1
|
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.
Collapse
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
| |
Collapse
|
2
|
Iwaniuk EE, Adebayo T, Coleman S, Villaros CG, Nesterova IV. Activatable G-quadruplex based catalases for signal transduction in biosensing. Nucleic Acids Res 2023; 51:1600-1607. [PMID: 36727464 PMCID: PMC9976883 DOI: 10.1093/nar/gkad031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
Discovery of oxidative catalysis with G-quadruplex•hemin constructs prompted a range of exciting developments in the field of biosensor design. Thus, G-quadruplex based DNAzymes with peroxidase activity found a niche as signal transduction modules in a wide range of analytical applications. The ability of nucleic acid scaffolds to recognise a variety of practically meaningful markers and to translate the recognition events into conformational changes powers numerous sensor design possibilities. In this work, we establish a catalase activity of G-quadruplex•hemin scaffolds. Catalase activated hydrogen peroxide decomposition generates molecular oxygen that forms bubbles. Observation of bubbles is a truly equipment free signal readout platform that is highly desirable in limited resources or do-it-yourself environments. We take a preliminary insight into a G-quadruplex structure-folding topology-catalase activity correlation and establish efficient operating conditions. Further, we demonstrate the platform's potential as a signal transduction modality for reporting on biomolecular recognition using an oligonucleotide as a proof-of-concept target. Ultimately, activatable catalases based on G-quadruplex•hemin scaffolds promise to become valuable contributors towards accessible molecular diagnostics applications.
Collapse
Affiliation(s)
- Elzbieta E Iwaniuk
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Thuwebat Adebayo
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Seth Coleman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Caitlin G Villaros
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
El‐Deeb 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] [MESH Headings] [Grants] [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 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.
Collapse
Affiliation(s)
- Ahmed A. El‐Deeb
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Sofia S. Zablotskaya
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Maria S. Rubel
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Moustapha A. Y. Nour
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Liubov I. Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological ProductsRussian Academy of SciencesInstitute of PoliomyelitisMoscowRussia
| | - Anna A. Shtro
- Smorodintsev Research Institute of Influenza197376Saint PetersburgRussia
| | | | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
- Chemistry DepartmentUniversity of Central FloridaOrlandoFL 32816USA
- Burnett School of Biomedical SciencesUniversity of Central FloridaOrlandoFL 32827USA
| |
Collapse
|
5
|
Bae SW, Kim J, Kwon S. Recent Advances in Polymer Additive Engineering for Diagnostic and Therapeutic Hydrogels. Int J Mol Sci 2022; 23:2955. [PMID: 35328375 PMCID: PMC8955662 DOI: 10.3390/ijms23062955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Hydrogels are hydrophilic polymer materials that provide a wide range of physicochemical properties as well as are highly biocompatible. Biomedical researchers are adapting these materials for the ever-increasing range of design options and potential applications in diagnostics and therapeutics. Along with innovative hydrogel polymer backbone developments, designing polymer additives for these backbones has been a major contributor to the field, especially for expanding the functionality spectrum of hydrogels. For the past decade, researchers invented numerous hydrogel functionalities that emerge from the rational incorporation of additives such as nucleic acids, proteins, cells, and inorganic nanomaterials. Cases of successful commercialization of such functional hydrogels are being reported, thus driving more translational research with hydrogels. Among the many hydrogels, here we reviewed recently reported functional hydrogels incorporated with polymer additives. We focused on those that have potential in translational medicine applications which range from diagnostic sensors as well as assay and drug screening to therapeutic actuators as well as drug delivery and implant. We discussed the growing trend of facile point-of-care diagnostics and integrated smart platforms. Additionally, special emphasis was given to emerging bioinformatics functionalities stemming from the information technology field, such as DNA data storage and anti-counterfeiting strategies. We anticipate that these translational purpose-driven polymer additive research studies will continue to advance the field of functional hydrogel engineering.
Collapse
Affiliation(s)
- Sang-Wook Bae
- Bio-MAX/N-Bio, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 08826, Korea
| | - Jiyun Kim
- School of Materials Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
- Center for Multidimensional Programmable Matter, Ulsan 44919, Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 08826, Korea
| |
Collapse
|
6
|
Kovtunov EA, Shkodenko LA, Goncharova EA, Nedorezova DD, Sidorenko SV, Koshel EI, Kolpashchikov DM. Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid. ChemistrySelect 2020. [DOI: 10.1002/slct.202003869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Evgeny A. Kovtunov
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Liubov A. Shkodenko
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Ekaterina A. Goncharova
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
- Saint-Petersburg Pasteur Institute Mira st.14, St. Petersburg 197101 Russian Federation
| | - Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Sergey V. Sidorenko
- Department of Medical Microbiology and Molecular Epidemiology Pediatric Research and Clinical Center for Infectious Diseases Saint Petersburg 197022 Russian Federation
- North Western State Medical University named after I.I. Mechnikov Kirochnaya Str. 41, St. Petersburg Russia 191015
| | - Elena I. Koshel
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
- University of Central Florida Chemistry Department 4111 Libra Drive, Physical Sciences 255 Orlando FL USA 32816-2366
| |
Collapse
|
7
|
Khajouei S, Ravan H, Ebrahimi A. DNA hydrogel-empowered biosensing. Adv Colloid Interface Sci 2020; 275:102060. [PMID: 31739981 PMCID: PMC7094116 DOI: 10.1016/j.cis.2019.102060] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 01/28/2023]
Abstract
DNA hydrogels as special members in the DNA nanotechnology have provided crucial prerequisites to create innovative gels owing to their sufficient stability, biocompatibility, biodegradability, and tunable multifunctionality. These properties have tailored DNA hydrogels for various applications in drug delivery, tissue engineering, sensors, and cancer therapy. Recently, DNA-based materials have attracted substantial consideration for the exploration of smart hydrogels, in which their properties can change in response to chemical or physical stimuli. In other words, these gels can undergo switchable gel-to-sol or sol-to-gel transitions upon application of different triggers. Moreover, various functional motifs like i-motif structures, antisense DNAs, DNAzymes, and aptamers can be inserted into the polymer network to offer a molecular recognition capability to the complex. In this manuscript, a comprehensive discussion will be endowed with the recognition capability of different kinds of DNA hydrogels and the alternation in physicochemical behaviors upon target introducing. Finally, we offer a vision into the future landscape of DNA based hydrogels in sensing applications.
Collapse
Affiliation(s)
- Sima Khajouei
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Ali Ebrahimi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
8
|
Wang X, Huang K, Zhang H, Zeng L, Zhou Y, Jing T. Preparation of molecularly imprinted polymers on hemin-graphene surface for recognition of high molecular weight protein. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 105:110141. [DOI: 10.1016/j.msec.2019.110141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/08/2019] [Accepted: 08/26/2019] [Indexed: 01/21/2023]
|
9
|
Ma Y, Geng F, Wang Y, Xu M, Shao C, Qu P, Zhang Y, Ye B. Novel strategy to improve the sensing performances of split ATP aptamer based fluorescent indicator displacement assay through enhanced molecular recognition. Biosens Bioelectron 2019; 134:36-41. [PMID: 30954924 DOI: 10.1016/j.bios.2019.03.047] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/24/2022]
Abstract
Split aptamer strategy was often used to improve the sensitivity of aptasensor. However, traditional split aptamer strategy can not be directly used to improve the label-free aptamer based Thioflavin T (ThT) displacement assay for ATP because the split ATP aptamer display much lower enhancement effects on the fluorescence of ThT than intact aptamer. In order to address this issue, this is the first report using G-rich DNA sequence to enhance the affinity of the two split ATP aptamer halves to ThT and offer lower limit of detection (LOD), wider linear range and higher selectivity through the enhanced molecular recognition. Compared to the intact aptamer/ThT complex, the ensemble of two G-rich split ATP aptamer fragments/ThT are higher fluorescent. Consequently, G-rich sequences would improve the fluorescent signal and thus the sensing performance of the proposed assay. In the optimized conditions, the LOD of the proposed fluorescent ATP aptasensor is 2 nM, which is lower than the reported ThT/ATP aptamer based methods. Additionally, our aptasensor has a wider dynamic linear range (0.1 μM - 120 μM) and higher selectivity. The proposed aptasensor has been successfully applied to detect ATP in 15% human serum. More importantly, the current study not only provides a novel method for ATP assay but also presents a way to construct a label-free split aptamer based fluorescent sensor for other species where aptamer can be generated.
Collapse
Affiliation(s)
- Yu Ma
- College of Chemistry and Molecular Engeering, Zhengzhou University, Zhengzhou, 450001, China
| | - Fenghua Geng
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engeering, Henan Joint International Research Laboratory of Chemo, Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China
| | - Yongxiang Wang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engeering, Henan Joint International Research Laboratory of Chemo, Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China; College of Chemistry and Material Science, Huaibei Normal University, Huaibei, 235000, China.
| | - Maotian Xu
- College of Chemistry and Molecular Engeering, Zhengzhou University, Zhengzhou, 450001, China; Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engeering, Henan Joint International Research Laboratory of Chemo, Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China
| | - Congying Shao
- College of Chemistry and Material Science, Huaibei Normal University, Huaibei, 235000, China
| | - Peng Qu
- College of Chemistry and Molecular Engeering, Zhengzhou University, Zhengzhou, 450001, China; Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engeering, Henan Joint International Research Laboratory of Chemo, Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China
| | - Yintang Zhang
- College of Chemistry and Molecular Engeering, Zhengzhou University, Zhengzhou, 450001, China; Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engeering, Henan Joint International Research Laboratory of Chemo, Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China
| | - Baoxian Ye
- College of Chemistry and Molecular Engeering, Zhengzhou University, Zhengzhou, 450001, China
| |
Collapse
|
10
|
Lanchuk YV, Ulasevich SA, Fedotova TA, Kolpashchikov DM, Skorb EV. Towards sustainable diagnostics: replacing unstable H 2O 2 by photoactive TiO 2 in testing systems for visible and tangible diagnostics for use by blind people. RSC Adv 2018; 8:37735-37739. [PMID: 35558580 PMCID: PMC9089394 DOI: 10.1039/c8ra06711b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/31/2018] [Indexed: 11/23/2022] Open
Abstract
Blind and color blind people cannot use colorimetric diagnostics; the problem is especially severe in rural areas where high temperatures and the absence of electricity challenge modern diagnostics. Here we propose to replace the unstable component of a diagnostic test, H2O2, with stable TiO2. Under UV irradiation, TiO2 forms reactive oxygen species that initiate polymerization of acrylamide causing liquid-to-gel transition in an analyte-dependent manner. We demonstrate that specific DNA sequences can be detected using this approach. This development may enable the detection of biological molecules by users with limited resources, for example in developing countries or for travelers in remote areas.
Collapse
Affiliation(s)
- Yulia V Lanchuk
- ITMO University Lomonosova St. 9 191002 St. Petersburg Russian Federation
| | | | | | - Dmitry M Kolpashchikov
- ITMO University Lomonosova St. 9 191002 St. Petersburg Russian Federation
- Chemistry Department University of Central Florida Orlando FL USA
| | - Ekaterina V Skorb
- ITMO University Lomonosova St. 9 191002 St. Petersburg Russian Federation
| |
Collapse
|