Universal platform for sensitive and label-free nuclease assay based on conjugated polymer and DNA/intercalating dye complex

A lysosome-targeted near-infrared fluorescent probe for imaging of acid phosphatase in living cells

Fluorescent probes for the detection of acid phosphatases (ACP) are important in the investigation of the pathology and diagnosis of diseases. We reported a lysosome-targeted near-infrared (NIR) fluorescent probe SHCy-P based on a novel NIR-emitting thioxanthene-indolium dye for the detection of ACP. The probe showed a long wavelength fluorescence emission at λ_em = 765 nm. Due to the ACP-catalyzed cleavage of the phosphate group in SHCy-P, the probe exhibited high selectivity and sensitivity for the 'turn-on' detection of ACP with a limit of detection as low as 0.48 U L^-1. The probe SHCy-P could also be used to detect and image endogenous ACP in lysosomes. In light of these prominent properties, we envision that SHCy-P will be an efficient optical imaging approach for investigating the ACP activity in disease diagnosis.

A label-free protamine-assisted colorimetric sensor for highly sensitive detection of S1 nuclease activity

A label-free, simple and rapid colorimetric method for the sensitive detection of S1 nuclease activity based on protamine-assisted aggregation of gold nanoparticles.

Sensitive monitoring of RNA transcription by optical amplification of cationic conjugated polymers

We reported a new strategy for sensitive monitoring in vitro RNA synthesis in real time based on fluorescence resonance energy transfer (FRET) from water-soluble conjugated polymer poly (9, 9-bis (6'-N, N, N,-trimethylammonium) hexyl) fluorene-co-alt-1,4-phenylene) bromide (PFP) to fluorogenic RNA aptamer/fluorophore (Spanich2/DFHBI and Broccoli/DFHBI) system. In this strategy, RNA of interest was transcribed accompanied by the Spanich2 or Broccoli. Then the 3, 5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) bound to the RNA aptamer sequence and thereby induced a fluorescence signal. PFP was used as the fluorescence energy donor, and Spanich2/DFHBI was the fluorescence energy acceptor. The fluorescence signal of Spanich2/DFHBI was amplified by light-harvesting and fluorescence amplification ability of PFP via FRET. And the limit of detection (LOD) (0.29 nM) was near 10-fold lower than that of RNA aptamer/DFHBI (LOD is 2.8 nM) alone by measuring the FRET ratio, which greatly reduced the variation of background signals. Most importantly, the addition of PFP did not interfere with RNA transcription in vitro, so this method was successfully applied to sensitively monitor RNA transcription and effect of T7 RNA polymerase inhibitor in real time, supplying a sensitive and simple method to study the modulation and inhibitor of RNA polymerase in vitro.

Fluorescent S1 nuclease assay utilizing exponential strand displacement amplification

We devise a simple, label-free S1 nuclease activity assay by exploiting target-induced inhibition of exponential strand displacement amplification (eSDA).

Coupling coumarin to gold nanoparticles by DNA chains for sensitive detection of DNase I

A kind of coumarin-modified gold nanoparticle by the bridge of dsDNA chains was designed and synthesized for sensitive detection of DNase I. The fluorescence of coumarin 343 at emission wavelengths of 491 nm excited at 440 nm was quenched by the gold nanoparticles due to the energy transfer process after the coumarin 343 was connected on the gold nanoparticles by DNA chains. When dsDNA chains were cut off by DNase I, the coumarin 343 molecules were released from gold nanoparticles and the fluorescence of coumarin 343 would be restored. The DNase I activity could be detected by this fluorescence assay with a high sensitivity based on the change of the energy transfer efficiency. The intensity of restored fluorescence is linearly related to the quantity of DNase I in the range from 1.0 to 40 mU/mL with a detection limit of 0.22 mU/mL. This design idea could render a useful way to develop similar molecular or enzyme sensor in analytical or biological fields.

A Target-Lighted dsDNA-Indicator for High-Performance Monitoring of Mercury Pollution and Its Antagonists Screening

As well-known, the excessive discharge of heavy-metal mercury not only destroys the ecological environment, bust also leads to severe damage of human health after ingestion via drinking and bioaccumulation of food chains, and mercury ion (Hg²⁺) is designated as one of most prevalent toxic metal ions in drinking water. Thus, the high-performance monitoring of mercury pollution is necessary. Functional nucleic acids have been widely used as recognition probes in biochemical sensing. In this work, a carbazole derivative, ethyl-4-[3,6-bis(1-methyl-4-vinylpyridium iodine)-9H-carbazol -9-yl)] butanoate (EBCB), has been synthesized and found as a target-lighted DNA fluorescent indicator. As a proof-of-concept, Hg²⁺ detection was carried out based on EBCB and Hg²⁺-mediated conformation transformation of a designed DNA probe. By comparison with conventional nucleic acid indicators, EBCB held excellent advantages, such as minimal background interference and maximal sensitivity. Outstanding detection capabilities were displayed, especially including simple operation (add-and-read manner), ultrarapidity (30 s), and low detection limit (0.82 nM). Furthermore, based on these advantages, the potential for high-performance screening of mercury antagonists was also demonstrated by the fluorescence change of EBCB. Therefore, we believe that this work is meaningful in pollution monitoring, environment restoration and emergency treatment, and may pave a way to apply EBCB as an ideal signal transducer for development of high-performance sensing strategies.

Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator

As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.

Sensitive and versatile fluorescent enzymatic assay of nucleases and DNA methyltransferase based on a supercharged fluorescent protein

The ScGFP-based platform takes advantage of the DNA length-dependent binding affinity between ScGFP and DNA for multiple DNA enzyme detection including nucleases and DNA MTase.

Thioflavin T as an Efficient G-Quadruplex Inducer for the Highly Sensitive Detection of Thrombin Using a New Föster Resonance Energy Transfer System

We report a new Föster resonance energy transfer (FRET) system that uses a special dye, thioflavin T (ThT), as an energy acceptor and a water-soluble conjugated polymer (CP) with high fluorescence as an energy donor. A simple, label-free, and sensitive strategy for the detection of thrombin in buffer and in diluted serum was designed based on this new system using ThT as an efficient inducer of the G-quadruplex. The difference between the blank and the positive samples was amplified due to distinctive FRET signals because thrombin has little effect on the intercalation of ThT into the G-quadruplex. In the absence of the target, ThT induces the aptamer to form a G-quadruplex and intercalates into it with strong fluorescence. The electrostatic attractions between the negatively charged G-quadruplex and positively charged CP allow a short donor-acceptor distance, resulting in a high FRET signal. However, in the presence of the target, the aptamer forms a G-quadruplex-thrombin complex first, followed by the intercalation of ThT into the G-quadruplex. A long distance exists between the donor and acceptor due to the strong steric hindrance from the large-sized thrombin, which leads to a low FRET signal. Compared with previously reported strategies based on the FRET between the CP and dye, our strategy is label-free, and the sensitivity was improved by an order of magnitude. Our strategy also shows the advantages of being simple, rapid (about 50 min), sensitive, label-free, and low-cost in comparison to strategies based on the FRET between quantum dots and dyes.

Plasmon coupling-enhanced two-photon photoluminescence of Au@Ag core-shell nanoparticles and applications in the nuclease assay

Au and Ag nanoparticles (NPs) have been known to display significantly enhanced two-photon photoluminescence (2PPL) upon the formation of nanoparticle aggregates. The enhancement effect of the core-shell nanoparticles has not been explored so far. Here we have prepared Au@Ag bimetallic core-shell nanoparticles with different thicknesses (1.1, 2.1, 3.5, 4.5, and 5.5 nm) of silver coating on 19 nm Au NPs to investigate the composition effects on plasmon coupling-enhanced 2PPL. A maximum 2PPL enhancement factor (IcoupledNPs/IisolatedNPs) of up to 840-fold was obtained for Au@Ag NPs with ∼3.5 nm Ag nanoshells. These Au@Ag NPs were subsequently utilized in two-photon detection of S1 nuclease as a photoluminescence turn on probe. This method displayed high sensitivity with the limit of detection of 1.4 × 10(-6) U μL(-1) and an excellent selectivity.

Superior fluorescent probe for detection of potassium ion

Here, a simple, and highly sensitive fluorescent assay is designed to monitor K(+). The versatile, robust biosensing strategy is based on the specific recognition utility of label-free aptamers with their targets and PicoGreen dye as the signal probe. The aptamers undergo a conformational change to a secondary structure such as G-quadruplex in the presence of targets. In addition to a conformational change with its targets, the remaining single-stranded DNA (ssDNA) aptamer form a duplex structure with its complete complementary sequence. Conformational changes of aptamers as well as fluorescence amplification produce clear signal-off in the presence of targets. Fluorescent assay employing this mechanism for the detection of K(+) is highly sensitive, and selective. The detection limit of the K(+) assay is determined to be 2.37 pM. The sensing strategy is low-cost and simple in its operation without requirement for complex labeling of probe DNA or sophisticated synthesis of the fluorescent compound. Also, the method has less structural requirement of complexes of aptamers with their targets, thus rending its wilder applications for various targets.

A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity

A G-triplex luminescent switch-on probe for the detection of nuclease activity.

Ca2+-controlled assembly for visualized detection of conformation changes of calmodulin

A new strategy has been designed for visualized detection of the conformation changes of calmodulin bound to target peptide (CaM-M13) based on the conformation sensitive property of a water-soluble conjugated polythiophene derivative (PMNT) and the electrostatic interactions of PMNT/CaM-M13. Interestingly, the direct visualized PMNT color changes under UV irradiation and the turbidity changes of samples in aqueous medium can be applied to detect the conformation changes as well as the controllable assembly of PMNT/CaM-M13 with Ca(2+) in aqueous medium. Because of the specific binding of Ca(2+), the assembly of PMNT/CaM-M13 can be applied to sense calcium as well.

A new label-free and turn-on strategy for endonuclease detection using a DNA-silver nanocluster probe

Endonuclease plays a vital role in a variety of biological processes and the assay of endonuclease activity and inhibitors is of high importance in the fields ranging from biotechnology to pharmacology. Howerer, traditional techniques usually suffer from time intensive, laborious, and cost-expensive. This work aims to develop a facile and sensitive method for endonuclease activity assay by making use of the fluorescence enhancement effect when DNA-silver nanoclusters (DNA-Ag NCs) are in proximity to guanine-rich DNA sequences. The system mainly consists of block DNA (B-DNA), G-DNA and Ag-DNA. B-DNA serves as the substrate of the endonuclease (S1 nuclease as the model enzyme). G-DNA, which is predesigned entirely complementary to B strand, contains a guanine-rich overhang sequence and hybridization part at the 5'-end. Ag-DNA involves a sequence for Ag NCs synthesis and a sequence complementary to the hybridization part of the G-DNA. In the "off" state, B-DNA plays the role as a blocker that inhibit the proximity between Ag NCs and guanine-rich DNA sequences, resulting in a low fluorescence readout. However, if S1 nuclease is introduced into the system, B-DNA was cleaved into mono- or short-oligonucleotides fragments, which could not hybridize with G-DNA. As a result, the subsequent addition of DNA-Ag NCs could bring guanine-rich DNA sequences close to the Ag NCs, accompanied by a significant fluorescence enhancement. Therefore, endonuclease activity could be successfully quantified by monitoring the variation in fluorescence intensity. In addition, this approach can also be applied for inhibitor screening of endonuclease. This label-free and turn-on fluorescent assays employing the mechanism proposed here for the detection of nuclease and inhibitors turn out to be sensitive, selective, and convenient.

Streptavidin sensor and its sensing mechanism based on water-soluble fluorescence conjugated polymer

Fluorescence quenching effect of water-soluble anionic conjugated polymer (CP) (poly[5-methoxy-2-(3-sulfopoxy)-1,4-phenylenevinylene] (MPS-PPV)) by [Re(N-N)(CO)3(py-CH2-NH-biotin)](PF6) [N-N=2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline; py-CH2-NH-biotin=N-[(4-pyridyl) methyl] biotinamide] (Re-Biotin) and fluorescence recovery in the presence of streptavidin (or avidin) were investigated using Re-Biotin as quencher tether ligand (QTL) probe. Meanwhile, the mechanisms of fluorescence quenching and recovery were discussed to provide new thoughts to design biosensor based on water-soluble CPs. The results indicate that the sensing mechanisms of streptavidin sensor or avidin sensor, using Re-Biotin as QTL probe, are the same and stable, whether in non-buffer system (aqueous solution) or different buffer systems [0.01 mol·L(-1) phosphate buffered solution (pH=7.4), 0.1 mol·L(-1) ammonium carbonate buffered solution (pH=8.9)]. There exists specific interactions between streptavidin (or avidin) and biotin of Re-Biotin. Fluorescence quenching and recovery processes of MPS-PPV are reversible. Mechanisms of Re-Biotin quenching MPS-PPV fluorescence can be interpreted as strong electrostatic interactions and charge transferences between Re-Biotin and MPS-PPV. Fluorescence recovery mechanisms of Re-Biotin-MPS-PPV system can be interpreted as specific interactions between streptavidin (or avidin) and biotin of Re-Biotin making Re-Biotin far away from MPS-PPV. Avidin or strptavidin as re-Biotin probe can not only be quantitatively determinated, but also be identified.

An ultrasensitive fluorometric platform for S1 nuclease assay based on cytochrome c

An ultrasensitive and straightforward fluorescent sensing platform for S1 nuclease activity has been developed based on cytochrome c.

Interaction of single-stranded DNA with graphene oxide: fluorescence study and its application for S1 nuclease detection

The mechanism for short ssDNA having weaker affinity to graphene oxide than long ssDNA was systematically investigated.

Poly(thymine)-templated fluorescent copper nanoparticles for ultrasensitive label-free nuclease assay and its inhibitors screening

Noble-metal fluorescent nanoparticles have attracted considerable interest on account of their excellent properties and potential applicable importance in many fields. Particularly, we recently found that poly(thymine) (poly T) could template the formation of fluorescent copper nanoparticles (CuNPs), offering admirable potential as novel functional biochemical probes. However, exploration of poly T-templated CuNPs for application is still at a very early stage. We report herein for the first example to develop a novel ultrasensitive label-free method for the nuclease (S1 nuclease as a model system) assay, and its inhibitors screening using the poly T-templated fluorescent CuNPs. In this assay, the signal reporter of poly T of 30 mer (T30) kept the original long state in the absence of nuclease, which could effectively template the formation of fluorescent CuNPs. In the presence of nuclease, poly T was digested to mono- or oligonucleotide fragments with decrease of fluorescence. The proposed method was low-cost and simple in its operation without requirement for complex labeling of probe DNA or sophisticated synthesis of the fluorescent compound. The assay process was very rapid with only 5 min for the formation of fluorescent CuNPs. The capabilities for target detection from complex fluids and screening of nuclease inhibitors were verified. A high sensitivity exhibited with a detectable minimum concentration of 5 × 10(-7) units μL(-1) S1 nuclease, which was about 1-4 orders of magnitude more sensitive than the developed approaches.

Assaying multiple restriction endonucleases functionalities and inhibitions on DNA microarray with multifunctional gold nanoparticle probes

Herein, a double-stranded (ds) DNA microarray-based resonance light scattering (RLS) assay with multifunctional gold nanoparticle (GNP) probes has been developed for studying restriction endonuclease functionality and inhibition. Because of decreasing significantly melting temperature, the enzyme-cleaved dsDNAs easily unwind to form single-stranded (ss) DNAs. The ssDNAs are hybridized with multiplex complementary ssDNAs functionalized GNP probes followed by silver enhancement and RLS detection. Three restriction endonucleases (EcoRI, BamHI and EcoRV) and three potential inhibitors (doxorubicin hydrochloride (DOX), ethidium bromide (EB) and an EcoRI-derived helical peptide (α4)) were selected to demonstrate capability of the assay. Enzyme activities of restriction endonucleases are detected simultaneously with high specificity down to the limits of 2.0 × 10(-2)U/mL for EcoRI, 1.1 × 10(-2)U/mL for BamHI and 1.6 × 10(-2)U/mL for EcoRV, respectively. More importantly, the inhibitory potencies of three inhibitors are showed quantitatively, indicating that our approach has great promise for high-throughput screening of restriction endonuclease inhibitors.

Selective fluorogenic chemosensors for distinct classes of nucleases

NUCLEASE SENSOR TRIO: Fluorogenic DNA sensors were developed for distinct classes of nucleases: 3'-exonucleases, 5'-exonucleases, and endonucleases. The highly selective sensors, built from very small modified DNA oligomers containing the unnatural fluorescent base pyrene, and employing thymine as a quencher, were found to function in a variety of complex biological media.

An ultra-high sensitive platform for fluorescence detection of micrococcal nuclease based on graphene oxide

Micrococcal nuclease (MNase) is the extracellular nuclease of Staphylococcus aureus (S. aureus). It preferentially digests single-stranded nucleic acids. The existence of MNase can be the standard to identify S. aureus and the content of MNase can be used to evaluate the pathogenicity of S. aureus. Herein, an ultra-high sensitive and selective fluorescent sensing platform for MNase is developed based on MNase-induced DNA strand scission and the difference in affinity of graphene oxide (GO) for single-stranded DNA containing different numbers of bases in length. In the absence of MNase, the adsorption of the dye-labeled ssDNA on GO makes the dyes close proximity to GO surface resulting in high efficiency quenching of fluorescence of the dyes. Conversely, and very importantly, in the presence of MNase, it cleaves the dye-labeled ssDNA into small fragments. The introduction of GO into the sensing solution results in weak quenching of the fluorescence of the dyes due to the weak affinity of the short dye-labeled oligonuleotide fragment to GO, and the fluorescence intensity gradually increases with increasing concentration of MNase. MNase can be detected in a range of 8×10⁻⁵ to 1.6×10⁻³ unit/mL with a detection limit of 2.7×10⁻⁵ unit/mL and good selectivity. The detection limit is of two orders of magnitude lower than those reported fluorescence MNase assays. Moreover, when the GO-based biosensor is used in S. aureus sample assays, preeminent fluorescence signals are obtained, thus the platform of the GO-based biosensor can be used to detect MNase in real-world samples.

Continuous and sensitive acid phosphatase assay based on a conjugated polyelectrolyte

We report a novel continuous and sensitive fluorescence turn-on assay for ACPs, which consists of a cationic conjugated polyelectrolyte (PPE4+) and a commonly used phosphatase substrate p-nitrophenyl phosphate (pNPP). The kinetics of the ACP catalyzed hydrolysis of the substrate pNPP was monitored by the fluorescence change of PPE4+ and corresponding kinetic parameters were derived to be consistent with the literature reports. The applications of PPE4+/pNPP-based ACP assay in high-throughput screening of ACP inhibitors and detection of prostatic acid phosphotase (PAP) in vitro were demonstrated.

Label-free fluorescent assay for real-time monitoring site-specific DNA cleavage by EcoRI endonuclease

DNA cleavage reaction catalyzed by nucleases is essential in many important biological processes and medicinal chemistry. Therefore, it is important to develop reliable and facile methods to assay nuclease activity. With this goal in mind, we report a fluorescent assay for label-free, facile, and real-time monitoring of DNA cleavage by EcoRI endonuclease using SYBR Green I (SGI) as a signal probe. The fluorescence of SGI dramatically increased when the free SGI was mixed with double-stranded DNA (dsDNA) substrate. Upon interacting with EcoRI, which cleaves the dsDNA into small fragments, the weakened interaction between SGI and the shortened DNA fragments caused a decrease in fluorescence of SGI. EcoRI-DNA interaction was real-time studied by monitoring fluorescence change with the prolonging of interaction time. The important kinetic parameters, including Michaelis-Menten constant (K(M)) and maximum initial velocity (V(max)), were accurately calculated, which is consistent with previously reported studies. Site-specific DNA cleavage by EcoRI endonuclease has also been verified by gel electrophoresis analysis, which indicated that this method is a simple and effective approach to assay DNA cleavage reaction. Specificity investigation demonstrated that EcoRI-DNA interactions can be studied with high selectivity. Compared with previously reported methods, this approach is selective, simple, convenient and cost-efficient without any labeling of the probe or of the target.

Naked-eye sensitive detection of nuclease activity using positively-charged gold nanoparticles as colorimetric probes

Positively-charged gold nanoparticles can effectively differentiate long DNA and fragmented DNA, thus providing a simple and visual approach to colorimetric detection of nuclease activity.

An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices

In a traditional sandwich assay, a DNA target hybridizes to a single copy of the signal probe. Here we employ a modified signal probe containing a methylene blue (a redox moiety) label and a "sticky end." When a DNA target hybridizes this signal probe, the sticky end remains free to hybridize another target leading to the creation of a supersandwich structure containing multiple labels. This leads to large signal amplification upon monitoring by voltammetry.