Nanoparticles-Free Fluorescence Anisotropy Amplification Assay for Detection of RNA Nucleotide-Cleaving DNAzyme Activity

Ultralow background one-pot detection of Lead(II) using a non-enzymatic double-cycle system mediated by a hairpin-involved DNAzyme

A double-cycle system has been developed for specifically detecting trace amounts of Pb2+ by significantly decreasing the background signal. The detection involves two types of RNA cleavage reactions: one using a Pb2+-specific GR5 DNAzyme (PbDz) and the other utilizing a newly constructed 10-23 DNAzyme with two hairpins embedded in its catalytic center (hpDz). The ring-structured hpDz (c-hpDz) exhibits significantly lower activity compared to the circular 10-23 DNAzyme without hairpin structures, which plays a crucial role in reducing the background signal. When Pb2+ is present, PbDz cleaves c-hpDz to its active form, which then disconnects the molecular beacon to emit the fluorescent signal. The method allows for rapid and sensitive Pb2+ detection within 40 min for 10 fM of Pb2+ and even as short as 10 min for 100 nM of Pb2+. Additionally, visual detection is possible through the non-crosslinking assembly of Au nanoparticles. The entire process can be performed in one pot and even one step, making it highly versatile and suitable for a wide range of applications, including food safety testing and environmental monitoring.

DNAzyme-Based Microscale Thermophoresis Sensor

Microscale thermophoresis (MST) technology has emerged as a powerful growing method in a molecular interaction study by measuring fluorescence responses of molecules inside a capillary to infrared (IR) laser heating with the benefits of rapid ratiometric measurement, separation-free, no immobilization, and low sample consumption. Combining the advantages of RNA-cleaving DNAzymes in target recognition and enzymatic catalysis and the strength of MST technology for fluorescence signaling, here, we reported a DNAzyme-based MST method for sensitive target detection. We introduced a fluorescein terminal label at the RNA-cleaving DNAzyme, and the substrate was linked to DNAzyme together with a poly-T sequence in a unimolecular design or not conjugated with DNAzyme in a bimolecular design. The presence of the cofactor activated DNAzyme to catalytically cleave the substrate, causing molecular structure alteration and significant changes in MST signals. This DNAzyme MST sensor enabled sensitively detecting activator targets Pb²⁺ and l-histidine, with a detection limit of 49 pM Pb²⁺ and 3.9 μM l-histidine. This biosensing strategy is universal and promising for wide applications.

Recent advances in fluorescence anisotropy/polarization signal amplification

Fluorescence anisotropy/polarization is an attractive and versatile technique based on molecular rotation in biochemical/biophysical systems. Traditional fluorescence anisotropy/polarization assays showed relatively low sensitivity for molecule detection, because widespread molecular masses are too small to produce detectable changes in fluorescence anisotropy/polarization value. In this review, we discuss in detail how the potential of fluorescence anisotropy/polarization signal approach considerably expanded through the implementation of mass amplification, recycle the target amplification, fluorescence probes structure-switching amplification, resonance energy transfer amplification, and provide perspectives at future directions and applications.

Framework nucleic acid-wrapped protein-inorganic hybrid nanoflowers with three-stage amplified fluorescence polarization for terminal deoxynucleotidyl transferase activity biosensing

Herein, we proposed a terminal deoxynucleotidyl transferase (TdT), a potential biomarker of lymphoid tumors, responsive fluorescence polarization (FP)- sensing protocol based on framework nucleic acid (FNA)-wrapped protein-inorganic hybrid nanoflowers. To achieve this goal, a pair of poly-A-composed extension primers (EPa and EPb) was designed, and protein-inorganic hybrid nanoflowers were synthesized by a biomineralization reaction. EPa was labeled with carboxyfluorescein (FAM) fluorophore to create the preliminary FP signal. EPb was labeled with biotin to conjugate with hybrid nanoflowers. Upon introduction of TdT into the dTTP pool, both EPa and EPb can be catalyzed by TdT to incorporate numerous T bases, thereby facilitating intermolecular hybridization between 'A' and 'T' bases. The final assembled FNA-wrapped hybrid nanoflowers with greatly enhanced molecular volume and weight restrict the free rotation of attached FAMs, causing a great FP enhancement from a designated three-stage FP amplification. Under optimized conditions, the TdT can be detected with a detection limit of 0.023 U/mL and a linear detection from 0.1 U/mL to 100 U/mL within 20 min. As a proof-of-concept study, the first exploitation of FNA and protein-inorganic nanoflowers to improve the FP signal and the merit of FP without sample separation and washing opens a new avenue for biochemical study and disease diagnosis.

Advances in the Functional Nucleic Acid Biosensors for Detection of Lead Ions

Lead ions (Pb²⁺) are destructive to the natural environment and public health, so the efficient detection of Pb²⁺ is particularly important. Although the instrumental analysis methods have high accuracy, they require high cost and precise operation, which limits their wide application. Therefore, many strategies have been extensively studied for detecting Pb²⁺ by biosensors. Functional nucleic acids have become an efficient tool in this field. This review focuses on the recent biosensors of detecting Pb²⁺ based on functional nucleic acids from 2010 to 2020, in which DNAzyme, DNA G-quadruplex and aptamer will be introduced. The biosensors are divided into three categories that colorimetric, fluorometric and electrochemical biosensors according to the different reported signals. The action mechanism and detection effect of each biosensor are explained. Finally, the present situation of nucleic acid biosensor for the detection of Pb²⁺ is summarized and the future research direction is prospected.

A crosslinked submicro-hydrogel formed by DNA circuit-driven protein aggregation amplified fluorescence anisotropy for biomolecules detection

Protein is an excellent molecular mass amplifier without fluorescence quenching effect for fluorescence anisotropy (FA) assay. However, in traditional protein amplified FA methods, the binding ratio between amplifier and dye-modified probe is 1:1 or one target can only induce FA change of one fluorophore on probe, resulting in low sensitivity. Herein, we developed a simple FA strategy with high accuracy and sensitivity by using a crosslinked submicro-hydrogel that was formed through a catalyzed hairpin assembly (CHA) assisted protein aggregation as a novel FA amplifier. In the presence of catalyst, the CHA process was initiated through the toehold-mediated strand exchange reaction, which led to the formation of a dye and biotin-labeled Y-shaped H1-H2 duplex (YHD) and recycling of catalyst. With the introduction of streptavidin, a crosslinked submicro-hydrogel was formed by strong binding affinity between biotin on YHD and streptavidin, resulting in an increased FA of fluorescent dye. After rational design of the catalyst sequence, this method has been utilized for the detection of miRNA-145, staphylococcal enterotoxin B (SEB) and ATP with an LOD of 2.5 nM, 92 pg mL^-1 and 3.6 μM, respectively. Moreover, this FA assay has been successfully applied for direct detection of target in biological samples, demonstrating its practicality in complex biological systems.

Review of recent progress on DNA-based biosensors for Pb2+ detection

Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb²⁺ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb²⁺ has become a rapidly growing topic in the analytical community. Pb²⁺ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb²⁺ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb²⁺ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb²⁺ sensing. In this article, these Pb²⁺ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.

DNA nanosheet as an excellent fluorescence anisotropy amplification platform for accurate and sensitive biosensing

Recently, various inorganic nanomaterials have been used as fluorescence anisotropy (FA) enhancers for biosensing successfully. However, most of them are size-uncontrollable and possess an intensive fluorescence quenching ability, which will seriously reduce the accuracy and sensitivity of FA method. Herein, we report a two-dimensional DNA nanosheet (DNS) without fluorescence quenching effect as a novel FA amplification platform. In our strategy, fluorophore-labeled probe DNA (pDNA) is linked onto the DNS surface through the hybridization with the handle DNA (hDNA) that extended from the DNS, resulting in the significantly enhanced FA value. After the addition of target, the pDNA was released from the DNS surface due to the high affinity between the hDNA and target, and the FA was decreased. Thus, target could be detected by the significantly decreased FA value. The linear range was 10-50 nM and the limit of detection was 8 nM for the single-stranded DNA detection. This new method is general and has been also successfully applied for the detection of ATP and thrombin sensitively. Our method improved the accuracy of FA assay and has great potential to detect series of biological analytes in complex biosensing systems.

Fluorescence Anisotropy Reduction of An Allosteric G-Rich Oligonucleotide for Specific Silver Ion and Cysteine Detection Based on the G-Ag+-G Base Pair

Silver is a common heavy metal, and the detection of silver ion (Ag⁺) is of great importance because of its wide application and hazardous effect on the environment and human health. However, it is a great challenge to produce a large fluorescence anisotropy (FA) change for small molecules (e.g, Ag⁺). Herein, we describe a novel fluorescence anisotropy reduction approach for the sensitive and specific detection of Ag⁺. The feasibility of this method is demonstrated through screening a number of guanine-rich oligonucleotide probes. By selectively labeling the oligonucleotides with a single fluorophore tetramethylrhodamine (TMR), the reduction in FA response is associated with the conformation change from the unfolded to a hairpin-like folded structure by inducing formation of the intermolecular G-Ag⁺-G base pair, which diminishes the interaction between guanine and TMR by photoinduced electron transfer (PET). The change in FA allows the selective detection of Ag⁺ at a concentration as low as 0.5 nM with a dynamic range from 2.0 to 100 nM. The interference from the other 14 metal ions with a 100-fold even to a 1000-fold excess amount is negligible. This simple and cost-effective probe was further explored to determine cysteine (Cys) based on competing with a guanine-rich oligonucelotide for Ag⁺-binding.

Paper-based point-of-care test with xeno nucleic acid probes

Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.

DNA-templated Au nanoclusters coupled with proximity-dependent hybridization and guanine-rich DNA induced quenching: a sensitive fluorescent biosensing platform for DNA detection

In this paper, the fluorescence signal of poly(A) DNA-templated Au nanoclusters (AuNCs) is found to be greatly quenched by photoinduced electron transfer (PET) when they are close to guanine (G)-rich DNA. Based on the findings, we have designed a low-cost fluorescence biosensing strategy for the sensitive detection of DNA. Highly luminescent and photo-stable poly(A) DNA-AuNCs were utilized as the fluorescent indicator and G-rich DNA was utilized as the fluorescent quencher. In the absence of target DNA, DNA-AuNCs failed to hybridize with the G-rich DNA and did not form the duplex DNA structure. Strong fluorescence intensity at 475 nm was observed due to the DNA-AuNCs being far away from the G-rich DNA. However, in the presence of target DNA, the DNA-AuNCs together with G-rich DNA could hybridize with the target DNA, leading to the 5' terminus of the DNA-AuNCs and the 3' terminus of G-rich DNA being in close proximity and promoting the cooperative hybridization. Therefore, a "Y" junction structure was formed and the G-rich sequences were brought close to the AuNCs. Therefore, the fluorescence intensity of the sensing system decreased significantly. Taking advantage of the poly(A) DNA-templated Au nanoclusters and G-rich DNA proximity-induced quenching, the strategy could be extended to determine other biomolecules by designing appropriate sequences of DNA probes.

Chimeric Aptamers-Based and MoS2 Nanosheet-Enhanced Label-Free Fluorescence Polarization Strategy for Adenosine Triphosphate Detection

Adenosine triphosphate (ATP) as a primary energy source plays a unique role in the regulation of all cellular events. The necessity to detect ATP requires sensitive and accurate quantitative analytical strategies. Herein, we present our study of developing a MoS₂ nanosheet-enhanced aptasensor for fluorescence polarization-based ATP detection. A bifunctional DNA strand was designed to consist of chimeric aptamers that recognize and capture ATP and berberine, a fluorescence enhancer. In the absence of ATP, the DNA strand bound to berberine will be hydrolyzed when Exonuclease I (Exo I) is introduced, releasing berberine as a result. In contrast, when ATP is present, ATP aptamer folds into a G-quadruplex structure; thus, the complex can resist degradation by Exo I to maintain berberine for fluorescent detection purpose. In addition, to magnify the fluorescence polarization (FP) signal, MoS₂ nanosheets were also adopted in the system. This nanosheets-enhanced FP strategy is simple and facile which does not require traditional dye-labeled DNA strands and complex operation steps. The developed fluorescence polarization aptasensor showed high sensitivity for the quantification of ATP with a detection limit of 34.4 nM, performing well both in buffer solution and in biological samples.

Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms

Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.

A high-sensitivity electrochemical aptasensor of carcinoembryonic antigen based on graphene quantum dots-ionic liquid-nafion nanomatrix and DNAzyme-assisted signal amplification strategy

In this work, we have developed an electrochemical aptasensor for high-sensitivity determination of carcinoembryonic antigen (CEA) based on lead ion (Pb²⁺)-dependent DNAzyme-assisted signal amplification and graphene quantum dot-ionic liquid-nafion (GQDs-IL-NF) composite film. We designed hairpin DNA containing CEA-specific aptamers and DNAzyme chains. In the presence of CEA, hairpin DNA recognized the target and performed a DNAzyme-assisted signal amplification reaction to yield a large number of single-stranded DNA. The GQDs-IL-NF composite film was immobilized on the glassy carbon electrode for the interaction with single-stranded DNA through noncovalent π-π stacking interaction. Therefore, the methylene blue-labeled substrate DNA (MB-substrate) was fixed on the electrode and exhibited an initial electrochemical signal. Under optimal conditions, the response current change was proportional to the concentration of CEA, demonstrating a wide linear range from 0.5fgmL^-1 to 0.5ngmL^-1, with a low detection limit of 0.34fgmL^-1. Furthermore, the proposed aptasensor was successfully applied in determining CEA in serum samples, showing its superior prospects in clinical diagnosis.

Use of anchor protein modules in fluorescence polarisation aptamer assay for ochratoxin A determination

A new strategy for sensitive fluorescence polarisation (FP) analysis is proposed which uses aptamer as the receptor and anchor protein modules as the enhancers by including the aptamers in complexes with protein modules. This approach is based on increasing the size differences of bound and unbound fluorophores. The strategy was applied in an ochratoxin A (ОТА) assay with the competitive binding of fluorophore-labelled and free OTA with aptamer-based receptors. We showed that the binding of labelled OTA with aptamer included in complexes with anchors led to higher a FP than binding with free aptamer. This allowed the aptamer concentration to be reduced, thus lowering the limit of detection by a factor of 40, down to 3.6 nM. The assay time was 15 min. To evaluate the applicability of the FP assay with aptamer-anchor complex to real samples, we conducted OTA measurements in spiked white wine. The OTA limit of detection in wine was 2.8 nM (1.1 μg/kg), and the recoveries ranged from 83% to 113%. The study shows that the proposed anchor strategy is efficient for increasing the sensitivity of FP-based aptamer assays.

Phosphate-perylene modified G-quadruplex probes for the detection of Pb2+ using fluorescence anisotropy

A simple and universal phosphate-perylene modification strategy was applied in the development of G-quadruplex probes with thrombin binding aptamer (TBA) and [d(TGGGT)₄] (G4) sequences. A perylene moiety was inserted at different phosphate positions of oligonucleotides without a significant effect on the G-quadruplex structures. Upon binding with K⁺ or Pb²⁺, these probes showed different perylene fluorescence anisotropy responses due to the different labeling positions and G-quadruplex structures. Two probes (G4-9 and TBA-9) were successfully used in Pb²⁺ detection through fluorescence anisotropy. Once the complexes of Pb²⁺ with G4-9 or TBA-9 were formed, the rotational diffusion of the perylene moiety was limited, resulting in a significant increase in fluorescence anisotropy. Both probes showed good sensitivity to Pb²⁺ and their fluorescence anisotropy signals demonstrated good linear responses to the logarithm of Pb²⁺ concentrations and the detection limits were 24.5 nM and 30.0 nM for TBA-9 and G4-9, respectively.

Exonuclease III-assisted graphene oxide amplified fluorescence anisotropy strategy for ricin detection

Graphene oxide (GO) is an excellent fluorescence anisotropy (FA) amplifier. However, in the conventional GO amplified FA strategy, one target can only induce the FA change of one fluorophore on probe, which limits the detection sensitivity. Herein, we developed an exonuclease III (Exo III) aided GO amplified FA strategy by using aptamer as an recognition element and ricin B-chain as a proof-of-concept target. The aptamer was hybridized with a blocker sequence and linked onto the surface of magnetic beads (MBs). Upon the addition of ricin B-chain, blocker was released from the surface of MBs and hybridized with the dye-modified probe DNA on the surface of GO through the toehold-mediated strand exchange reaction. The formed blocker-probe DNA duplex triggered the Exo III-assisted cyclic signal amplification by repeating the hybridization and digestion of probe DNA, liberating the fluorophore with several nucleotides (low FA value). Thus, ricin B-chain could be sensitively detected by the significantly decreased FA. The linear range was from 1.0μg/mL to 13.3μg/mL and the limit of detection (LOD) was 400ng/mL. This method improved the sensitivity of FA assay and it could be generalized to any kind of target detection based on the use of an appropriate aptamer.

Ultrasensitive, Specific, Recyclable, and Reproducible Detection of Lead Ions in Real Systems through a Polyadenine-Assisted, Surface-Enhanced Raman Scattering Silicon Chip

It is of great significance to accurately and reliably detect trace lead(II) (Pb(2+)) ions, preferably at sub-nM level due to the possible long-term accumulation of Pb(2+) in the human body, which may cause serious threats to human health. However, a suitable Pb(2+) sensor meeting the demands is still scanty. Herein, we develop a polyadenine-assisted, surface-enhanced Raman scattering (SERS) silicon chip (0.5 cm × 0.5 cm) composed of core (Ag)-satellite (Au) nanoparticles (Ag-Au NPs)-decorated silicon wafers (Ag-Au NPs@Si) for high-performance Pb(2+) detection. Typically, strong SERS signals could be measured when DNAzyme conjugated on the SERS silicon chip is specifically activated by Pb(2+), cleaving the substrate strand into two free DNA strands. A good linearity exists between the normalized Raman intensities and the logarithmic concentrations of Pb(2+) ranging from 10 pM to 1 μM with a good correlation coefficient, R(2) of 0.997. Remarkably, Pb(2+) ions with a low concentration of 8.9 × 10(-12) M can be readily determined via the SERS silicon chip ascribed to its superior SERS enhancement, much lower than those (∼nM) reported by other SERS sensors. Additionally, the developed chip features good selectivity and recyclability (e.g., ∼11.1% loss of Raman intensity after three cycles). More importantly, the as-prepared chip can be used for accurate and reliable determination of unknown Pb(2+) ions in real systems including lake water, tap water and industrial wastewater, with the RSD value less than 12%.

Fluorescence Polarization Based Nucleic Acid Testing for Rapid and Cost-Effective Diagnosis of Infectious Disease

A new nucleic acid detection method was developed for a rapid and cost-effective diagnosis of infectious disease. This approach relies on the three unique elements: 1) detection probes that regulate DNA polymerase activity in response to the complementary target DNA; 2) universal reporters conjugated with a single fluorophore; and 3) fluorescence polarization (FP) detection. As a proof-of-concept, the assay was used to detect and sub-type Salmonella bacteria with sensitivities down to a single bacterium in less than three hours.

A novel graphene oxide amplified fluorescence anisotropy assay with improved accuracy and sensitivity

A novel and versatile graphene oxide (GO) amplified fluorescence anisotropy (FA) strategy with improved accuracy and sensitivity has been successfully developed.