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Hussein Z, Nour MAY, Kozlova AV, Kolpashchikov DM, Komissarov AB, El-Deeb AA. DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection. Anal Chem 2023; 95:18667-18672. [PMID: 38079240 DOI: 10.1021/acs.analchem.3c04420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.
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Affiliation(s)
- Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816, United States
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, United States
| | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
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Yang S, Zhao Z, Wang B, Feng L, Luo J, Deng R, Sheng J, Gao X, Xie S, Chen M, Chang K. Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules. ACS APPLIED MATERIALS & INTERFACES 2023; 15:23662-23670. [PMID: 37140536 DOI: 10.1021/acsami.3c02614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
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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Affiliation(s)
- Sha Yang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Zhuyang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Binpan Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Liu Feng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Jie Luo
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Ruijia Deng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Jing Sheng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Xueping Gao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Shuang Xie
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
- College of Pharmacy and Laboratory Medicine, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, China
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Maltzeva YI, Gorbenko DA, Nikitina EV, Rubel MS, Kolpashchikov DM. Visual Detection of Stem-Loop Primer Amplification (SPA) Products without Denaturation Using Peroxidase-like DNA Machines (PxDM). Int J Mol Sci 2023; 24:7812. [PMID: 37175522 PMCID: PMC10177805 DOI: 10.3390/ijms24097812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Rapid, inexpensive, and accurate determination of nucleic acids is a decisive factor in evaluating population's health and monitoring treatment at point-of-care (POC) settings. Testing systems with visual outputs can provide instrument-free signal detection. Isothermal amplification technologies can substitute conventional polymerase chain reaction (PCR) testing due to compatibility with the POC diagnostic. Here, we have visually detected DNA fragments obtained by stem-loop-primer-assisted isothermal amplification (SPA), but not those obtained by PCR or LAMP amplification using DNA nanomachines with peroxidase-like activity (PxDM) with sensitivity to a single nucleotide substitution. Compared to the diagnostics with conventional loop-mediated isothermal amplification (LAMP), the PxDM method produces no false positive signals with the non-specific amplification products. The study suggests that PxDM, in conjunction with SPA isothermal amplification, can become a valid platform for POC testing systems.
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Affiliation(s)
- Yulia I. Maltzeva
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Daria A. Gorbenko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Ekaterina V. Nikitina
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St Petersburg, Russia
| | - Maria S. Rubel
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA;
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32826, USA
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Ateiah M, Gandalipov ER, Rubel AA, Rubel MS, Kolpashchikov DM. DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species. Int J Mol Sci 2023; 24:ijms24054473. [PMID: 36901903 PMCID: PMC10003685 DOI: 10.3390/ijms24054473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for "opening up" the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10-23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of B. thuringiensis 16S rRNA at fluorescein and B. mycoides at Cy5 channels with a limit of detection of 30 × 103 and 35 × 103 CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification.
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Affiliation(s)
- Muhannad Ateiah
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Erik R. Gandalipov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya enb. 7-9, St. Petersburg 199034, Russia;
| | - Maria S. Rubel
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Dmitry M. Kolpashchikov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- Correspondence:
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Rubel MS, Shkodenko LA, Gorbenko DA, Solyanikova VV, Maltzeva YI, Rubel AA, Koshel EI, Kolpashchikov DM. Detection of Multiplex NASBA RNA Products Using Colorimetric Split G Quadruplex Probes. Methods Mol Biol 2023; 2709:287-298. [PMID: 37572289 DOI: 10.1007/978-1-0716-3417-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Structural RNA is a challenging target for recognition by hybridization probes. This chapter addresses the recognition problem of RNA amplicons in samples obtained by multiplex nucleic acid sequence-based amplification (NASBA). The method describes the design of G-quadruplex binary (split) DNA peroxidase sensors that produces colorimetric signal upon recognition of NASBA amplicons.
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Affiliation(s)
- Maria S Rubel
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia.
| | - Liubov A Shkodenko
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | - Daria A Gorbenko
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | | | - Yulia I Maltzeva
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Elena I Koshel
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | - Dmitry M Kolpashchikov
- Department of Chemistry, University of Central Florida, Orlando, FL, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
- Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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ElDeeb AA, Zablotskaya SS, Rubel MS, Nour MAY, Kozlovskaya LI, Shtro AA, Komissarov AB, Kolpashchikov DM. Toward a Home Test for COVID 19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples. ChemMedChem 2022; 17:e202200382. [PMID: 36031581 PMCID: PMC9538286 DOI: 10.1002/cmdc.202200382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Indexed: 11/08/2022]
Abstract
Nucleic acid-based detection of RNA viruses requires annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structure of folded viral RNA. In this study, we designed a protein enzymes-free nano-construction, names four-armed DNA machine (4DNM), that requires neither amplification stage nor high temperature annealing step for SARS-CoV-2 detection. It uses binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with total of four RNA-binding arms. Additional arms improved limit of detection at least 10 times. 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 detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.
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Affiliation(s)
- Ahmed A ElDeeb
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and molecular biology, RUSSIAN FEDERATION
| | - Sofia S Zablotskaya
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Maria S Rubel
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Moustapha A Y Nour
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Liubov I Kozlovskaya
- FSBSI Institute of Engineering Science Ural Branch of the Russian Academy of Sciences: FGBUN Institut masinovedenia Ural'skogo otdelenia Rossijskoj akademii nauk, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Anna A Shtro
- Research Institute of Influenza: Naucno-issledovatel'skij institut grippa, diagnostics, RUSSIAN FEDERATION
| | - Andrey B Komissarov
- Research Institute of Influenza: Naucno-issledovatel'skij institut grippa, diagnostics, RUSSIAN FEDERATION
| | - Dmitry M Kolpashchikov
- University of Central Florida, Chemistry, 4000 Central Florida Blvd, P.O. Box 162366, 32816-2366, Orlando, UNITED STATES
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