Terminal Protection of Small Molecule-Linked DNA: A Versatile Biosensor Platform for Protein Binding and Gene Typing Assay

A versatile CRISPR/Cas12a-based biosensing platform coupled with a target-protected transcription strategy

Besides the critical role in gene editing, CRISPR/Cas system also brings a new signal amplification mechanism to the development of next generation biosensing technologies. Herein, we have developed a versatile CRISPR/Cas12a sensing platform by combining a target protection-based transcription amplification strategy with the Cas12a-based signal amplification mechanism, which allows for the sensitive detection of both nucleic acid and non-nucleic acid targets. In this design, a rationally designed transcription template sequence is able to avoid Exonuclease I (Exo I) degradation only in the existence of the target-mediated binding events including either nucleic acid hybridization or protein-based affinity interactions. This target binding-induced protection effect can facilitate the subsequent transcription amplification to generate crRNA and activate the subsequent Cas12a trans-cleavage signal amplification mechanism to yield target dosage-responsive fluorescence signal. In contrast, if the target is absent, the protection-free transcription template will be completely digested by Exo I, thus no fluorescence response is produced. This new strategy well eliminates the T7 polymerase-associated non-specific transcription background and realizes the sensitive detection of various kinds of biomolecules including microRNA, protein, as well as exosome, broadening the application scenarios of CRISPR/Cas system in the field of bioanalysis and biosensing.

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

Label-free fluorescence detection of protein–ligand interactions based on binding-induced enzymatic cleavage protection

Label-free fluorescence monitoring protein–ligand interaction based on binding induced enzymatic cleavage protection.

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.

Small molecule-protein interactions in branch migration thermodynamics: modelling and application in the homogeneous detection of proteins and small molecules

We have disclosed the unique inhibition effect of small molecule-protein interactions toward the DNA branch migration process and constructed a complete thermodynamic model for it. The disclosed effect was further coupled with the steric hindrance effect to establish a homogeneous assay for proteins and small molecules with ultra-high inhibition factors and sensitivity.

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.

Colorimetric detection of protein via the terminal protection of small-molecule-linked DNA and unmodified gold nanoparticles

A novel colorimetric strategy for protein detection was developed based on unmodified gold nanoparticles (AuNPs) and terminal protection from a target protein.

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.

A TiS2 nanosheet enhanced fluorescence polarization biosensor for ultra-sensitive detection of biomolecules

Development of new strategies for the sensitive and selective detection of ultra-low concentrations of specific cancer markers is of great importance for assessing cancer therapeutics due to its crucial role in early clinical diagnoses and biomedical applications. In this work, we have developed two types of fluorescence polarization (FP) amplification assay strategies for the detection of biomolecules by using TiS2 as a FP enhancer and Zn(2+)-dependent self-hydrolyzing deoxyribozymes as catalysts to realize enzyme-catalyzed target-recycling signal amplification. One approach is based on the terminal protection of small-molecule-linked DNA, in which biomolecular binding to small molecules in DNA-small-molecule chimeras can protect the conjugated DNA from degradation by exonuclease I (Exo I); the other approach is based on the terminal protection of biomolecular bound aptamer DNA, in which biomolecules directly bound to the single strand aptamer DNA can protect the ssDNA from degradation by Exo I. We select folate receptor (FR) and thrombin (Tb) as model analytes to verify the current concept. It is shown that under optimized conditions, our strategies exhibit high sensitivity and selectivity for the quantification of FR and Tb with low detection limits (0.003 ng mL(-1) and 0.01 pM, respectively). Additionally, this strategy is a simple "mix and detect" approach, and does not require any separation steps. This biosensor is also utilized in the analysis of real biological samples, the results agree well with those obtained by the enzyme-linked immunosorbent assay (ELISA).

Target-protecting dumbbell molecular probe against exonucleases digestion for sensitive detection of ATP and streptavidin

In this work, a versatile dumbbell molecular (DM) probe was designed and employed in the sensitively homogeneous bioassay. In the presence of target molecule, the DM probe was protected from the digestion of exonucleases. Subsequently, the protected DM probe specifically bound to the intercalation dye and resulted in obvious fluorescence signal which was used to determine the target molecule in return. This design allows specific and versatile detection of diverse targets with easy operation and no sophisticated fluorescence labeling. Integrating the idea of target-protecting DM probe with adenosine triphosphate (ATP) involved ligation reaction, the DM probe with 5'-end phosphorylation was successfully constructed for ATP detection, and the limitation of detection was found to be 4.8 pM. Thanks to its excellent selectivity and sensitivity, this sensing strategy was used to detect ATP spiked in human serum as well as cellular ATP. Moreover, the proposed strategy was also applied in the visual detection of ATP in droplet-based microfluidic platform with satisfactory results. Similarly, combining the principle of target-protecting DM probe with streptavidin (SA)-biotin interaction, the DM probe with 3'-end biotinylation was developed for selective and sensitive SA determination, which demonstrated the robustness and versatility of this design.

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.

Endonuclease IV cleaves apurinic/apyrimidinic sites in single-stranded DNA and its application for biosensing

The cleaving capability of endonuclease IV to apurinic/apyrimidinic sites in single-stranded DNA has been demonstrated. It was further applied to construct a novel dual signal amplified sensing system for highly sensitive enzyme and protein detection.

Novel selection methods for DNA-encoded chemical libraries

Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.

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.

Fluorescence amplification detection via terminal protection of small molecule–protein interactions

A novel fluorescence assay was developed for detecting small molecule–protein interactions on the basis of terminal protection.

Programmable Mg2+-dependent DNAzyme switch by the catalytic hairpin DNA assembly for dual-signal amplification toward homogeneous analysis of protein and DNA

The catalytic hairpin DNA assembly-programmed Mg²⁺-dependent DNAzyme switch was proposed for dual-signal amplified detection of protein and DNA.

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.

Gold nanoparticle-based exonuclease III signal amplification for highly sensitive colorimetric detection of folate receptor

By combining terminal protection of small molecule (folate)-capped DNA probes, exonuclease III signal amplification and gold nanoparticles, we developed a simple and label-free colorimetric assay for highly sensitive detection of folate receptor (FR). A detection limit of 50 fM FR was obtained using UV-vis spectrometry and 10 pM FR could be visualized by the naked eye.

Dual-color determination of protein via terminal protection of small-molecule-linked DNA and the enzymolysis of exonuclease III

We have developed a new dual-color fluorescent biosensor for protein detection based on terminal protection of small-molecule-linked DNA and the enzymolysis of exonuclease III (Exo III). The determination of streptavidin (SA) was realized via fluorescence signals of the green color from quantum dots (QDs) and the red from [Ru(phen)2(dppx)](2+). In the absence of SA, biotin-DNA was degradated by the Exo III, thus making the [Ru(phen)2(dppx)](2+) employed as a fluorescence quencher to the QDs. With the addition of SA, dual-color response appeared because of the specific binding between SA and biotin so that the biotin-dsDNA was protected and combined with [Ru(phen)2(dppx)](2+), leading to the QDs recovery and the generating of [Ru(phen)2(dppx)](2+) fluorescence. This sensor exhibited high sensitivity with a low detection limit (2.11ng/mL) and firstly introduced dual-color QDs-ruthenium complex dyads to protein assay.

Graphene oxide-based fluorescent biosensor for protein detection via terminal protection of small-molecule-linked DNA

A fluorescence method for protein detection is developed based on terminal protection of small-molecule-linked DNA by target protein and a graphene oxide-assisted DNA assay strategy. This design results in fluorescence-enhanced detection that is sensitive and selective for the target protein.

Versatile DNAzyme-based amplified biosensing platforms for nucleic acid, protein, and enzyme activity detection

DNAzymes have been widely applied as signal amplifiers for enzyme-free and highly sensitive detection of DNA. A few of them have also been employed for amplified detection of other biomolecules via a target-triggered assembly of split or mutated DNAzyme strategy. However, most of these designs adopt Mg(2+)-dependent DNAzyme as the catalytic unit, which suffered from low catalytic cleavage activity. Meanwhile, some DNAzymes with high catalytic activity are not suitable for these designs because the slight modification of the catalytic core might results in remarkably decreased or even no catalytic activity of these DNAzymes. On the basis of DNAzyme topological effect or the terminal protection of small-molecule-linked DNA, we developed two versatile sensing platforms for amplified detection of different biotargets. Since no modification is necessary for the catalytic core of the DNAzyme in these designs, they can employ any DNAzyme with high catalytic activity as amplified unit, which affords a high amplified efficiency for the sensing platform. A catalytic and molecular beacon design was further employed to realize the true enzymatic multiple turnover of DNAzyme. These designs together allow a high sensitivity for the biotargets, resulting in a detection limit of 20 pM, 0.2 U/mL, and 1 ng/mL for target DNA, DNA adenine methylation methyltransferase (Dam MTase), and streptavidin, respectively, much lower than previously reported biosensors. In addition, the proposed sensing strategy is versatile. By conjugating with various recognition units, it can be employed to detect a wide range of biotargets, varying from nucleic acids to proteins with high sensitivity.