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Lee M, Kim M, Lee M, Kim S, Park N. Nanosized DNA Hydrogel Functionalized with a DNAzyme Tetrahedron for Highly Efficient Gene Silencing. Biomacromolecules 2024; 25:4913-4924. [PMID: 38963792 DOI: 10.1021/acs.biomac.4c00356] [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: 07/06/2024]
Abstract
DNAzymes are DNA oligonucleotides that have catalytic activity without the assistance of protein enzymes. In particular, RNA-cleaving DNAzymes were considered as ideal candidates for gene therapy due to their unique characteristics. Nevertheless, efforts to use DNAzyme as a gene therapeutic agent are limited by issues such as their low physiological stability in serum and intracellular delivery efficiency. In this study, we developed a nanosized synthetic DNA hydrogel functionalized with a DNAzyme tetrahedron (TDz Dgel) to overcome these limitations. We observed remarkable improvement in the gene-silencing effect as well as intracellular uptake without the support of gene transfection reagents using TDz Dgel. The improved catalytic activity of the DNAzyme resulted from the combination of the cell-penetrating DNA tetrahedron structure and high stability of DNA hydrogel. We envision that this approach will become a convenient and efficient strategy for gene-silencing therapy using DNAzyme in the future.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Minchul Kim
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
| | - Minjae Lee
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
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Wang Q, Du Y, Zheng J, Shi L, Li T. G-Quadruplex-Programmed Versatile Nanorobot Combined with Chemotherapy and Gene Therapy for Synergistic Targeted Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400267. [PMID: 38805747 DOI: 10.1002/smll.202400267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/29/2024] [Indexed: 05/30/2024]
Abstract
Developing synergistic targeted therapeutics to improve treatment efficacy while reducing side effects has proven promising for anticancer therapies, but how to conveniently modulate multidrug cooperation remains a challenge. Here, a novel synergistic strategy using a G-quadruplex-programmed versatile nanorobot (G4VN) containing two subunits of DNAzyme (DzG4) and ligand-drug conjugates (LDCs) is proposed to precisely target tumors and then execute both gene silencing and chemotherapy. As the core module of this nanorobot, a well-designed G4 responding to a high level of K+ in tumor microenvironment smartly kills three birds with one stone, which makes two TfR aptamers proximate to improve their efficiency of targeting tumor cells, and in situ activates a split 10-23 DNAzyme to downregulate target mRNA expression, meanwhile promotes the cell uptake of a GSH-responsive LDCs to enhance drug efficacy. Such a design enables a potently synergistic anticancer therapy with low side effects in vivo, showing great promise for broad applications in precision disease treatment.
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Affiliation(s)
- Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Jiao Zheng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Lili Shi
- Department of Chemistry, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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3
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Chen M, Li M, Ren X, Zhou F, Li Y, Tan L, Luo Z, Cai K, Hu Y. DNAzyme Nanoconstruct-Integrated Autonomously-Adaptive Coatings Enhance Titanium-Implant Osteointegration by Cooperative Angiogenesis and Vessel Remodeling. ACS NANO 2023; 17:15942-15961. [PMID: 37566558 DOI: 10.1021/acsnano.3c04049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Orthopedic implants have a high failure rate due to insufficient interfacial osseointegration, especially under osteoporotic conditions. Type H vessels are CD31+EMCN+ capillaries with crucial roles in mediating new bone formation, but their abundance in osteoporotic fracture site is highly limited. Herein, we report a nanoengineered composite coating to improve the in situ osseointegration of a Ti implant for osteoporotic fracture repair, which is realized through inhibiting the stimulator of interferon genes (STING) in endothelial cells (ECs) to stimulate type H vessel formation. Autonomously catalytic DNAzyme-ZnO nanoflowers (DNFzns) were prepared through rolling circle amplification (RCA) of STING mRNA-degrading DNAzymes, which were then integrated on the Ti surface and further sequentially complexed with thioketal-bridged polydopamine and naringenin (Ti/DNFzn/PDA-Nar). ECs and mesenchymal stem cells (MSCs) can be recruited to the implant surface by galvanotaxis, accounting for the negative charges of DNFzn/PDA-Nar, subsequently released Nar under reactive oxygen species (ROS) stimulation to upregulate endothelial nitric oxide synthase (eNOS) in recruited ECs, leading to enhanced local angiogenesis. Meanwhile, the coordinately released DNFzns would abolish STING expression in ECs to transform the newly formed vessels into Type H vessels, thus substantially promoting the osseointegration of Ti implants. This study provides application prospects for improving implant osteointegration for osteoporotic fracture treatment.
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Affiliation(s)
- Maohua Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Menghuan Li
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Xijiao Ren
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Fei Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yanan Li
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Lu Tan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Zhong Luo
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yan Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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Chiba K, Yamaguchi T, Obika S. Development of 8-17 XNAzymes that are functional in cells. Chem Sci 2023; 14:7620-7629. [PMID: 37476720 PMCID: PMC10355097 DOI: 10.1039/d3sc01928d] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
DNA enzymes (DNAzymes), which cleave target RNA with high specificity, have been widely investigated as potential oligonucleotide-based therapeutics. Recently, xeno-nucleic acid (XNA)-modified DNAzymes (XNAzymes), exhibiting cleavage activity in cultured cells, have been developed. However, a versatile approach to modify XNAzymes that function in cells has not yet been established. Here, we report an X-ray crystal structure-based approach to modify 8-17 DNAzymes; this approach enables us to effectively locate suitable XNAs to modify. Our approach, combined with a modification strategy used in designing antisense oligonucleotides, rationally designed 8-17 XNAzyme ("X8-17") that achieved high potency in terms of RNA cleavage and biostability against nucleases. X8-17, modified with 2'-O-methyl RNA, locked nucleic acid and phosphorothioate, successfully induced endogenous MALAT-1 and SRB1 RNA knockdown in cells. This approach may help in developing XNAzyme-based novel therapeutic agents.
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Affiliation(s)
- Kosuke Chiba
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
- National Institutes of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi Ibaraki Osaka 567-0085 Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University 1-1 Yamadaoka Suita Osaka 565-0871 Japan
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Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
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Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
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Hu O, Li Z, Wu J, Tan Y, Chen Z, Tong Y. A Multicomponent Nucleic Acid Enzyme-Cleavable Quantum Dot Nanobeacon for Highly Sensitive Diagnosis of Tuberculosis with the Naked Eye. ACS Sens 2023; 8:254-262. [PMID: 36579361 DOI: 10.1021/acssensors.2c02114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Clinical tuberculosis (TB) screening and diagnosis are crucial for controlling the spread of this life-threatening infectious disease. In this work, a novel, rapid, and simple colorimetric detection platform for TB was developed based on a quantum dot-based nanobeacon (QD-NB) and multicomponent nucleic acid enzyme (MNAzyme). In the presence of target DNA (IS1081 gene fragment), the recombinase polymerase amplification (RPA) was performed and the amplicons were chemically DNA-denatured and then subjected to MNAzyme reaction. RNA-cleaving MNAzyme assembly included the recognition of target DNA and hybridization with a QD-NB fluorescence probe. Under the addition of Mg2+, the RNA-containing QD-NB as a cleavable substrate could be broken into two DNA fragments, leading to green fluorescence release due to their departure from a black hole quencher (BHQ2). The TB detection could be achieved with the naked eye under a portable and inexpensive UV flashlight. Our results demonstrated that QD-NB-based MNAzyme colorimetric assays improved the detection sensitivity by 1 order of magnitude compared with the detection using RPA. The limit of detection (LOD) of the visual reading was as low as 2 copies/μL (3.3 amol/L). Excellent specificity and reproducibility could also be achieved. Furthermore, the practical application of the colorimetric method for TB diagnosis was verified by 36 clinical TB patients and 20 healthy individuals. The developed QD-NB-based MNAzyme colorimetric assays provided a rapid, convenient, sensitive, and accurate alternative for clinical TB screening and diagnosis.
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Affiliation(s)
- Ou Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, P. R. China
| | - Zeyu Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, P. R. China
| | - Jinghao Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, P. R. China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, Guangzhou 510095, P. R. China
| | - Zuanguang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, P. R. China
| | - Yanli Tong
- Guangdong Second Provincial General Hospital, Guangzhou, Guangzhou 510317, P. R. China
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Taylor AI, Wan CJK, Donde MJ, Peak-Chew SY, Holliger P. A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat Chem 2022; 14:1295-1305. [PMID: 36064973 PMCID: PMC7613789 DOI: 10.1038/s41557-022-01021-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/08/2022] [Indexed: 11/07/2022]
Abstract
Nucleic-acid catalysts (ribozymes, DNA- and XNAzymes) cleave target (m)RNAs with high specificity but have shown limited efficacy in clinical applications. Here we report on the in vitro evolution and engineering of a highly specific modular RNA endonuclease XNAzyme, FR6_1, composed of 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid (FANA). FR6_1 overcomes the activity limitations of previous DNA- and XNAzymes and can be retargeted to cleave highly structured full-length (>5 kb) BRAF and KRAS mRNAs at physiological Mg2+ concentrations with allelic selectivity for tumour-associated (BRAF V600E and KRAS G12D) mutations. Phosphorothioate-FANA modification enhances FR6_1 biostability and enables rapid KRAS mRNA knockdown in cultured human adenocarcinoma cells with a G12D-allele-specific component provided by in vivo XNAzyme cleavage activity. These results provide a starting point for the development of improved gene-silencing agents based on FANA or other XNA chemistries.
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Affiliation(s)
- Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK.
| | | | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
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Targeting non-coding RNA family members with artificial endonuclease XNAzymes. Commun Biol 2022; 5:1010. [PMID: 36153384 PMCID: PMC9509326 DOI: 10.1038/s42003-022-03987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractNon-coding RNAs (ncRNAs) offer a wealth of therapeutic targets for a range of diseases. However, secondary structures and high similarity within sequence families make specific knockdown challenging. Here, we engineer a series of artificial oligonucleotide enzymes (XNAzymes) composed of 2’-deoxy-2’-fluoro-β-D-arabino nucleic acid (FANA) that specifically or preferentially cleave individual ncRNA family members under quasi-physiological conditions, including members of the classic microRNA cluster miR-17~92 (oncomiR-1) and the Y RNA hY5. We demonstrate self-assembly of three anti-miR XNAzymes into a biostable catalytic XNA nanostructure, which targets the cancer-associated microRNAs miR-17, miR-20a and miR-21. Our results provide a starting point for the development of XNAzymes as a platform technology for precision knockdown of specific non-coding RNAs, with the potential to reduce off-target effects compared with other nucleic acid technologies.
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Spitale RC, Chaput JC. Reply to: On gene silencing by the X10-23 DNAzyme. Nat Chem 2022; 14:859-861. [DOI: 10.1038/s41557-022-00983-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
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