Stress Biomarkers in Biological Fluids and Their Point-of-Use Detection

Hormones produced by glands in the endocrine system and neurotransmitters produced by the nervous system control many bodily functions. The concentrations of these molecules in the body are an indication of its state, hence the use of the term biomarker. Excess concentrations of biomarkers, such as cortisol, serotonin, epinephrine, and dopamine, are released by the body in response to a variety of conditions, for example, emotional state (euphoria, stress) and disease. The development of simple, low-cost modalities for point-of-use (PoU) measurements of biomarkers levels in various bodily fluids (blood, urine, sweat, saliva) as opposed to conventional hospital or lab settings is receiving increasing attention. This paper starts with a review of the basic properties of 12 primary stress-induced biomarkers: origin in the body (i.e., if they are produced as hormones, neurotransmitters, or both), chemical composition, molecular weight (small/medium size molecules and polymers, ranging from ∼100 Da to ∼100 kDa), and hydro- or lipophilic nature. Next is presented a detailed review of the published literature regarding the concentration of these biomarkers found in several bodily fluids that can serve as the medium for determination of the condition of the subject: blood, urine, saliva, sweat, and, to a lesser degree, interstitial tissue fluid. The concentration of various biomarkers in most fluids covers a range of 5-6 orders of magnitude, from hundreds of nanograms per milliliter (∼1 μM) down to a few picograms per milliliter (sub-1 pM). Mechanisms and materials for point-of-use biomarker sensors are summarized, and key properties are reviewed. Next, selected methods for detecting these biomarkers are reviewed, including antibody- and aptamer-based colorimetric assays and electrochemical and optical detection. Illustrative examples from the literature are discussed for each key sensor approach. Finally, the review outlines key challenges of the field and provides a look ahead to future prospects.

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.

Determination of hypoxia-inducible factor-1 by using a ratiometric colorimetric test based on click-mediated growth of gold nanoparticles

The authors describe a significantly improved colorimetric nanoprobe for the determination of transcription factors (TFs). It is making use of click-mediated growth of gold nanoparticles (AuNPs) to amplify the signal-to-noise ratio. Hypoxia-inducible factor-1 (HIF-1) is an important TF that acts as a mediator of cell response to hypoxia. So, the detection of HIF-1 was chosen as the model analyte. Specifically, target HIF-1 is designed to bind to the hypoxia response element within DNA duplex. The click chemistry between the DNA duplex and alkynyl-functionalized AuNPs (AF-AuNPs) is then inhibited because of significant steric hindrance. As a result, the AF-AuNPs grow into larger-sized highly-aggregated irregular nanostructures, which in turn enable colorimetric determination. The ratio of absorbances at 620 and 560 nm increases in the 0.5 to 10 nM HIF-1 concentration range, and the detection limit is 0.27 nM. This is better by a factor of 100 than that of aggregation-based colorimetric assays. The nanoprobe is selective and can be used in complex samples. Conceivably, it may also be extended to the determination of other TFs by simply changing the used DNA duplex. Graphical abstract Schematic of a nanoprobe for detecting hypoxia-inducible factor-1 (HIF-1). Three concepts are involved: the binding of HIF-1 and hypoxia response element, the Cu⁺-catalyzed click chemistry between P1/P2 duplex and alkynyl-functionalized AuNPs (AF-AuNPs), and the AuNPs growth with hydroxylamine and HAuCl₄.

Aptamer-Based Lateral Flow Test Strip for Rapid Detection of Zearalenone in Corn Samples

An aptamer-based lateral flow test strip was developed for the detection of zearalenone (ZEN). This assay was based on the competition for the aptamer between ZEN and its complementary sequence. Several experimental conditions that could influence sensitivity have been investigated, including the concentration of aptamer and NaCl used in the probe preparation, the mole ratio of streptavidin and biotinylated DNA used in the preparation of test line and control line, and the loading quantity of gold nanoparticles-aptamer conjugates (AuNPs-Apt). Under the optimal experimental conditions, we successfully detected ZEN within a detection range of 5-200 ng/mL and the visual limit of detection of 20 ng/mL. This aptamer-based strip was successfully applied to the determination of ZEN in spiked corn samples, and the recoveries were from 93.4% to 114.2%. All detections can be achieved within 5 min. The results demonstrated that the developed aptamer-based lateral flow test strip is a potential alternative tool for the rapid and sensitive detection of ZEN.

Aptamer-based Resonance Light Scattering for Sensitive Detection of Acetamiprid

In this work, an aptasensor-based resonance light-scattering (RLS) method was developed for the sensitive and selective detection of acetamiprid. The ABA (acetamiprid binding aptamer)-stabilized gold nanoparticles (ABA-AuNPs) were used as a probe. Highly specific single-strand DNA (ssDNA, i.e, aptamers) that bind to acetamiprid with high affinity were employed to discriminate other pesticides, such as edifenphos, kanamycin, metribuzin et. al. The sensing approach is based on a specific interaction between acetamiprid and ABA. Aggregation of AuNPs was specifically induced by the desorption of the ABA from the surface of AuNPs, which caused the RLS signal intensity to be enhanced at 700 nm. The alteration of AuNPs' aggregation has been successfully optimized by controlling several conditions. Under the optimal conditions, the RLS intensity changes (I/I0) of AuNPs were linearly correlated with the acetamiprid concentration in the range of 0 - 100 nM. The detection limit is 1.2 nM (3σ). This method had also been used for acetamiprid detection in lake water samples.

Probing transcription factor binding activity and downstream gene silencing in living cells with a DNA nanoswitch

Transcription factor DNA binding activity is of pivotal importance in living systems because of its primary involvement in the regulation of genetic machinery. The analysis of transient expression levels of transcription factors in response to a certain cell status is a powerful means for investigating cellular dynamics at the biomolecular level. Herein, a DNA-based molecular switch that enables probing of transcription factor DNA binding activity is directly used in living cells. We demonstrate that the DNA nanoswitch allows for dynamic fluorescence imaging of NF-κB and quantification of downstream gene silencing in real time. The present strategy is based on a functional DNA nanodevice that transduces, through a binding-induced conformational change, the recognition of a specific transcription factor into a fluorescent signal. In addition, stochastic optical resolution microscopy, a super-resolution microscopy technique, is used to track the internalization and intracellular trafficking of the DNA nanodevice with high spatial resolution. Overall, it has been shown that a rationally designed DNA nanodevice can be used to achieve rapid, simple, and cost-effective real-time determination of transcription factor binding activity and downstream gene silencing.

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.

Exploiting pH-Regulated Dimer-Tetramer Transformation of Concanavalin A to Develop Colorimetric Biosensing of Bacteria

Gold nanoparticles (AuNPs) aggregation-based colorimetric biosensing remains a challenge for bacteria due to their large size. Here we propose a novel colorimetric biosensor for rapid detection of Escherichia coli O157:H7 (E. coli O157:H7) in milk samples based on pH-regulated transformation of dimer/tetramer of Concanavalin A (Con A) and the Con A-glycosyl recognition. Briefly, antibody-modified magnetic nanoparticles was used to capture and concentrate E. coli O157:H7 and then to label with Con A; pH adjusted to 5 was then applied to dissociate Con A tetramer to release dimer, which was collected and re-formed tetramer at pH of 7 to cause the aggregation of dextran-modified AuNPs. The interesting pH-dependent conformation-transformation behavior of Con A innovated the design of the release from the bacteria surface and then the reconstruction of Con A. Therefore, we realized the sensitive colorimetric biosensing of bacteria, which are much larger than AuNPs that is generally not suitable for this kind of method. The proposed biosensor exhibited a limit of detection down to 41 CFU/mL, short assay time (~95 min) and satisfactory specificity. The biosensor also worked well for the detection in milk sample, and may provide a universal concept for the design of colorimetric biosensors for bacteria and virus.

Mechanism of adsorption of single and double stranded DNA on gold and silver nanoparticles: Investigating some important parameters in bio-sensing applications

The mechanism of adsorption of single and double stranded DNAs on colloidal gold and silver nanoparticles has been studied by measuring the resistance of the nanoparticles, surrounded by various oligonucleotides, against salt induced aggregation. It is shown that both single and double stranded DNAs can be adsorbed on the metal nanoparticles and the adsorption strength is determined by the interaction between various bases of DNA and the nanoparticles. By changing the salt concentration, the difference between adsorption of various DNA strands on the nanoparticles can be specified. The results indicate that a key parameter in success of a sensing assay of DNA hybridization is the salt concentration which should be greater than a minimum threshold depending on the nanoparticles characteristics. We have also investigated the interaction mechanism between various DNA bases with the metal nanoparticles. For both gold and silver nanoparticles, adenine has the highest and thymine has the lowest attachment to the nanoparticles. From surface enhanced Raman spectroscopy (SERS) data of various bases in the presence of gold nanoparticles, the probable interaction points in the bases with the nanoparticles have been determined, which are mainly the nitrogen sites of these oligonucleotides.

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.

A duplex DNA–gold nanoparticle probe composed as a colorimetric biosensor for sequence-specific DNA-binding proteins

The SPL-12-mediated change of Au aggregation via duplex DNA–SPL-12 interactions could be utilized for colorimetric sensing of SPL-12 using duplex DNA–Au.

Gold nanoparticles as sensitive optical probes

Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.

Recent advances in transcription factor assays in vitro

We review the recent advances in transcription factor assaysin vitroand highlight the emerging trends as well.

DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection

We have developed a unique DNA-assembled gold nanoparticles (AuNPs) dimer for dynamic light scattering (DLS) sensing of transcription factors, exemplified by estrogen receptor (ER) that binds specifically to a double-stranded (ds) DNA sequence containing estrogen response element (ERE). Here, ERE sequence is incorporated into the DNA linkers to bridge the AuNPs dimer for ER binding. Coupled with DLS, this AuNP dimer-based DLS detection system gave distinct readout of a single ‘complex peak’ in the presence of the target molecule (i.e., ER). This unique signature marked the first time that such nanostructures can be used to study transcription factor-DNA interactions, which DLS alone cannot do. This was also unlike previously reported AuNP-DLS assays that gave random and broad distribution of particles size upon target binding. In addition, the ERE-containing AuNP dimers could also suppress the light-scattering signal from the unbound proteins and other interfering factors (e.g., buffer background), and has potential for sensitive detection of target proteins in complex biological samples such as cell lysates. In short, the as-developed AuNP dimer probe coupled with DLS is a simple (mix and test), rapid (readout in ~5 min) and sensitive (low nM levels of ER) platform to detect sequence-specific protein-DNA binding event.

Heat induced aggregation of gold nanorods for rapid visual detection of lysozyme

Gold nanorods have been nominated as propitious candidates for nanobiodiagnostic applications. Herein, a technique has been introduced for rapid visual detection of lysozyme, as its high level of excretion in biological fluids is a characteristic sign of leukemia and kidney disorders. Gold nanorods were biofunctionalized with lysozyme aptamer and characterized with UV-Visible and FTIR spectroscopy, zeta potential analyzer and transmission electron microscopy. Exposure of the nanoprobe to nano molar levels of lysozyme (20 nmol l(-1)) lead to dictated aggregation of the nanostructures at ambient temperature; which was significantly improved by heat induced morphological perturbations and rapid detection by the naked eye (down to pico molar level). Qualitative analysis of Acute myeloid leukemia, Acute lymphocytic leukemia and Lymphoma blood serums showed sensitivity and specificity of the fabricated aptasensor under both temperature conditions. This report encourages utilization of heat-induced aggregation of gold nanorods as a promising nanodiagnostic technique for the emerging nanotechnologies.

Transportation and fate of gold nanoparticles in oilseed rape

In this work, we demonstrate the mild effect of AuNPs on the growth of oilseed rape seedlings and suggest their potential application as vehicles for gene delivery in plants.

Sensitive colorimetric detection of protein by gold nanoparticles and rolling circle amplification

A sensitive and selective colorimetric biosensor for the detection of protein, which combines gold nanoparticles and rolling circle amplification, is described.

A new visible-light-driven photoelectrochemical biosensor for probing DNA–protein interactions

A novel photoelectrochemical approach was achieved for the detection of a DNA binding protein via the protein–DNA interaction.

Trends in protein-based biosensor assemblies for drug screening and pharmaceutical kinetic studies

The selection of natural and chemical compounds for potential applications in new pharmaceutical formulations constitutes a time-consuming procedure in drug screening. To overcome this issue, new devices called biosensors, have already demonstrated their versatility and capacity for routine clinical diagnosis. Designed to perform analytical analysis for the detection of a particular analyte, biosensors based on the coupling of proteins to amperometric and optical devices have shown the appropriate selectivity, sensibility and accuracy. During the last years, the exponential demand for pharmacokinetic studies in the early phases of drug development, along with the need of lower molecular weight detection, have led to new biosensor structure materials with innovative immobilization strategies. The result has been the development of smaller, more reproducible biosensors with lower detection limits, and with a drastic reduction in the required sample volumes. Therefore in order to describe the main achievements in biosensor fields, the present review has the main aim of summarizing the essential strategies used to generate these specific devices, that can provide, under physiological conditions, a credible molecule profile and assess specific pharmacokinetic parameters.

An electrochemical sensing platform based on local repression of electrolyte diffusion for single-step, reagentless, sensitive detection of a sequence-specific DNA-binding protein

In this paper, we report for the first time an electrochemical biosensor for single-step, reagentless, and picomolar detection of a sequence-specific DNA-binding protein using a double-stranded, electrode-bound DNA probe terminally modified with a redox active label close to the electrode surface. This new methodology is based upon local repression of electrolyte diffusion associated with protein-DNA binding that leads to reduction of the electrochemical response of the label. In the proof-of-concept study, the resulting electrochemical biosensor was quantitatively sensitive to the concentrations of the TATA binding protein (TBP, a model analyte) ranging from 40 pM to 25.4 nM with an estimated detection limit of ∼10.6 pM (∼80 to 400-fold improvement on the detection limit over previous electrochemical analytical systems).