DNA nanomachine for visual detection of structured RNA and double stranded DNA

Gorbenko, Daria A.; Shkodenko, Liubov A.; Rubel, Maria S.; Слита, Александр В.; Nikitina, E. V.; Martens, E. A.; Kolpashchikov, Dmitry M.

doi:10.1039/d2cc00325b

Cited by 13 publications

(18 citation statements)

References 40 publications

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“…Benefiting from the specificity and thermodynamics of Watson–Crick base pairing rules, artificial DNA nanomachines combine the advantages of programmability, self-assembly, and predictability, and they have been applied in the smart detection/diagnosis of diseases or controllable drug release. − Wang et al proposed a well-directed three-dimensional walking nanomachine based on a DNA dendrimer track for the intracellular detection and imaging of microRNA (miRNA) . Miao et al.…”

Section: Introductionmentioning

confidence: 99%

Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules

Yang

Zhao

Wang

et al. 2023

ACS Appl. Mater. Interfaces

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Bioactive small molecules serve as invaluable biomarkers for recognizing modulated organismal metabolism in correlation with numerous diseases. Therefore, sensitive and specific molecular biosensing and imaging in vitro and in vivo are particularly critical for the diagnosis and treatment of a large group of diseases. Herein, a modular DNA tetrahedron-based nanomachine was engineered for the ultrasensitive detection of intracellular small molecules. The nanomachine was composed of three self-assembled modules: an aptamer for target recognition, an entropy-driven unit for signal reporting, and a tetrahedral oligonucleotide for the transportation of the cargo (e.g., the nanomachine and fluorescent markers). Adenosine triphosphate (ATP) was used as the molecular model. Once the target ATP bonded with the aptamer module, an initiator was released from the aptamer module to activate the entropy-driven module, ultimately activating the ATP-responsive signal output and subsequent signal amplification. The performance of the nanomachine was validated by delivering it to living cells with the aid of the tetrahedral module to demonstrate the possibility of executing intracellular ATP imaging. This innovative nanomachine displays a linear response to ATP in the 1 pM to 10 nM concentration range and demonstrates high sensitivity with a low detection limit of 0.40 pM. Remarkably, our nanomachine successfully executes endogenous ATP imaging and is able to distinguish tumor cells from normal ones based on the ATP level. Overall, the proposed strategy opens up a promising avenue for bioactive small molecule-based detection/diagnostic assays.

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Section: Introductionmentioning

confidence: 99%

Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules

Yang

Zhao

Wang

et al. 2023

ACS Appl. Mater. Interfaces

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“…This study presents a NA detection strategy based on peroxidase-like DNA-nanomachine (PxDm) [12,13]. The sensor is based on the G-quadruplex (G-4).…”

Section: Introductionmentioning

confidence: 99%

Chemiluminescent detection of nucleic acids induced by peroxidase-like targeted DNA-nanomachines (PxDm) mixed with plasmonic nanoparticles

Gorbenko,

Filatov,

Dadadzhanov

et al. 2023

Molecular and Nanophotonic Machines VI

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One of the most critical issues in the field of molecular diagnostics and medicine is the development of compact and sensitive assay devices for the precise detection of nucleic acids. Although there are several effective methods for detecting unique nucleic acid sequences, the high cost of equipment and reagents, as well as the need for highly trained personnel, necessitate the design of new and more affordable diagnostic assays that are comparable in selectivity and sensitivity to existing methods that can be used in developing countries and/or outside of specialized diagnostic laboratories. Sensing methods based on guanine quadruplexes (G-4)/hemin complexes, that have peroxidase activity are one of the promising directions for the detection of target nucleic acids. Target nucleic acid was analyzed by peroxidase-like DNA-nanomachine (PxDm) equipped with 1-3 long analyte binding arms to tightly bind and unwind single-stranded analytes. In this study, we present a technique for sequence-specific detection of nucleic acid. The technique is based on the measuring of a chemiluminescent (CL) emission induced by luminol oxidation utilizing a closed-type detection device. Moreover, the optical properties and potential use of plasmonic silver nanoparticles (Ag NPs) to enhance the CL intensity of chemiluminophore were investigated. Particular attention was paid to the possibility of synthesizing the silver nanoparticles with different spectral positions of plasmon resonance band, depending on the method and duration of synthesis. The CL intensity of luminol in the presence of the post-centrifuged colloidal Ag NPs obtained by laser ablation has been increased 3 times. The combination of AgNPs-luminol-DNA-nanomachine systems in the presence of a target analyte led to the significant increase of limit of detection and reached clinically relevant quantitative indications.

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“…However, such assays have high limits of detection (LOD) and thus doomed to be dependent on nucleic acid amplification. [ 10d , 10e ] We turned our attention to fluorescent binary RNA‐cleaving deoxyribozyme (BiDz) probe. [12] BiDz can reach LOD down to 1–10 pM, [13] which is, to the best of our knowledge, the lowest among protein enzyme‐free testing systems that do not use amplification cascades.…”

Section: Introductionmentioning

confidence: 99%

“…Visual [10] or tactile [11] signal outputs could be the most user‐friendly as they would not require equipment. However, such assays have high limits of detection (LOD) and thus doomed to be dependent on nucleic acid amplification [10e,d] . We turned our attention to fluorescent binary RNA‐cleaving deoxyribozyme (BiDz) probe [12] .…”

Section: Introductionmentioning

confidence: 99%

Toward a Home Test for COVID‐19 Diagnosis: DNA Machine for Amplification‐Free SARS‐CoV‐2 Detection in Clinical Samples

et al. 2022

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Nucleic acid‐based detection of RNA viruses requires an annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structures of folded viral RNA. In this study, we designed a protein‐enzyme‐free nano‐construction, named four‐armed DNA machine (4DNM), that requires neither an amplification stage nor a high‐temperature annealing step for SARS‐CoV‐2 detection. It uses a binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with a total of four RNA‐binding arms. Additional arms were found to improve the limit of detection at least 10‐fold. The sensor distinguished SARS‐CoV‐2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT‐qPCR). The strategy reported here can be used for the detection of long natural RNA and can become a basis for a point‐of‐care or home diagnostic test.

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DNA nanomachine for visual detection of structured RNA and double stranded DNA

Abstract: Modern medical diagnosis relies on identifying specific nucleic acids using hybridization probes, often failing to detect single-stranded (ss) RNA folded in stable secondary structures or double-stranded (ds) DNA. In this...

Cited by 13 publications

References 40 publications

Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules

Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules

Chemiluminescent detection of nucleic acids induced by peroxidase-like targeted DNA-nanomachines (PxDm) mixed with plasmonic nanoparticles

Toward a Home Test for COVID‐19 Diagnosis: DNA Machine for Amplification‐Free SARS‐CoV‐2 Detection in Clinical Samples

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