Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques

Bezerra, Andresa B.; Kurian, Amanda S. N.; Easley, Christopher J.

doi:10.1021/acs.analchem.0c04364

Cited by 25 publications

(26 citation statements)

References 111 publications

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“…As shown in Figure S5, the 165 Ho signal intensity increases with the concentration of amplifier. It is noted that the appropriate concentration of P1 in LGM-Ln is crucial for recognizing the input target to avoid the Hook effect . Meanwhile, too many substrates in the amplifier would decrease the coverage of P1, resulting in low affinity binding for target recognition.…”

Section: Resultsmentioning

confidence: 99%

Lanthanide Encoded Logically Gated Micromachine for Simultaneous Detection of Nucleic Acids and Proteins by Elemental Mass Spectrometry

Yang

Zhou

et al. 2022

Anal. Chem.

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DNA-based logic computing potentially for analysis of biomarker inputs and generation of oligonucleotide signal outputs is of great interest to scientists in diverse areas. However, its practical use for sensing of multiple biomarkers is limited by the universality and robustness. Based on a proximity assay, a lanthanide encoded logically gated micromachine (LGM-Ln) was constructed in this work, which is capable of responding to multiplex inputs in biological matrices. Under the logic function controls triggered by inputs and a Boolean “AND” algorithm, it is followed by an amplified “ON” signal to indicate the analytes (inputs). In this logically gated sensing system, the whole computational process does not involve strand displacement in an intermolecular reaction, and a threshold-free design is employed to generate the 0 and 1 computation via intraparticle cleavage, which facilitates the computation units and makes the “computed values” more reliable. By simply altering the affinity ligands for inputs’ biorecognition, LGM-Ln can also be extended to multi-inputs mode and produce the robust lanthanide encoded outputs in the whole human serum for sensing nucleic acids (with the detection limit of 10 pM) and proteins (with the detection limit of 20 pM). Compared with a logically gated micromachine encoded with fluorophores, the LGM-Ln has higher resolution and no spectral overlaps for multiple inputs, thus holding great promise in multiplex analyses and clinical diagnosis.

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Section: Resultsmentioning

confidence: 99%

Lanthanide Encoded Logically Gated Micromachine for Simultaneous Detection of Nucleic Acids and Proteins by Elemental Mass Spectrometry

Yang

Zhou

et al. 2022

Anal. Chem.

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“…The DNA3 was designed to be complementary with the partial sequence of DNA2. The simultaneous recognition of the anti-dig antibody with the two dig elements conjugated onto DNA2 and DNA3 brought about their proximity hybridization owing to the increased local concentrations, − inducing the partial sequence at the 5′-terminus of DNA1 to be displaced and dissociated from DNA2. This promoted the redox reporter to approach the electrode for the increased electron transfer.…”

Section: Results and Discussionmentioning

confidence: 99%

“…For example, the rigid double-stranded nucleic acid scaffold, with the labeled redox molecule as a signal reporter and the small-molecule moiety as a recognition element, was proposed for single-step protein detection. , The steric hindrance effect was also explored to develop single-step DNA-based biosensors in which antibody binding with the redox-active signaling strand altered its hybridization kinetics with a capture DNA. , Unfortunately, these platforms could only operate in a signal-off fashion, limiting the signal gain of the sensor. To improve the signal gain, the proximity-based nucleic acid hybridization strategy became popular for single-step and signal-on protein analysis. − It was also confronted by the complex thermodynamic optimization of the involved multiple DNA sequences, which was responsible for the cooperative recognition effect. Thus, the design of a more flexible, versatile, and easy-to-use sensing platform for highly accurate protein assay was still desirable.…”

Section: Introductionmentioning

confidence: 99%

Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System

Wang

Chen

et al. 2022

Anal. Chem.

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Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge was deployed for the fabrication of a simple and general DNA-based electrochemical sensing platform. It could be harnessed for different signal output behaviors (one signal-off and two signal-on modes) toward a single-step analysis of the target protein. The detection limit toward the target protein could reach about 0.1 nM. Also, it could be used as a streamlined electrochemical workflow for the successive monitoring of protein binding. Furthermore, such an electrochemical sensing platform could be explored for the operation of the concatenated AND logic gates as a molecular keypad lock system. The current sensing platform based on only one duplex DNA scaffold presented features such as simple biosensor design and fabrication, flexible operation for different signal outputs, sensitive and selective protein detection, and expandable logic operation. It thus would pave a broad road toward the development of high-performance biosensors or logic devices to be applied for molecular diagnosis or computing.

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“…New biosensing platforms have been developed over the last two decades to achieve reagentless, single-step detection of antibodies (or proteins) directly in untreated biological fluids. [13][14][15] These platforms exploit synthetic, redox-labeled nucleic acid molecules as responsive recognition elements that generate electrochemical signals in response to the presence of the selected target. [16][17][18] For example, biosensors based on DNA aptamers or antigen-tagged DNA probes can fold/unfold in the presence of the biomolecular target (i.e., they undergo a binding-induced conformational change) generating a specific electrochemical signal.…”

Section: Introductionmentioning

confidence: 99%

A Programmable Electrochemical Y‐Shaped DNA Scaffold Sensor for the Single‐Step Detection of Antibodies and Proteins in Untreated Biological Fluids

Bonini

Parolo

Álvarez-Diduk

et al. 2022

Adv Funct Materials

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Proteins and antibodies are key biomarkers for diagnosing and monitoring specific medical conditions. Currently, gold standard techniques used for their quantification require laborious multi‐step procedures, involving high costs and slow response times. It is possible to overcome these limitations by exploiting the chemistry and programmability of DNA to design a reagentless electrochemical sensing platform. Specifically, three DNA single strands are engineered that can self‐assemble into a Y‐shaped DNA nanostructure that resembles one of the IgGs. In order to convert this DNA nanostructure into a responsive DNA‐scaffold bioreceptor, it is modified including two recognition elements, two redox tag molecules, and a thiol group. In the absence of the target, the scaffold receptor can efficiently collide with the electrode surface and generate a strong electrochemical signal. The presence of the target induces its bivalent binding, which produces steric hindrance interactions that limit the receptor's collisional activity. In its bound state, the redox tags can therefore approach the surface at a slower rate, leading to a signal decrease that is quantitatively related to the target concentration. The Y‐shape DNA scaffold sensor can detect nanomolar concentrations of antibodies and proteins in <15 min with a single‐step procedure directly in untreated biological fluids.

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Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques

Cited by 25 publications

References 111 publications

Lanthanide Encoded Logically Gated Micromachine for Simultaneous Detection of Nucleic Acids and Proteins by Elemental Mass Spectrometry

Lanthanide Encoded Logically Gated Micromachine for Simultaneous Detection of Nucleic Acids and Proteins by Elemental Mass Spectrometry

Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System

A Programmable Electrochemical Y‐Shaped DNA Scaffold Sensor for the Single‐Step Detection of Antibodies and Proteins in Untreated Biological Fluids

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