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Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
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Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
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Nedorezova DD, Dubovichenko MV, Eldeeb AA, Nur MAY, Bobkov GA, Ashmarova AI, Kalnin AJ, Kolpashchikov DM. Cleaving Folded RNA by Multifunctional DNAzyme Nanomachines. Chemistry 2024; 30:e202401580. [PMID: 38757205 DOI: 10.1002/chem.202401580] [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: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Both tight and specific binding of folded biological mRNA is required for gene silencing by oligonucleotide gene therapy agents. However, this is fundamentally impossible using the conventional oligonucleotide probes according to the affinity/specificity dilemma. This study addresses this problem for cleaving folded RNA by using multicomponent agents (dubbed 'DNA nanomachine' or DNM). DNMs bind RNA by four short RNA binding arms, which ensure tight and highly selective RNA binding. Along with the improved affinity, DNM maintain the high sequence selectivity of the conventional DNAzymes. DNM enabled up to 3-fold improvement in DNAzymes catalytic efficiency (kcat/Km) by facilitating both RNA substrate binding and product release steps of the catalytic cycle. This study demonstrates that multicomponent probes organized in sophisticated structures can help to achieve the balance between affinity and selectivity in recognizing folded RNA and thus creates a foundation for applying complex DNA nanostructures derived by DNA nanotechnology in gene therapy.
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Affiliation(s)
- Daria D Nedorezova
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Mikhail V Dubovichenko
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Ahmed A Eldeeb
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Moustapha A Y Nur
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Gleb A Bobkov
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Anna I Ashmarova
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Arsenij J Kalnin
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816
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Wu L, Yuan R, Wen T, Qin Y, Wang Y, Luo X, Liu JW. Recent advances in functional nucleic acid decorated nanomaterials for cancer imaging and therapy. Biomed Pharmacother 2024; 174:116546. [PMID: 38603885 DOI: 10.1016/j.biopha.2024.116546] [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] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
Nanomaterials possess unusual physicochemical properties including unique optical, magnetic, electronic properties, and large surface-to-volume ratio. However, nanomaterials face some challenges when they were applied in the field of biomedicine. For example, some nanomaterials suffer from the limitations such as poor selectivity and biocompatibility, low stability, and solubility. To address the above-mentioned obstacles, functional nucleic acid has been widely served as a powerful and versatile ligand for modifying nanomaterials because of their unique characteristics, such as ease of modification, excellent biocompatibility, high stability, predictable intermolecular interaction and recognition ability. The functionally integrating functional nucleic acid with nanomaterials has produced various kinds of nanocomposites and recent advances in applications of functional nucleic acid decorated nanomaterials for cancer imaging and therapy were summarized in this review. Further, we offer an insight into the future challenges and perspectives of functional nucleic acid decorated nanomaterials.
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Affiliation(s)
- Liu Wu
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Ruitao Yuan
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Tong Wen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Yingfeng Qin
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Yumin Wang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| | - Xiaoling Luo
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China.
| | - Jin-Wen Liu
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China.
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Nedorezova DD, Dubovichenko MV, Kalnin AJ, Nour MAY, Eldeeb AA, Ashmarova AI, Kurbanov GF, Kolpashchikov DM. Cleaving Folded RNA with DNAzyme Agents. Chembiochem 2024; 25:e202300637. [PMID: 37870555 DOI: 10.1002/cbic.202300637] [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: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Cleavage of biological mRNA by DNAzymes (Dz) has been proposed as a variation of oligonucleotide gene therapy (OGT). The design of Dz-based OGT agents includes computational prediction of two RNA-binding arms with low affinity (melting temperatures (Tm ) close to the reaction temperature of 37 °C) to avoid product inhibition and maintain high specificity. However, RNA cleavage might be limited by the RNA binding step especially if the RNA is folded in secondary structures. This calls for the need for two high-affinity RNA-binding arms. In this study, we optimized 10-23 Dz-based OGT agents for cleavage of three RNA targets with different folding energies under multiple turnover conditions in 2 mM Mg2+ at 37 °C. Unexpectedly, one optimized Dz had each RNA-binding arm with a Tm ≥60 °C, without suffering from product inhibition or low selectivity. This phenomenon was explained by the folding of the RNA cleavage products into stable secondary structures. This result suggests that Dz with long (high affinity) RNA-binding arms should not be excluded from the candidate pool for OGT agents. Rather, analysis of the cleavage products' folding should be included in Dz selection algorithms. The Dz optimization workflow should include testing with folded rather than linear RNA substrates.
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Affiliation(s)
- Daria D Nedorezova
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Mikhail V Dubovichenko
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Arseniy J Kalnin
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Ahmed A Eldeeb
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Anna I Ashmarova
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Gabdulla F Kurbanov
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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Wang S, Shang J, Zhao B, Wang H, Yang C, Liu X, Wang F. Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications. Chempluschem 2023; 88:e202300432. [PMID: 37706615 DOI: 10.1002/cplu.202300432] [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] [Received: 08/06/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023]
Abstract
The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.
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Affiliation(s)
- Siyuan Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Jinhua Shang
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Bingyue Zhao
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Huimin Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Changying Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Xiaoqing Liu
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Fuan Wang
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
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Pine AC, Brooke GN, Marco A. A computational approach to identify efficient RNA cleaving 10-23 DNAzymes. NAR Genom Bioinform 2023; 5:lqac098. [PMID: 36632612 PMCID: PMC9830538 DOI: 10.1093/nargab/lqac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
DNAzymes are short pieces of DNA with catalytic activity, capable of cleaving RNA. DNAzymes have multiple applications as biosensors and in therapeutics. The high specificity and low toxicity of these molecules make them particularly suitable as therapeutics, and clinical trials have shown that they are effective in patients. However, the development of DNAzymes has been limited due to the lack of specific tools to identify efficient molecules, and users often resort to time-consuming/costly large-scale screens. Here, we propose a computational methodology to identify 10-23 DNAzymes that can be used to triage thousands of potential molecules, specific to a target RNA, to identify those that are predicted to be efficient. The method is based on a logistic regression and can be trained to incorporate additional DNAzyme efficiency data, improving its performance with time. We first trained the method with published data, and then we validated, and further refined it, by testing additional newly synthesized DNAzymes in the laboratory. We found that although binding free energy between the DNAzyme and its RNA target is the primary determinant of efficiency, other factors such as internal structure of the DNAzyme also have an important effect. A program implementing the proposed method is publicly available.
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Affiliation(s)
- Angela C Pine
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Greg N Brooke
- Correspondence may also be addressed to Greg N. Brooke.
| | - Antonio Marco
- To whom correspondence should be addressed. Tel: +44 1206 87 3339;
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Nedorezova DD, Dubovichenko MV, Belyaeva EP, Grigorieva ED, Peresadina AV, Kolpashchikov DM. Specificity of oligonucleotide gene therapy (OGT) agents. Theranostics 2022; 12:7132-7157. [PMID: 36276652 PMCID: PMC9576606 DOI: 10.7150/thno.77830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide gene therapy (OGT) agents (e. g. antisense, deoxyribozymes, siRNA and CRISPR/Cas) are promising therapeutic tools. Despite extensive efforts, only few OGT drugs have been approved for clinical use. Besides the problem of efficient delivery to targeted cells, hybridization specificity is a potential limitation of OGT agents. To ensure tight binding, a typical OGT agent hybridizes to the stretch of 15-25 nucleotides of a unique targeted sequence. However, hybrids of such lengths tolerate one or more mismatches under physiological conditions, the problem known as the affinity/specificity dilemma. Here, we assess the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTE) in vitro, in animal models and clinical studies. All OGT agents except deoxyribozymes exhibit HD OTE in vitro, with most thorough evidence of poor specificity reported for siRNA and CRISPR/Cas9. Notably, siRNA suppress non-targeted genes due to (1) the partial complementarity to mRNA 3'-untranslated regions (3'-UTR), and (2) the antisense activity of the sense strand. CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. Contribution of this effects to the observed in vivo toxicity of OGT agents is unclear and requires further investigation. Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo.
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Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Mikhail V. Dubovichenko
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina P. Belyaeva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina D. Grigorieva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Arina V. Peresadina
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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