Amplified terminal protection assay of small molecule/protein interactions via a highly characteristic solid-state Ag/AgCl process

A Fluorescent Biosensor for Streptavidin Detection Based on Double-Hairpin DNA-Templated Copper Nanoparticles

In this paper, we developed a sensitive, label-free and facile fluorescent strategy for detecting streptavidin (SA) based on double-hairpin DNA-templated copper nanoparticles (CuNPs) and terminal protection of small molecule-linked DNA. Herein, a special DNA hairpin probe was designed and synthesized, which contained two poly T single-stranded loops and a nick point in the middle of the stem. Inspired by the concept of the terminal protection interaction, the specific binding of SA to the biotinylated DNA probe can prevent the exonuclease degradation and keep the integrity of DNA probe, which can be used for synthesizing fluorescent CuNPs as a template. Conversely, the DNA probe would be digested by exonucleases and therefore, would fail to form CuNPs without SA. After systematic optimization, the detection range of SA concentration is from 0.5 to 150 nM with a low detection limit of 0.09 nM. Additionally, the proposed method was also successfully applied in the biological samples. Finally, the proposed method is sensitive, effective and simple, and can be potentially applied for predicting diseases and discovering new drugs.

A simple and sensitive detection of small molecule-protein interactions based on terminal protection-mediated exponential strand displacement amplification

We herein describe a simple and sensitive strategy to detect a small molecule-protein interaction based on terminal protection-mediated exponential strand displacement amplification (eSDA). In principle, the small molecule linked to a DNA probe protects the DNA probe against the exonuclease I-catalyzed degradation after its binding to the corresponding target protein. The protected DNA probe then serves as a template to promote eSDA. Consequently, a large number of duplexes are produced, which leads to a high fluorescence from a double-stranded DNA specific fluorescent dye, SYBR Green I. As a model system to prove this sensing strategy, the interaction between biotin and streptavidin (SA), which is known to be the strongest among the non-covalent biological interactions, was selected and its analytical performance was thoroughly investigated. As a result, SA was sensitively detected with the limit of detection of 16 pM. In addition, the practical applicability of this method was successfully demonstrated by reliably determining the SA in human serum.

A novel bioluminescent detection of exonuclease I activity based on terminal deoxynucleotidyl transferase-mediated pyrophosphate release

Here we report a novel bioluminescence (BL) method for exonuclease I (Exo I) detection based on terminal deoxynucleotidyl transferase (TdT)-mediated pyrophosphate release. An inert hairpin probe with a blocked protruding 3'-terminal biotinylated nucleotide was designed, and a blocked 3'-terminal nucleotide of the probe would be removed only in the presence of Exo I, thus rendering the probe with a free 3'-hydroxyl group. Subsequently, with nucleotide incorporation by TdT, huge amounts of pyrophosphates were generated. After the conversion of pyrophosphate to adenosine triphosphate (ATP) through ATP sulfurylase, BL was emitted by the reaction of d-luciferin and ATP with firefly luciferase. Therefore, Exo I activity was indirectly quantified in the range 1-500 mU with a detection limit of 0.05 mU/μl. Moreover, the developed approach was successfully applied to investigate the inhibitory effect of streptavidin on cleavage of Exo I and also determine Exo I activity in spiked serum samples. Overall, the proposed method has high sensitivity and selectivity, and can be universally extended to the detection of other nucleases using terminal extension as a signal amplification method and BL as a detection signal, having potential application in the diagnosis of nuclease-related diseases or evaluation of nuclease functions in biological systems.

Allosteric kissing complex-based electrochemical biosensor for sensitive, regenerative and versatile detection of proteins

Herein, an allosteric kissing complex-based electrochemical biosensor was ingeniously proposed for the simple, sensitive, regenerative and versatile detection of proteins. Two hairpins (Hp1 and Hp2) were designed and the Hp1 was immobilized on the electrode surface, which could form a kissing complex with Hp2 through the apical loop-loop or kissing interaction of the RNA-RNA base sequences. The Hp2 possesses the appended single-stranded tails on each end, which hybridize with the recognition element-conjugated DNA strands to construct a protein responsive switch of Hp2 scaffold. After kissing complex formation between the Hp2 scaffold and the immobilized Hp1, the streptavidin-labeled alkaline phosphatase (SA-ALP) can be introduced onto the electrode surface for the generation of electrochemical signal. In the presence of target protein, its binding to the recognition elements linked onto the Hp2 scaffold endows the steric strain to open the Hp2 stem, propagated by the disruption of the kissing complex structure, resulting into a decreased electrochemical signal related with the protein quantification. Also, the Hp1 immobilized electrode can be directly regenerated after protein-induced kissing complex dissociation. The current kissing complex-based electrochemical biosensing strategy can be easily extended for the detection toward different protein targets of interest by simply changing the recognition elements conjugated onto the Hp2 scaffold. The sensitive and selective detection toward proteins could be achieved with the detection limits toward Anti-Dig antibody and thrombin of about 1ng/mL and 10pM, respectively. The developed kissing complex-based protein biosensing strategy should be a beneficial supplement in current biosensor field, providing a promising means for the applications in bioanalysis, disease diagnostics, and clinical biomedicine.

A novel steric effect-regulated isothermal exponential amplification technology for the one-step homogeneous sensing of proteins

A novel approach utilizing the steric effect and isothermal exponential amplification for one-step homogeneous sensing of proteins.

Revealing and Resolving the Restrained Enzymatic Cleavage of DNA Self-Assembled Monolayers on Gold: Electrochemical Quantitation and ESI-MS Confirmation

Herein, we report a combined electrochemical and ESI-MS study of the enzymatic hydrolysis efficiency of DNA self-assembled monolayers (SAMs) on gold, platform systems for understanding nucleic acid surface chemistry, and for constructing DNA-based biosensors. Our electrochemical approach is based on the comparison of the amounts of surface-tethered DNA nucleotides before and after exonuclease I (Exo I) incubation using electrostatically bound [Ru(NH₃)₆]³⁺ as redox indicators. It is surprising to reveal that the hydrolysis efficiency of ssDNA SAMs does not depend on the packing density and base sequence, and that the cleavage ends with surface-bound shorter strands (9-13 mers). The ex-situ ESI-MS observations confirmed that the hydrolysis products for ssDNA SAMs (from 24 to 56 mers) are dominated with 10-15 mer fragments, in contrast to the complete digestion in solution. Such surface-restrained hydrolysis behavior is due to the steric hindrance of the underneath electrode to the Exo I/DNA binding, which is essential for the occurrence of Exo I-catalyzed processive cleavage. More importantly, we have shown that the hydrolysis efficiency of ssDNA SAMs can be remarkably improved by adopting long alkyl linkers (locating DNA strands further away from the substrates).

The analysis of proteins and small molecules based on sterically tunable nucleic acid hyperbranched rolling circle amplification

In this work, we succeeded in establishing a new method for proteins and small molecules analysis based on the small molecule-linked DNA and nucleic acid hyperbranched rolling circle amplification (HRCA). Small molecule linked DNA by chemical modification was used as a flexible tool to study protein-small molecule interactions. The HRCA reaction which would produce signal amplification was regulated by the steric effect depending on whether the target proteins were present. In the implement of the proposed strategy, streptavidin (SA)-biotin and anti-digoxin antibody (anti-Dig)-digoxin were chosen as two model partners. Experimental results showed that the quantitative detection of SA and anti-Dig was realized both with nanomolar detection limits. The small molecules biotin and digoxin were also detected at nanomolar levels in a wide range of 1nM~100µM and 1nM~10µM, respectively. Meanwhile, the results indicated that the method had a favorable specificity in analyzing proteins or small molecules. Thus, it may be expected to quantitatively analyze some protein markers and small molecular drugs in complex biological samples.

A dual-signal strategy for the solid detection of both small molecules and proteins based on magnetic separation and highly fluorescent copper nanoclusters

Recently, a variety of analytical methods for the detection of small molecules or proteins based on small molecule-protein interaction have been developed. However, these methods often focus on either small molecules or proteins. Few efforts are made to detect both of them in the same system. In this work, a dual-signal strategy for the solid detection of both small molecules and proteins based on small molecule-protein interaction is proposed by using the streptavidin-biotin couple as a model. In our strategy, magnetic nanoparticles (MNPs) are adopted for target separation, and highly fluorescent copper nanoclusters (CuNCs) are synthesized in situ to give signals. In the absence of the targets, CuNCs are associated with the MNPs and present in the precipitate under magnetic field; whereas in the presence of either streptavidin or biotin, the CuNCs will present in the supernate. By monitoring the fluorescent intensity of each, dual-signal can be obtained for the solid detection of either the protein or the small molecule. Results show that sensitive and specific detection of both streptavidin (detection limit: 0.47nM) and biotin (detection limit: 3.1nM) can be achieved. This method can be extended for the detection of other small molecule-protein couples, and thereby has the potential for biomedical and clinical applications.

A one-pot strategy for the detection of proteins based on sterically and allosterically tunable hybridization chain reaction

In this work, we report a facile one-pot strategy for protein detection based on sterically and allosterically tunable hybridization chain reaction (HCR). In our strategy, DNA hairpins H1 and H2 are dual-labeled with pyrene moieties through a six-carbon-atom spacer at each end; and a single-stranded DNA primer is designed to contain two small molecules near each end. In the absence of target protein, the primer can trigger HCR events between alternating H1 and H2 hairpins to form a nicked double-helix. As a result, the pyrene excimers are formed to emit at approximately 485nm. On the contrary, upon binding of the specific target protein onto the primer through the protein-small molecule interaction, the HCR will be inhibited due to the steric and allosteric effect. The changes of the fluorescent signals of pyrene excimers are in response to the concentration of target protein, so that the detection of protein can be realized. We have demonstrated the feasibility of this strategy by using streptavidin (SA) and folate receptor (FR) as model targets. Results show that both of them can be well detected with a detection limit of 1.07nM and 2.7nM, respectively. The developed method for protein assay is flexible, so we infer that the one-pot strategy holds great potential for the detection of other proteins.

Studies on the binding of pepsin with three pyrethroid insecticides by multi-spectroscopic approaches and molecular docking

In this study, the molecular interactions between pepsin and three pyrethroid insecticides, including fenvalerate, cyhalothrin and deltamethrin, were investigated by multi-spectroscopic and molecular docking methods under mimic physiological pH conditions. The results indicated that all of these insecticides could interact with pepsin to form insecticide-pepsin complexes. The binding constants, number of binding sites and thermodynamic parameters measured at different temperatures indicated that these three pyrethroid insecticides could spontaneously bind with pepsin mainly through electrostatic forces and hydrophobic interactions with one binding site. According to the theory of Föster's non-radioactive energy transfer, the distance (r) between pepsin and three pyrethroid insecticides were all found to be less than 7 nm, which implied that the energy transfer occurred between pepsin and these insecticides, leading to the quenching of pepsin fluorescence. Synchronous and three-dimensional fluorescence, CD spectra and molecular docking results indicated that all tested pyrethroid insecticides bound directly into the enzyme cavity site and the binding of insecticides into the cavity influenced the microenvironment of the pepsin activity site which resulted in the extension of peptide strands of pepsin with loss of α-helix structures.Copyright © 2016 John Wiley & Sons, Ltd.

A WS2 nanosheet-based nanosensor for the ultrasensitive detection of small molecule–protein interaction via terminal protection of small molecule-linked DNA and Nt.BstNBI-assisted recycling amplification

A novel, ultrasensitive and specific fluorescent nanosensor for the detection of small molecule–protein interaction based on the terminal protection of small molecule-linked DNA and Nt.BstNBI-assisted recycling amplification was reported.

High performance system for protein assays: synergistic effect of terminal protection strategy and graphene oxide platform

A straightforward biosensor for protein assay has been developed based on terminal protection of small molecule-linked DNA by target protein and the difference in affinity of graphene oxide for ssDNA containing different numbers of bases in length.

Terminal protection of small molecule-linked ssDNA for label-free and highly sensitive colorimetric detection of folate receptor biomarkers

Protection of ssDNA from digesting by Exo I generates amplified color transition for label-free and sensitive detection of folate receptors.

Study on the interaction of catalase with pesticides by flow injection chemiluminescence and molecular docking

The interaction mechanisms of catalase (CAT) with pesticides (including organophosphates: disulfoton, isofenphos-methyl, malathion, isocarbophos, dimethoate, dipterex, methamidophos and acephate; carbamates: carbaryl and methomyl; pyrethroids: fenvalerate and deltamethrin) were first investigated by flow injection (FI) chemiluminescence (CL) analysis and molecular docking. By homemade FI-CL model of lg[(I0-I)/I]=lgK+nlg[D], it was found that the binding processes of pesticides to CAT were spontaneous with the apparent binding constants K of 10(3)-10(5) L mol(-1) and the numbers of binding sites about 1.0. The binding abilities of pesticides to CAT followed the order: fenvalerate>deltamethrin>disulfoton>isofenphos-methyl>carbaryl>malathion>isocarbophos>dimethoate>dipterex>acephate>methomyl>methamidophos, which was generally similar to the order of determination sensitivity of pesticides. The thermodynamic parameters revealed that CAT bound with hydrophobic pesticides by hydrophobic interaction force, and with hydrophilic pesticides by hydrogen bond and van der Waals force. The pesticides to CAT molecular docking study showed that pesticides could enter into the cavity locating among the four subdomains of CAT, giving the specific amino acid residues and hydrogen bonds involved in CAT-pesticides interaction. It was also found that the lgK values of pesticides to CAT increased regularly with increasing lgP, Mr, MR and MV, suggesting that the hydrophobicity and steric property of pesticide played essential roles in its binding to CAT.

Terminal protection of small molecule-linked DNA for small molecule-protein interaction assays

Methods for the detection of specific interactions between diverse proteins and various small-molecule ligands are of significant importance in understanding the mechanisms of many critical physiological processes of organisms. The techniques also represent a major avenue to drug screening, molecular diagnostics, and public safety monitoring. Terminal protection assay of small molecule-linked DNA is a demonstrated novel methodology which has exhibited great potential for the development of simple, sensitive, specific and high-throughput methods for the detection of small molecule–protein interactions. Herein, we review the basic principle of terminal protection assay, the development of associated methods, and the signal amplification strategies adopted for performance improving in small molecule–protein interaction assay.

Ultrasensitive detection of small molecule-protein interaction via terminal protection of small molecule linked DNA and Exo III-aided DNA recycling amplification

Terminal protection of small molecule linked DNA assays amplified by Exo III-aided DNA recycling is developed for the detection of streptavidin-biotin interaction, with a detection limit of 0.8 fM streptavidin in the "turn-on" state, indicating that the proposed method is an ultrasensitive platform for the detection of small molecule-protein interactions.