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Wang S, Guang J, Gao Y, Fan B, Liang Y, Pan J, Li L, Meng W, Hu F. Fluorescent DNA tetrahedral probe with catalytic hairpin self-assembly reaction for imaging of miR-21 and miR-155 in living cells. Mikrochim Acta 2024; 191:462. [PMID: 38990374 DOI: 10.1007/s00604-024-06529-4] [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: 03/29/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
A CHA-based fluorescent DNA tetrahedral probe (FDTp) has been designed to detect the microRNAs miR-21 and miR-155 sensitively and specifically in living cells. The design consisted of functional elements (H1, H2, and Protector) connected to a DNA tetrahedron modified with two pairs of fluorophores and quenching groups. In the presence of miR-21, the chain displacement effect was triggered and Cy3 fluorescence was emitted. In the presence of miR-155, the signal of the catalytic hairpin assembly (CHA) between H1 and H2 on FDTp was amplified, making the fluorescence of FAM sensitive to miR-155. Using this method, the detection limit for miR-155 was 5 pM. The FDTp successfully imaged miR-21 and miR-155 in living cells and distinguished a variety of cell lines based on their expression levels of miR-21 and miR-155. The detection and imaging of dual targets in this design ensured the accuracy of tumor diagnosis and provided a new method for early tumor diagnosis.
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Affiliation(s)
- Shan Wang
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiejie Guang
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
- Pharmacy Department, Huangshan City People's Hospital, Liyuan Road, Tunxi District, Huangshan, 245000, China
| | - Yahui Gao
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Bingyuan Fan
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Yan Liang
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Jinru Pan
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Li
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.
| | - Wei Meng
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China.
| | - Fang Hu
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China.
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2
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Cao G, Yang N, Yang J, Li J, Wang L, Nie F, Huo D, Hou C. Label-Free and DNAzyme-Mediated Biosensor with a High Signal-to-Noise Ratio for a Lumpy Skin Disease Virus Assay. Anal Chem 2024; 96:10927-10934. [PMID: 38934225 DOI: 10.1021/acs.analchem.4c00962] [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: 06/28/2024]
Abstract
Lumpy skin disease virus (LSDV) is a severe and highly contagious form of cowpox. As LSDV continues to mutate and there is no vaccine and treatment in nonendemic countries, early detection of LSDV becomes an important basis for epidemic prevention and control, especially for detection of conserved sequences. A new label-free and sensitive fluorescence method was developed based on a light-up RNA aptamer for detecting LSDV. The method integrated recombinase polymerase amplification (RPA), CRISPR/Cas12a, 10-23 DNAzyme, and Baby Spinach RNA aptamer for triple cascade signal amplification. Based on highly sensitive and specific RPA and CRISPR/Cas12a, DNAzyme achieved a third signal amplification. Additionally, the Baby Spinach RNA aptamer had stronger fluorescence signals and higher quantum yields. The label-free method had ultrahigh sensitivity with the actual detection limit as 1.29 copies·μL-1. The method was 100-fold more sensitive compared to RPA with Cas12a. Moreover, it had no cross-reactivity with viruses belonging to the Capripoxvirus, such as sheep pox virus and goat pox virus with genetic homology as 97%. Furthermore, the method displayed 100% accuracy in 50 actual samples. Therefore, the method based on RPA, Cas12a, and 10-23 DNAzyme had advantages in LSDV detection and provided a new solution for LSD prevention and control.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Nannan Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Jun Yang
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Jiali Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Lin Wang
- Science and Technology Research Center of China Customs, Beijing 100026, PR China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, PR China
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3
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Sun J, Chen X, Lin Y, Cai X. MicroRNA-29c-tetrahedral framework nucleic acids: Towards osteogenic differentiation of mesenchymal stem cells and bone regeneration in critical-sized calvarial defects. Cell Prolif 2024; 57:e13624. [PMID: 38414296 PMCID: PMC11216942 DOI: 10.1111/cpr.13624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Certain miRNAs, notably miR29c, demonstrate a remarkable capacity to regulate cellular osteogenic differentiation. However, their application in tissue regeneration is hampered by their inherent instability and susceptibility to degradation. In this study, we developed a novel miR29c delivery system utilising tetrahedral framework nucleic acids (tFNAs), aiming to enhance its stability and endocytosis capability, augment the efficacy of miR29c, foster osteogenesis in bone marrow mesenchymal stem cells (BMSCs), and significantly improve the repair of critical-sized bone defects (CSBDs). We confirmed the successful synthesis and biocompatibility of sticky ends-modified tFNAs (stFNAs) and miR29c-modified stFNAs (stFNAs-miR29c) through polyacrylamide gel electrophoresis, microscopy scanning, a cell counting kit-8 assay and so on. The mechanism and osteogenesis effects of stFNAs-miR29c were explored using immunofluorescence staining, western blotting, and reserve transcription quantitative real-time polymerase chain reaction. Additionally, the impact of stFNAs-miR29c on CSBD repair was assessed via micro-CT and histological staining. The nano-carrier, stFNAs-miR29c was successfully synthesised and exhibited exemplary biocompatibility. This nano-nucleic acid material significantly upregulated osteogenic differentiation-related markers in BMSCs. After 2 months, stFNAs-miR29c demonstrated significant bone regeneration and reconstruction in CSBDs. Mechanistically, stFNAs-miR29c enhanced osteogenesis of BMSCs by upregulating the Wnt signalling pathway, contributing to improved bone tissue regeneration. The development of this novel nucleic acid nano-carrier, stFNAs-miR29c, presents a potential new avenue for guided bone regeneration and bone tissue engineering research.
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Affiliation(s)
- Jiafei Sun
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduChina
- Sichuan Provincial Engineering Research Center of Oral BiomaterialsChengduSichuanChina
| | - Xingyu Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduChina
- Sichuan Provincial Engineering Research Center of Oral BiomaterialsChengduSichuanChina
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduChina
- Sichuan Provincial Engineering Research Center of Oral BiomaterialsChengduSichuanChina
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduChina
- Sichuan Provincial Engineering Research Center of Oral BiomaterialsChengduSichuanChina
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4
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Volek M, Kurfürst J, Kožíšek M, Srb P, Veverka V, Curtis EA. Apollon: a deoxyribozyme that generates a yellow product. Nucleic Acids Res 2024:gkae490. [PMID: 38869058 DOI: 10.1093/nar/gkae490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024] Open
Abstract
Colorimetric assays in which the color of a solution changes in the presence of an input provide a simple and inexpensive way to monitor experimental readouts. In this study we used in vitro selection to identify a self-phosphorylating kinase deoxyribozyme that produces a colorimetric signal by converting the colorless substrate pNPP into the yellow product pNP. The minimized catalytic core, sequence requirements, secondary structure, and buffer requirements of this deoxyribozyme, which we named Apollon, were characterized using a variety of techniques including reselection experiments, high-throughput sequencing, comparative analysis, biochemical activity assays, and NMR. A bimolecular version of Apollon catalyzed multiple turnover phosphorylation and amplified the colorimetric signal. Engineered versions of Apollon could detect oligonucleotides with specific sequences as well as several different types of nucleases in homogenous assays that can be performed in a single tube without the need for washes or purifications. We anticipate that Apollon will be particularly useful to reduce costs in high-throughput screens and for applications in which specialized equipment is not available.
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Affiliation(s)
- Martin Volek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Jaroslav Kurfürst
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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5
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Volek M, Kurfürst J, Drexler M, Svoboda M, Srb P, Veverka V, Curtis EA. Aurora: a fluorescent deoxyribozyme for high-throughput screening. Nucleic Acids Res 2024:gkae467. [PMID: 38860424 DOI: 10.1093/nar/gkae467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Fluorescence facilitates the detection, visualization, and tracking of molecules with high sensitivity and specificity. A functional DNA molecule that generates a robust fluorescent signal would offer significant advantages for many applications compared to intrinsically fluorescent proteins, which are expensive and labor intensive to synthesize, and fluorescent RNA aptamers, which are unstable under most conditions. Here, we describe a novel deoxyriboyzme that rapidly and efficiently generates a stable fluorescent product using a readily available coumarin substrate. An engineered version can detect picomolar concentrations of ribonucleases in a simple homogenous assay, and was used to rapidly identify novel inhibitors of the SARS-CoV-2 ribonuclease Nsp15 in a high-throughput screen. Our work adds an important new component to the toolkit of functional DNA parts, and also demonstrates how catalytic DNA motifs can be used to solve real-world problems.
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Affiliation(s)
- Martin Volek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Jaroslav Kurfürst
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Matúš Drexler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Michal Svoboda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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6
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Ali M, Nair P, Capretta A, Brennan JD. In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes. Chembiochem 2024; 25:e202400085. [PMID: 38574237 DOI: 10.1002/cbic.202400085] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.
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Affiliation(s)
- Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, and, Firestone Institute of Respiratory Health at St. Joseph's Health Care, Hamilton, ON, L8N 4A6, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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7
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Wieruszewska J, Pawłowicz A, Połomska E, Pasternak K, Gdaniec Z, Andrałojć W. The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor. Nat Commun 2024; 15:4218. [PMID: 38760331 PMCID: PMC11101458 DOI: 10.1038/s41467-024-48638-x] [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: 04/13/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
DNAzymes - synthetic enzymes made of DNA - have long attracted attention as RNA-targeting therapeutic agents. Yet, as of now, no DNAzyme-based drug has been approved, partially due to our lacking understanding of their molecular mode of action. In this work we report the solution structure of 8-17 DNAzyme bound to a Zn2+ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb2+-bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb2+ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions - Mg2+, Na+, and Pb2+ - suggest that at DNAzyme concentrations used in NMR all these ions induce a similar tertiary fold. Based on these findings, we propose a model for 8-17 DNAzyme interactions with metal ions postulating the existence of only a single catalytically-active structure, yet populated to a different extent depending on the metal ion cofactor. Our results provide structural information on the 8-17 DNAzyme in presence of non-Pb2+ cofactors, including the biologically relevant Mg2+ ion.
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Affiliation(s)
- Julia Wieruszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Aleksandra Pawłowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Ewa Połomska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland.
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Wang M, Liu Z, Liu C, He W, Qin D, You M. DNAzyme-based ultrasensitive immunoassay: Recent advances and emerging trends. Biosens Bioelectron 2024; 251:116122. [PMID: 38382271 DOI: 10.1016/j.bios.2024.116122] [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: 10/18/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Immunoassay, as the most commonly used method for protein detection, is simple to operate and highly specific. Sensitivity improvement is always the thrust of immunoassays, especially for the detection of trace quantities. The emergence of artificial enzyme, i.e., DNAzyme, provides a novel approach to improve the detection sensitivity of immunoassay. Simultaneously, its advantages of simple synthesis and high stability enable low cost, broad applicability and long shelf life for immunoassay. In this review, we summarized the recent advances in DNAzyme-based immunoassay. First, we summarized the existing different DNAzymes based on their catalytic activities. Next, the common signal amplification strategies used for DNAzyme-based immunoassays were reviewed to cater to diverse detection requirements. Following, the wide applications in disease diagnosis, environmental monitoring and food safety were discussed. Finally, the current challenges and perspectives on the future development of DNAzyme-based immunoassays were also provided.
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Affiliation(s)
- Meng Wang
- Department of Biomedical Engineering, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Zhe Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China; Department of Rehabilitation Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, PR China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Wanghong He
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China; Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, PR China
| | - Dui Qin
- Department of Biomedical Engineering, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China.
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
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9
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Wang B, Pan X, Teng IT, Li X, Kobeissy F, Wu ZY, Zhu J, Cai G, Yan H, Yan X, Liang M, Yu F, Lu J, Yang Z, Biondi E, Haskins W, Cao YC, Benner SA, Tan W, Wang KK. Functional Selection of Tau Oligomerization-Inhibiting Aptamers. Angew Chem Int Ed Engl 2024; 63:e202402007. [PMID: 38407551 DOI: 10.1002/anie.202402007] [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: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Pathological hyperphosphorylation and aggregation of microtubule-associated Tau protein contribute to Alzheimer's Disease (AD) and other related tauopathies. Currently, no cure exists for Alzheimer's Disease. Aptamers offer significant potential as next-generation therapeutics in biotechnology and the treatment of neurological disorders. Traditional aptamer selection methods for Tau protein focus on binding affinity rather than interference with pathological Tau. In this study, we developed a new selection strategy to enrich DNA aptamers that bind to surviving monomeric Tau protein under conditions that would typically promote Tau aggregation. Employing this approach, we identified a set of aptamer candidates. Notably, BW1c demonstrates a high binding affinity (Kd=6.6 nM) to Tau protein and effectively inhibits arachidonic acid (AA)-induced Tau protein oligomerization and aggregation. Additionally, it inhibits GSK3β-mediated Tau hyperphosphorylation in cell-free systems and okadaic acid-mediated Tau hyperphosphorylation in cellular milieu. Lastly, retro-orbital injection of BW1c tau aptamer shows the ability to cross the blood brain barrier and gain access to neuronal cell body. Through further refinement and development, these Tau aptamers may pave the way for a first-in-class neurotherapeutic to mitigate tauopathy-associated neurodegenerative disorders.
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Affiliation(s)
- Bang Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Xiaoshu Pan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - I-Ting Teng
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Xiaowei Li
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Firas Kobeissy
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Zo-Yu Wu
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Jiepei Zhu
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Guangzheng Cai
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - He Yan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Xin Yan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Mingwei Liang
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Fahong Yu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Elisa Biondi
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080-7066, USA
| | - Y Charles Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Kevin K Wang
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080-7066, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, FL 32608, USA
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10
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [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: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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11
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Smirnov VV, Drozd VS, Patra CK, Hussein Z, Rybalko DS, Kozlova AV, Nour MAY, Zemerova TP, Kolosova OS, Kalnin AY, El-Deeb AA. Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs. Analyst 2024; 149:1947-1957. [PMID: 38385166 DOI: 10.1039/d3an02178e] [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: 02/23/2024]
Abstract
Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.
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Affiliation(s)
- Viktor V Smirnov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Valerya S Drozd
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Christina K Patra
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Daria S Rybalko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Tatiana P Zemerova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Olga S Kolosova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Faculty of Industrial Drug Technology, Saint Petersburg State Chemical and Pharmaceutical University, 14, lit. A, st. Professor Popov, 197022, St. Petersburg, Russian Federation
| | - Arseniy Y Kalnin
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Institute of Chemistry, Saint Petersburg University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
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12
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Takezawa Y, Zhang H, Mori K, Hu L, Shionoya M. Ligase-mediated synthesis of Cu II-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases. Chem Sci 2024; 15:2365-2370. [PMID: 38362437 PMCID: PMC10866359 DOI: 10.1039/d3sc05042d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both hydrogen-bonded caU-A and metal-mediated caU-CuII-caU base pairs. The base sequence was logically designed based on a known RNA-cleaving DNAzyme so that the caU-modified DNAzyme (caU-DNAzyme) can form a catalytically inactive structure containing three caU-A base pairs and an active form with three caU-CuII-caU pairs. The caU-DNAzyme was synthesized by joining short caU-containing fragments with a standard DNA ligase. The activity of caU-DNAzyme was suppressed without CuII, but enhanced 21-fold with the addition of CuII. Furthermore, the DNAzyme activity was turned on and off during the reaction by the addition and removal of CuII ions. Both ligase-mediated synthesis and CuII-dependent allosteric regulation were achieved by the bifacial base pairing properties of caU. This study provides a new strategy for designing stimuli-responsive DNA molecular systems.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hanci Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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13
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Kennebeck MM, Kaminsky CK, Massa MA, Das PK, Boyd RD, Bishka M, Tricarico JT, Silverman SK. DNAzyme-Catalyzed Site-Specific N-Acylation of DNA Oligonucleotide Nucleobases. Angew Chem Int Ed Engl 2024; 63:e202317565. [PMID: 38157448 PMCID: PMC10873475 DOI: 10.1002/anie.202317565] [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: 11/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
We used in vitro selection to identify DNAzymes that acylate the exocyclic nucleobase amines of cytidine, guanosine, and adenosine in DNA oligonucleotides. The acyl donor was the 2,3,5,6-tetrafluorophenyl ester (TFPE) of a 5'-carboxyl oligonucleotide. Yields are as high as >95 % in 6 h. Several of the N-acylation DNAzymes are catalytically active with RNA rather than DNA oligonucleotide substrates, and eight of nine DNAzymes for modifying C are site-specific (>95 %) for one particular substrate nucleotide. These findings expand the catalytic ability of DNA to include site-specific N-acylation of oligonucleotide nucleobases. Future efforts will investigate the DNA and RNA substrate sequence generality of DNAzymes for oligonucleotide nucleobase N-acylation, toward a universal approach for site-specific oligonucleotide modification.
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Affiliation(s)
- Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Caroline K Kaminsky
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Maria A Massa
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Prakriti K Das
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Michelle Bishka
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - J Tomas Tricarico
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Scott K Silverman
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
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14
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Rath WH, Göstl R, Herrmann A. Mechanochemical Activation of DNAzyme by Ultrasound. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306236. [PMID: 38308193 PMCID: PMC10885644 DOI: 10.1002/advs.202306236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Controlling the activity of DNAzymes by external triggers is an important task. Here a temporal control over DNAzyme activity through a mechanochemical pathway with the help of ultrasound (US) is demonstrated. The deactivation of the DNAzyme is achieved by hybridization to a complementary strand generated through rolling circle amplification (RCA), an enzymatic polymerization process. Due to the high molar mass of the resulting polynucleic acids, shear force can be applied on the RCA strand through inertial cavitation induced by US. This exerts mechanical force and leads to the cleavage of the base pairing between RCA strand and DNAzyme, resulting in the recovery of DNAzyme activity. This is the first time that this release mechanism is applied for the activation of catalytic nucleic acids, and it has multiple advantages over other stimuli. US has higher penetration depth into tissues compared to light, and it offers a more specific stimulus than heat, which has also limited use in biological systems due to cell damage caused by hyperthermia. This approach is envisioned to improve the control over DNAzyme activity for the development of reliable and specific sensing applications.
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Affiliation(s)
- Wolfgang H. Rath
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Robert Göstl
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Andreas Herrmann
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
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15
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Wang X, Yu B, Sakurabayashi S, Paz-Villatoro JM, Iwahara J. Robust Enzymatic Production of DNA G-Quadruplex, Aptamer, DNAzyme, and Other Oligonucleotides: Applications for NMR. J Am Chem Soc 2024; 146:1748-1752. [PMID: 38191993 PMCID: PMC10926321 DOI: 10.1021/jacs.3c11219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Single-stranded DNA (ssDNA) oligonucleotides are widely used in biological research, therapeutics, biotechnology, and nanomachines. Large-scale enzymatic production of ssDNA oligonucleotides forming noncanonical structures has been difficult. Here, we present a simple and robust method named "palindrome-nicking-dependent amplification" (PaNDA) for enzymatic production of a large amount of ssDNA oligonucleotides. It utilizes a strand-displacing DNA polymerase and a nicking enzyme together with input DNA and deoxynucleotide triphosphates at 55 °C. Scaling up of PaNDA is straightforward due to its isothermal nature. The ssDNA products can easily be isolated through anion-exchange chromatography under nondenaturing conditions. We demonstrate applications of PaNDA to 13C/15N-labeling of various DNA strands, including a 22-nt telomere repeat G-quadruplex, a 26-nt therapeutic aptamer, and a 33-nt DNAzyme. The 13C/15N-labeling by PaNDA greatly facilitates the characterization of noncanonical DNA by nuclear magnetic resonance (NMR) spectroscopy. For example, the behavior of therapeutic DNA aptamers in human serum can be investigated.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Shuhei Sakurabayashi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Jonathan M Paz-Villatoro
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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16
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Liu J, Cui L, Shi X, Yan J, Wang Y, Ni Y, He J, Wang X. Generation of DNAzyme in Bacterial Cells by a Bacterial Retron System. ACS Synth Biol 2024; 13:300-309. [PMID: 38171507 DOI: 10.1021/acssynbio.3c00509] [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: 01/05/2024]
Abstract
DNAzymes are catalytically active single-stranded DNAs in which DNAzyme 10-23 (Dz 10-23) consists of a catalytic core and a substrate-binding arm that reduces gene expression through sequence-specific mRNA cleavage. However, the in vivo application of Dz 10-23 depends on exogenous delivery, which leads to its inability to be synthesized and stabilized in vivo, thus limiting its application. As a unique reverse transcription system, the bacterial retron system can synthesize single-stranded DNA in vivo using ncRNA msr/msd as a template. The objective of this work is to reduce target gene expression using Dz 10-23 generated in vivo by the retron system. In this regard, we successfully generated Dz 10-23 by cloning the Dz 10-23 coding sequence into the retron msd gene and tested its ability to reduce specific gene expression by examining the mRNA levels of cfp encoding cyan fluorescence protein and other functional genes such as mreB and ftsZ. We found that Dz had different repressive effects when targeting different mRNA regions, and in general, the repressive effect was stronger when targeting downstream of mRNAs. Our results also suggested that the reduction effect was due to cleavage of the substrate mRNA by Dz 10-23 rather than the antisense effect of the substrate-binding arm. Therefore, this study not only provided a retron-based method for the intracellular generation of Dz 10-23 but also demonstrated that Dz 10-23 could reduce gene expression by cleaving target mRNAs in cells. We believe that this new strategy would have great potential in the regulation of gene expression.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lina Cui
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xinyu Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jiahao Yan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yifei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuyang Ni
- College of Life Sciences, Shangrao Normal University, Shangrao 334001, PR China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xun Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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17
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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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18
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Takezawa Y, Hu L, Nakama T, Shionoya M. Metal-dependent activity control of a compact-sized 8-17 DNAzyme based on metal-mediated unnatural base pairing. Chem Commun (Camb) 2024; 60:288-291. [PMID: 38063055 DOI: 10.1039/d3cc05520e] [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: 01/03/2024]
Abstract
A compact 8-17 DNAzyme was modified with a CuII-meditated artificial base pair to develop a metal-responsive allosteric DNAzyme. The base sequence was rationally designed based on the reported three-dimensional structure. The activity of the modified DNAzyme was enhanced 5.1-fold by the addition of one equivalent of CuII ions, showing good metal responsiveness. Since it has been challenging to modify compactly folded DNAzymes without losing their activity, this study demonstrates the utility of the metal-mediated artificial base pairing to create stimuli-responsive functional DNAs.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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19
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Ma Y, Chen R, Zhang R, Liang J, Ren S, Gao Z. Application of DNA-fueled molecular machines in food safety testing. Compr Rev Food Sci Food Saf 2024; 23:1-22. [PMID: 38284608 DOI: 10.1111/1541-4337.13299] [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: 05/31/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
Food is consumed by humans, which is indispensable to human life. Therefore, considerable attention of the whole society has been paid to food safety. Over the last few years, dramatic social development has brought new challenges to food safety, making developing new and quick methods for on-site food safety testing an important necessity. As a result, DNA-fueled molecular machines, characterized by high efficiency, accuracy, and sensitivity in testing, have come into the spotlight, based on which sensors can be constructed to detect toxic and harmful substances in food products. This study reviewed recent research on several DNA-fueled molecular machines, including DNA tweezers, DNA walkers, and DNA origami, for rapidly detecting toxic and harmful substances. Based on the above studies, the sensitivity and timeliness of several DNA molecular machines were summarized and compared, and the development prospect of DNA fuel molecular machines in the field of food safety detection was prospected.
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Affiliation(s)
- Yujing Ma
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Rui Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Jun Liang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
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20
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Prešern U, Goličnik M. Enzyme Databases in the Era of Omics and Artificial Intelligence. Int J Mol Sci 2023; 24:16918. [PMID: 38069254 PMCID: PMC10707154 DOI: 10.3390/ijms242316918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Enzyme research is important for the development of various scientific fields such as medicine and biotechnology. Enzyme databases facilitate this research by providing a wide range of information relevant to research planning and data analysis. Over the years, various databases that cover different aspects of enzyme biology (e.g., kinetic parameters, enzyme occurrence, and reaction mechanisms) have been developed. Most of the databases are curated manually, which improves reliability of the information; however, such curation cannot keep pace with the exponential growth in published data. Lack of data standardization is another obstacle for data extraction and analysis. Improving machine readability of databases is especially important in the light of recent advances in deep learning algorithms that require big training datasets. This review provides information regarding the current state of enzyme databases, especially in relation to the ever-increasing amount of generated research data and recent advancements in artificial intelligence algorithms. Furthermore, it describes several enzyme databases, providing the reader with necessary information for their use.
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Affiliation(s)
| | - Marko Goličnik
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
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21
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Kuprikova N, Ondruš M, Bednárová L, Riopedre-Fernandez M, Slavětínská L, Sýkorová V, Hocek M. Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases. Nucleic Acids Res 2023; 51:11428-11438. [PMID: 37870471 PMCID: PMC10681718 DOI: 10.1093/nar/gkad893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/06/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
We designed and synthesized a set of four 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phosphate). The anion-linked dNTPs were used for enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase containing one, two, three, or four modified nucleotides. The polymerase was able to synthesize even long sequences of >100 modified nucleotides in a row by primer extension (PEX). We also successfully combined two anionic and two hydrophobic dNTPs bearing phenyl and indole moieties. In PCR, the combinations of one or two modified dNTPs gave exponential amplification, while most of the combinations of three or four modified dNTPs gave only linear amplification in asymmetric PCR. The hypermodified ONs were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies including hybridization, denaturation, CD spectroscopy and molecular modelling and dynamics suggest that the presence of anionic modifications in one strand decreases the stability of duplexes while still preserving the B-DNA conformation, whilst the DNA hypermodified in both strands adopts a different secondary structure.
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Affiliation(s)
- Natalia Kuprikova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Miguel Riopedre-Fernandez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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22
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Zerbetto M, Saint-Pierre C, Piserchia A, Torrengo S, Gambarelli S, Abergel D, Polimeno A, Gasparutto D, Sicoli G. Intrinsic Flexibility beyond the Highly Ordered DNA Tetrahedron: An Integrative Spectroscopic and Molecular Dynamics Approach. J Phys Chem Lett 2023; 14:10032-10038. [PMID: 37906734 DOI: 10.1021/acs.jpclett.3c02383] [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: 11/02/2023]
Abstract
Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process. To address such an issue, spin-labeled DNA sequences are chemically synthesized, self-assembled, and then analyzed by Continuous-Wave (CW) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopy. Interspin distance measurements based on PELDOR/DEER techniques combined with molecular dynamics (MD) thus revealed unexpected dynamic heterogeneity and flexibility of the assembled structures. The observation of flexibility in these ordered 3D structures demonstrates the sensitivity of this approach and its effectiveness in accessing the main dynamic and structural features with unprecedented resolution.
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Affiliation(s)
- Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Andrea Piserchia
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Simona Torrengo
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Daniel Abergel
- Laboratoire des biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Antonino Polimeno
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Giuseppe Sicoli
- CNRS UMRS 8516, LASIRE, University of Lille, Avenue Paul Langevin - C4 building, F-59655 Villeneuve d'Ascq Cedex, France
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23
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Wang J, Huang H, Hanpanich O, Shimada N, Maruyama A. Cationic copolymer and crowding agent have a cooperative effect on a Na +-dependent DNAzyme. Biomater Sci 2023; 11:7062-7066. [PMID: 37706516 DOI: 10.1039/d3bm01119d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
DNAzymes are promising agents for theranostics and biosensors. Sodium dependent DNAzymes have been developed for sensing and imaging of Na+, but these DNAzymes have low catalytic activity. Herein, we demonstrate that a molecular crowded environment containing 10 to 40 wt% PEG enhanced the catalytic activity of a Na+-dependent DNAzyme, EtNa, although dextran did not. The cationic copolymer poly(L-lysine)-graft-poly(ethylene glycol) at 0.03 wt% (0.3 g L-1) enhanced the reaction rate of EtNa by 10-fold, which is similar to the acceleration induced by 15 wt% (150 g L-1) PEG. A cooperative impact of the copolymer and crowding agent was observed: the combination resulted in an impressive 46-fold acceleration effect. Thus, the use of a cationic copolymer and a crowding agent is a promising strategy to improve the activity of Na+-dependent DNAzyme-based nanomachines, biosensors, and theranostics, especially in environments lacking divalent metal ions.
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Affiliation(s)
- Jun Wang
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - He Huang
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
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24
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Iwata T, Kurahashi Y, Wijaya IMM, Kandori H. Spectroscopic Investigation of Na +-Dependent Conformational Changes of a Cyclobutane Pyrimidine Dimer-Repairing Deoxyribozyme. ACS OMEGA 2023; 8:37274-37281. [PMID: 37841180 PMCID: PMC10569015 DOI: 10.1021/acsomega.3c05083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
UV1C is an enzymatically active DNA sequence (deoxyribozyme, DNAzyme) that functions as a cyclobutane pyrimidine dimer (CPD) photolyase. UV1C forms parallel guanine quadruplexes (G-quadruplexes) with a DNA substrate in the presence of 240 mM Na+, the structure of which is important for the enzymatic activity. To investigate the repair mechanism of CPD by UV1C, we designed light-induced Fourier transform infrared (FTIR) spectroscopy. Prior to FTIR measurements, circular dichroism (CD) spectroscopy was conducted to determine the Na+ concentration at which the most G-quadruplexes were formed. We found that UV1C also forms a hybrid G-quadruplex structure at over 500 mM Na+. By assuming a concentration equilibrium between G-quadruplexes and Na+, 1.3 and 1.8 Na+ were found to bind to parallel and hybrid G-quadruplexes, respectively. The hybrid G-quadruplex form of UV1C was also suggested to exhibit photolyase activity. Light-induced FTIR spectra recorded upon the photorepair of CPD by UV1C were compared for parallel G-quadruplex-rich and hybrid G-quadruplex-rich samples. Spectral variations were indicative of structural differences in parallel and hybrid G-quadruplexes before and after CPD cleavage. Differences were also observed when compared to the CPD repair spectrum by CPD photolyase. The spectral differences during CPD repair by either protein or DNAzyme suggest the local environment of the substrates, the surrounding protein, or the aqueous solution.
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Affiliation(s)
- Tatsuya Iwata
- Department
of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yuhi Kurahashi
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - I Made Mahaputra Wijaya
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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25
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Montserrat Pagès A, Hertog M, Nicolaï B, Spasic D, Lammertyn J. Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme. Int J Mol Sci 2023; 24:13686. [PMID: 37761982 PMCID: PMC10531344 DOI: 10.3390/ijms241813686] [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: 06/12/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.
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Affiliation(s)
- Aida Montserrat Pagès
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Maarten Hertog
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Bart Nicolaï
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
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26
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Su J, Sun C, Du J, Xing X, Wang F, Dong H. RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy. Adv Healthc Mater 2023; 12:e2300367. [PMID: 37084038 DOI: 10.1002/adhm.202300367] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Indexed: 04/22/2023]
Abstract
Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.
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Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Fang Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
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27
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Lee M, Kang S, Kim S, Park N. Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors. BIOSENSORS 2023; 13:856. [PMID: 37754090 PMCID: PMC10526965 DOI: 10.3390/bios13090856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023]
Abstract
miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea (S.K.)
| | - Seungjae Kang
- 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 (S.K.)
| | - 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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28
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Feng Q, Zakaria S, Morrison D, Tram K, Gu J, Salena BJ, Li Y. A Fluorogenic DNAzyme for A Thermally Stable Protein Biomarker from Fusobacterium nucleatum, a Human Bacterial Pathogen. Angew Chem Int Ed Engl 2023; 62:e202306272. [PMID: 37404195 DOI: 10.1002/anie.202306272] [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: 05/09/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/06/2023]
Abstract
Fusobacterium nucleatum has been correlated to many poor human conditions including oral infections, adverse pregnancies and cancer, and thus molecular tools capable of detecting this human pathogen can be used to develop diagnostic tests for them. Using a new selection method targeting thermally stable proteins without a counter-selection step, we derived an fluorogenic RNA-cleaving DNAzyme, named RFD-FN1, that can be activated by a thermally stable protein target that is unique to F. nucleatum subspecies. High thermal stability of protein targets is a very desirable attribute for DNAzyme-based biosensing directly with biological samples because nucleases found inherently in these samples can be heat-inactivated. We further demonstrate that RFD-FN1 can function as a fluorescent sensor in both human saliva and human stool samples. The discovery of RFD-FN1 paired with a highly thermal stable protein target presents opportunities for developing simpler diagnostic tests for this important pathogen.
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Affiliation(s)
- Qian Feng
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Sandy Zakaria
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Jim Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
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29
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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: 0] [Impact Index Per Article: 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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30
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Xing C, Lin Q, Chen Y, Zeng S, Wang J, Lu C. A Smart Metal-Polyphenol-DNAzyme nanoplatform for Gene-Chemodynamic Synergistic Tumor therapy. Acta Biomater 2023:S1742-7061(23)00305-7. [PMID: 37253417 DOI: 10.1016/j.actbio.2023.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
DNAzyme-based gene regulation shows great potential for the therapy of many cancers. However, ineffective delivery and insufficient cofactor supply pose challenges for potent gene therapy. In this study, we constructed a smart metal-polyphenol-DNAzyme nanoplatform (TA-Mn@Dz NPs) with intrinsic stability, effective delivery, and cofactor self-supply ability for gene-chemodynamic synergistic tumor therapy. Tannic acid, a plant-derived polyphenol, acts as an intermediate structural unit to mediate the assembly of Mn2+/DNAzyme and tumor acid environment-responsive nanocarriers. Intracellularly, the acidic environment triggers the decomposition of TA-Mn@Dz NPs to release DNAzyme and Mn2+. The Mn2+ ion not only boosts the catalytic cleavage of surviving mRNA for effective gene therapy but also activates chemodynamic therapy (CDT), generating highly toxic ·OH from endogenous H2O2. When tail intravenously injected into MCF-7 tumor-bearing mice, the TA-Mn@Dz NPs display desirable synergistic gene-chemodynamic antitumor effects, paving the way for developing DNAzyme-based multifunctional theranostic platforms for biomedical applications. STATEMENT OF SIGNIFICANCE: 1. A smart metal-polyphenol-DNAzyme nanoplatform was constructed for gene-chemodynamic synergistic tumor therapy. 2. Tannic acid act as intermediate structural units to mediate the assembly of Mn2+/DNAzyme and tumor acid environment-responsive nanocarriers. 3. The Mn2+-ion could not only boost the catalytic cleavage of surviving mRNA for effective gene therapy, but also catalyze endogenous H2O2 to form cytotoxic hydroxyl radicals for chemodynamic therapy. 4. Our work paves an extremely simple way to integrate gene therapy with CDT for the dual-catalytic tumor treatment.
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Affiliation(s)
- Chao Xing
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China; MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P.R. China.
| | - Qitian Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yiting Chen
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China
| | - Sijie Zeng
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China
| | - Jun Wang
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China.
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P.R. China.
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31
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Cao X, Dong J, Sun R, Zhang X, Chen C, Zhu Q. A DNAzyme-enhanced nonlinear hybridization chain reaction for sensitive detection of microRNA. J Biol Chem 2023; 299:104751. [PMID: 37100287 DOI: 10.1016/j.jbc.2023.104751] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 04/28/2023] Open
Abstract
As a typical biomarker, the expression of microRNA is closely related to the occurrence of cancer. However, in recent years, the detection methods have had some limitations in the research and application of microRNAs. In this paper, an autocatalytic platform was constructed through the combination of a nonlinear hybridization chain reaction and DNAzyme to achieve efficient detection of microRNA-21. Fluorescently labeled fuel probes can form branched nanostructures and new DNAzyme under the action of the target, and the newly formed DNAzyme can trigger a new round of reactions, resulting in enhanced fluorescence signals. This platform is a simple, efficient, fast, low-cost, and selective method for the detection of microRNA-21, which can detect microRNA-21 at concentrations as low as 0.004 nM and can distinguish sequence differences by single-base differences. In tissue samples from liver cancer patients, the platform shows the same detection accuracy as real-time PCR but with better reproducibility. In addition, through the flexible design of the trigger chain, our method could be adapted to detect other nucleic acids biomarkers.
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Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China
| | - Jiani Dong
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China
| | - Ruowei Sun
- Hunan Zaochen Nanorobot Co. Ltd, Liuyang 410300, Hunan, China
| | - Xun Zhang
- Hunan Zaochen Nanorobot Co. Ltd, Liuyang 410300, Hunan, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
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32
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Lauzon D, Vallée-Bélisle A. Functional advantages of building nanosystems using multiple molecular components. Nat Chem 2023; 15:458-467. [PMID: 36759713 DOI: 10.1038/s41557-022-01127-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/15/2022] [Indexed: 02/11/2023]
Abstract
Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.
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Affiliation(s)
- D Lauzon
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - A Vallée-Bélisle
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada.
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33
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Pandey R, Lu Y, McConnell EM, Osman E, Scott A, Gu J, Hoare T, Soleymani L, Li Y. Electrochemical DNAzyme-based biosensors for disease diagnosis. Biosens Bioelectron 2023; 224:114983. [PMID: 36640547 DOI: 10.1016/j.bios.2022.114983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023]
Abstract
DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| | - Yang Lu
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Enas Osman
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Alexander Scott
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Todd Hoare
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Chemical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
| | - Yingfu Li
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
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34
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Miao Q, Ding W, Bao X, Wang S, Lin Q, Xu Y, Lu J, Lyu M, Wang S. An efficient
DNAzyme
for the fluorescence detection of
Vibrio cholerae. Food Sci Nutr 2023. [DOI: 10.1002/fsn3.3304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Affiliation(s)
- Qingzhen Miao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Wen Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Xiuli Bao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Siyuan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Qianru Lin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Yingying Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
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35
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Yang S, Silverman SK. Defining the substrate scope of DNAzyme catalysis for reductive amination with aliphatic amines. Org Biomol Chem 2023; 21:1910-1919. [PMID: 36786764 DOI: 10.1039/d3ob00070b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Amines can be alkylated using various reactions, such as reductive amination of aldehydes. In this study, we sought DNAzymes as catalytic DNA sequences that promote reductive amination with aliphatic amines, including DNA-anchored peptide substrates with lysine residues. By in vitro selection starting with either N40 or N20 random DNA pools, we identified many DNAzymes that catalyze reductive amination between the DNA oligonucleotide-anchored aliphatic amino group of DNA-C3-NH2 (C3 = short three-carbon tether) and a DNA-anchored benzaldehyde group in the presence of NaCNBH3 as reducing agent. At pH 5.2, 6.0, 7.5, or 9.0 in the presence of various divalent metal ion cofactors including Mg2+, Mn2+, Zn2+ and Ni2+, the DNAzymes have kobs up to 0.12 h-1 and up to 130-fold rate enhancement relative to the DNA-splinted but uncatalyzed background reaction. However, analogous selection experiments did not lead to any DNAzymes that function with DNA-HEG-NH2 [HEG = long hexa(ethylene glycol) tether], or with short- and long-tethered DNA-AAAKAA and DNA-HEG-AAAKAA lysine-containing hexapeptide substrates (A = alanine, K = lysine). Including a variety of other amino acids in place of the neighboring alanines also did not lead to DNAzymes. These findings establish a practical limit on the substrate scope of DNAzyme catalysis for N-alkylation of aliphatic amines by reductive amination. The lack of DNAzymes for reductive amination with any substrate more structurally complex than DNA-C3-NH2 is likely related to the challenge in binding and spatially organizing those other substrates. Because other reactions such as aliphatic amine N-acylation are feasible for DNAzymes with DNA-anchored peptides, our findings show that the ability to identify DNAzymes depends strongly on both the investigated reaction and the composition of the substrate.
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Affiliation(s)
- Shukun Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| | - Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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36
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Su M, Lien J, Anilao A, Guo T. Enhanced Single-Strand Breaks of a Nucleic Acid by Gold Nanoparticles under X-ray Irradiation. J Phys Chem Lett 2023; 14:1214-1221. [PMID: 36716218 DOI: 10.1021/acs.jpclett.2c03885] [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: 06/18/2023]
Abstract
The hydroxyl radical concentration-dependent yield of single-strand breaks (SSBs), obtained through correction of scavenging and hindrance effects caused by gold nanoparticles (AuNPs), for fluorophore- and quencher-labeled DNA on AuNPs was 10 times that of free DNA based on fluorescence measurements of X-ray-irradiated DNA on AuNPs. By comparing the fluorescence data that revealed the number of SSBs with the results of mass spectrometry measurements that detected the total damage to DNA, we found that SSBs dominated DNA damage for DNA on AuNPs whereas non-SSB damage dominated for free DNA. The yield of RNA SSBs under X-ray irradiation was similar to that of DNA in the presence of AuNPs, whereas free RNA was more resistive to radiation than DNA. These results indicated the enhanced SSBs were likely catalyzed through the conversion from nucleobase damage to SSBs by AuNPs. The outcome of this work impacts materials and environmental science, sensing, nanotechnology, biology, and medicine.
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Affiliation(s)
- Mengqi Su
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Jennifer Lien
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Auddy Anilao
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Ting Guo
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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37
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Cao X, Chen C, Zhu Q. Biosensors based on functional nucleic acids and isothermal amplification techniques. Talanta 2023; 253:123977. [PMID: 36201957 DOI: 10.1016/j.talanta.2022.123977] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.
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Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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38
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Rajasree SC, Takezawa Y, Shionoya M. Cu II-mediated stabilisation of DNA duplexes bearing consecutive ethenoadenine lesions and its application to a metal-responsive DNAzyme. Chem Commun (Camb) 2023; 59:1006-1009. [PMID: 36524578 DOI: 10.1039/d2cc06179a] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal-mediated nucleobase pairing can play a central role in the expression of metal-responsive DNA functions. We report the CuII-mediated stabilisation of DNA duplexes bearing damaged nucleobases, 1,N6-ethenoadenine (εA), as metal-binding sites, which was utilised to construct a metal-responsive DNAzyme. Consecutive incorporation of three or more εA-εA mismatch pairs allowed for CuII-dependent significant duplex stabilisation through metal-mediated εA-CuII-εA base pairing. Subsequently, a split DNAzyme with three εA-CuII-εA base pairs was strategically designed. The activity of the εA-modified DNAzyme was enhanced by 5.3-fold upon addition of CuII ions. This study demonstrates the utility of εA lesions for building metal-responsive DNA architectures.
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Affiliation(s)
- Silpa Chandran Rajasree
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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39
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Du X, He PP, Wang C, Wang X, Mu Y, Guo W. Fast Transport and Transformation of Biomacromolecular Substances via Thermo-Stimulated Active "Inhalation-Exhalation" Cycles of Hierarchically Structured Smart pNIPAM-DNA Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206302. [PMID: 36268982 DOI: 10.1002/adma.202206302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Although smart hydrogels hold great promise in biosensing and biomedical applications, their response to external stimuli is governed by the passive diffusion-dependent substance transport between hydrogels and environments and within the 3D hydrogel matrices, resulting in slow response to biomacromolecules and limiting their extensive applications. Herein, inspired by the respiration systems of organisms, an active strategy to achieve highly efficient biomolecular substance transport through the thermo-stimulated "inhalation-exhalation" cycles of hydrogel matrices is demonstrated. The cryo-structured poly(N-isopropylacrylamide) (pNIPAM)-DNA hydrogels, composed of functional DNA-tethered pNIPAM networks and free-water-containing macroporous channels, exhibit thermally triggered fast and reversible shrinking/swelling cycles with high-volume changes, which drive the formation of dynamic water stream to accelerate the intake of external substances and expelling of endogenous substances, thus promoting the functional properties of hydrogel systems. Demonstrated by catalytic DNAzyme and CRISPR-Cas12a-incorporating hydrogels, significantly enhanced catalytic efficiency with up to 280% and 390% is achieved, upon the introduction of active "inhalation-exhalation" cycles, respectively. Moreover, remotely near-infrared (NIR)-triggering of "inhalation-exhalation" cycles is achieved after the introduction of NIR-responsive MXene nanosheets into the hydrogel matrix. These hydrogel systems with enhanced substance transport and transformation properties hold promise in the development of more effective biosensing and therapeutic systems.
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Affiliation(s)
- Xiaoxue Du
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Ping-Ping He
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Chunyan Wang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiaowen Wang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yali Mu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Weiwei Guo
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
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40
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Abstract
Natural enzymes catalyze biochemical transformations in superior catalytic efficiency and remarkable substrate specificity. The excellent catalytic repertoire of enzymes is attributed to the sophisticated chemical structures of their active sites, as a result of billions-of-years natural evolution. However, large-scale practical applications of natural enzymes are restricted due to their poor stability, difficulty in modification, and high costs of production. One viable solution is to fabricate supramolecular catalysts with enzyme-mimetic active sites. In this review, we introduce the principles and strategies of designing peptide-based artificial enzymes which display catalytic activities similar to those of natural enzymes, such as aldolases, laccases, peroxidases, and hydrolases (mainly the esterases and phosphatases). We also discuss some multifunctional enzyme-mimicking systems which are capable of catalyzing orthogonal or cascade reactions. We highlight the relationship between structures of enzyme-like active sites and the catalytic properties, as well as the significance of these studies from an evolutionary point of view.
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41
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Intelligent nanotherapeutic strategies for the delivery of CRISPR system. Acta Pharm Sin B 2022. [DOI: 10.1016/j.apsb.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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42
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Deng C, Yang H, Liu S, Zhao Z. Self-assembly of Dendrimer-DNA amphiphiles and their catalysis as G-quadruplex/hemin DNAzymes. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Discovery and translation of functional nucleic acids for clinically diagnosing infectious diseases: Opportunities and challenges. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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44
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Liu Y, Zhu P, Huang J, He H, Ma C, Wang K. Integrating DNA nanostructures with DNAzymes for biosensing, bioimaging and cancer therapy. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Recent advance of RNA aptamers and DNAzymes for MicroRNA detection. Biosens Bioelectron 2022; 212:114423. [DOI: 10.1016/j.bios.2022.114423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 02/02/2023]
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46
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Ekesan Ş, McCarthy E, Case DA, York DM. RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis. J Phys Chem B 2022; 126:5982-5990. [PMID: 35862934 PMCID: PMC9496635 DOI: 10.1021/acs.jpcb.2c03727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despite having only a limited repertoire of building blocks and available set of chemical functional groups. Ribozyme active sites usually occur at junctions where negatively charged helices come together, and in many cases leverage this strained electrostatic environment to recruit metal ions in solution that can assist in catalysis. Similar strategies have been implicated in related artificially engineered DNA enzymes. Herein, we apply Poisson-Boltzmann, 3D-RISM, and molecular simulations to study a set of metal-dependent small self-cleaving ribozymes (hammerhead, pistol, and Varkud satellite) as well as an artificially engineered DNAzyme (8-17) to examine electrostatic features and their relation to the recruitment of monovalent and divalent metal ions important for activity. We examine several fundamental roles for these ions that include: (1) structural integrity of the catalytically active state, (2) pKa tuning of residues involved in acid-base catalysis, and (3) direct electrostatic stabilization of the transition state via Lewis acid catalysis. Taken together, these examples demonstrate how RNA electrostatics orchestrates the site-specific and territorial binding of metal ions to play important roles in catalysis.
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David A. Case
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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47
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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48
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Sanford AA, Manuel BA, Romero-Reyes MA, Heemstra JM. Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids. Chem Sci 2022; 13:7670-7684. [PMID: 35865900 PMCID: PMC9258336 DOI: 10.1039/d2sc00117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Brea A Manuel
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Misael A Romero-Reyes
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Chemistry, Hanover College Hanover Indiana 47243 USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta GA 30332 USA
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49
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Zhang Q, Liang Y, Xing H. Caging-Decaging Strategies to Realize Spatiotemporal Control of DNAzyme Activity for Biosensing and Bioimaging. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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50
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Luo D, Lin X, Zhao Y, Hu J, Mo F, Song G, Zou Z, Wang F, Liu X. A dynamic DNA nanosponge for triggered amplification of gene-photodynamic modulation. Chem Sci 2022; 13:5155-5163. [PMID: 35655573 PMCID: PMC9093187 DOI: 10.1039/d2sc00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/18/2022] [Indexed: 12/19/2022] Open
Abstract
Nucleic acid therapeutics has reached clinical utility through modulating gene expression. As a potential oligonucleotide drug, DNAzyme has RNA-cleaving activity for gene silencing, but faces challenges due to the lack of a safe and effective delivery vehicle and low in vivo catalytic activity. Here we describe DNAzyme-mediated gene regulation using dynamic DNA nanomaterials with intrinsic biocompatibility, stability, tumor-targeted delivery and uptake, and self-enhanced efficacy. We assemble programmable DNA nanosponges to package and deliver diverse nucleic acid drugs and therapeutic agents such as aptamer, DNAzyme and its cofactor precursor, and photosensitizer in one pot through the rolling circle amplification reaction, formulating a controllable nanomedicine using encoded instructions. Upon environmental stimuli, DNAzyme activity increases and RNA cleavage accelerates by a supplementary catalytic cofactor. In addition, this approach induces elevated O2 and 1O2 generation as auxiliary treatment, achieving simultaneously self-enhanced gene-photodynamic cancer therapy. These findings may advance the clinical trial of oligonucleotide drugs as tools for gene modulation. Oligonucleotide drug delivery approach is provided with a biomimetic, dynamic DNA nanomaterial, which enables disease gene regulation and auxiliary therapy in a controllable and self-boosting manner.![]()
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Affiliation(s)
- Dan Luo
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Xue Lin
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Yun Zhao
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Jialing Hu
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Fengye Mo
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Gege Song
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Zhiqiao Zou
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
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