1
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Boyd R, Kennebeck M, Miranda A, Liu Z, Silverman S. Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination. Nucleic Acids Res 2024; 52:8702-8716. [PMID: 39051544 PMCID: PMC11347174 DOI: 10.1093/nar/gkae639] [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: 06/06/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
DNA and RNA nucleobase modifications are biologically relevant and valuable in fundamental biochemical and biophysical investigations of nucleic acids. However, directly introducing site-specific nucleobase modifications into long unprotected oligonucleotides is a substantial challenge. In this study, we used in vitro selection to identify DNAzymes that site-specifically N-alkylate the exocyclic nucleobase amines of particular cytidine, guanosine, and adenosine (C, G and A) nucleotides in DNA substrates, by reductive amination using a 5'-benzaldehyde oligonucleotide as the reaction partner. The new DNAzymes each require one or more of Mg2+, Mn2+, and Zn2+ as metal ion cofactors and have kobs from 0.04 to 0.3 h-1, with rate enhancement as high as ∼104 above the splinted background reaction. Several of the new DNAzymes are catalytically active when an RNA substrate is provided in place of DNA. Similarly, several new DNAzymes function when a small-molecule benzaldehyde compound replaces the 5'-benzaldehyde oligonucleotide. These findings expand the scope of DNAzyme catalysis to include nucleobase N-alkylation by reductive amination. Further development of this new class of DNAzymes is anticipated to facilitate practical covalent modification and labeling of DNA and RNA substrates.
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Affiliation(s)
- Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Aurora A Miranda
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Zehui Liu
- 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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2
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Xia L, Du L, Hou X, Zhou R, Cheng N, Chen J. Protein-Controlled Split DNAzyme to Enhance Catalytic Activity: Design and Performance. Anal Chem 2024. [PMID: 39010288 DOI: 10.1021/acs.analchem.3c05909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
In this study, we utilized proteins to control the assembly of split DNAzyme to establish protein-controlled split DNAzymes (Pc SD), with the aim of enhancing its catalytic activity. To achieve this, simultaneous recognition of protein by affinity ligands at both ends of split DNAzyme fragments induced an increased local concentration of each split fragment, leading to reassembly of the split catalytic core with a rigid conformation and higher affinity to its cofactor. As a result, under protein control, Pc SD exhibits unexpected cleavage efficiency compared to free split DNAzyme. To further explore the catalytic features, we then systematically positioned split sites within the catalytic core of three popular DNAzyme-based Pc SDs, thus revealing the important nucleic acids that influence Pc SDs activity. Based on the excellent analytical performance of Pc SD for streptavidin (with a LOD of 0.1 pM in buffer),we equipped Pc SD with antibodies as rapid diagnostic tools for inpatient care (AFP as biomarker) with a minimized workflow (with a LOD of 2 pM in 5% human serum). The results of this study offer fundamental insights into external factors for boosting DNAzyme catalysis and will be promising for applications that utilize split DNAzymes.
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Affiliation(s)
- Lingying Xia
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
- Biliary Surgical Department of West China Hospital, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Lijie Du
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Xiandeng Hou
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Nansheng Cheng
- Biliary Surgical Department of West China Hospital, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
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3
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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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4
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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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5
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Hu Q, Tong Z, Yalikong A, Ge LP, Shi Q, Du X, Wang P, Liu XY, Zhan W, Gao X, Sun D, Fu T, Ye D, Fan C, Liu J, Zhong YS, Jiang YZ, Gu H. DNAzyme-based faithful probing and pulldown to identify candidate biomarkers of low abundance. Nat Chem 2024; 16:122-131. [PMID: 37710046 DOI: 10.1038/s41557-023-01328-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Biomarker discovery is essential for the understanding, diagnosis, targeted therapy and prognosis assessment of malignant diseases. However, it remains a huge challenge due to the lack of sensitive methods to identify disease-specific rare molecules. Here we present MORAC, molecular recognition based on affinity and catalysis, which enables the effective identification of candidate biomarkers with low abundance. MORAC relies on a class of DNAzymes, each cleaving a sole RNA linkage embedded in their DNA chain upon specifically sensing a complex system with no prior knowledge of the system's molecular content. We show that signal amplification from catalysis ensures the DNAzymes high sensitivity (for target probing); meanwhile, a simple RNA-to-DNA mutation can shut down their RNA cleavage ability and turn them into a pure affinity tool (for target pulldown). Using MORAC, we identify previously unknown, low-abundance candidate biomarkers with clear clinical value, including apolipoprotein L6 in breast cancer and seryl-tRNA synthetase 1 in polyps preceding colon cancer.
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Affiliation(s)
- Qinqin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, and School of Global Health, Shanghai Jiao Tong University, Shanghai, China
| | - Zongxuan Tong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ayimukedisi Yalikong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li-Ping Ge
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiang Shi
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinyu Du
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Pu Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wuqiang Zhan
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xia Gao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Di Sun
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tong Fu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dan Ye
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunhai Fan
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, and School of Global Health, Shanghai Jiao Tong University, Shanghai, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Laboratory, Shanghai, China
| | - Jie Liu
- Department of Digestive Disease, Huashan Hospital, Fudan University, Shanghai, China
| | - Yun-Shi Zhong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Hongzhou Gu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Institutes of Biomedical Sciences, Fudan University Shanghai Cancer Center, Shanghai Stomatological Hospital, and Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, and School of Global Health, Shanghai Jiao Tong University, Shanghai, China.
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6
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Hussein Z, Nour MAY, Kozlova AV, Kolpashchikov DM, Komissarov AB, El-Deeb AA. DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection. Anal Chem 2023; 95:18667-18672. [PMID: 38079240 DOI: 10.1021/acs.analchem.3c04420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.
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Affiliation(s)
- Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816, United States
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, United States
| | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
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7
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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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8
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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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9
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Jastrzembski MG, Watson BC, Weissburg MJ, Bras B. Assessing the state of biologically inspired design from three perspectives: academic, public, and practitioners. BIOINSPIRATION & BIOMIMETICS 2023; 18:046005. [PMID: 37023773 DOI: 10.1088/1748-3190/accb31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Biologically inspired design (BID) applies natural solutions to engineering challenges. Due to the widespread success of BID, we examine the following research question: how does the purpose of applying, the inspiration source, and the application of BID differ between academics, the public, and practitioners? Answering this question can help us design the tools used to support BID, provide an understanding of the current 'state of BID' and identify where BID solutions have not been widely utilized. Identifying gaps in utilization could prompt investigations into BID methods in new fields. To answer this research question, 660 BID samples were gathered equally from three data sources: Google Scholar, Google News, and the Asknature.org 'Innovations' database. The data were classified across seven dimensions and 68 subcategories. The conclusions of our research deliver insights into three areas. First, we identify trends in BID independent of source. For example, 72.5% of the biomimicry samples had the purpose of improving functionality and 87.6% of the samples impacted the usage phase of a product's life cycle. Secondly, by examining the distribution of BID within each source, we identify areas for potential outreach or application. Finally, by contrasting BID results between three sources (academic, news, and practical case studies) we gain an understanding of the disparities between the three. This analysis provides BID researchers and practitioners with a useful insight into the present state of this field, with the goal of motivating future research and application.
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Affiliation(s)
- M G Jastrzembski
- Biomedical Engineering at Mercer University, 1501 Mercer University Drive, Macon, GA 31207, United States of America
| | - B C Watson
- Electrical Engineering and Computer Science Department at Embry-Riddle Aeronautical University, 1 Aerospace Boulevard, Daytona Beach, FL 32119, United States of America
- George W. Woodruff School of Mechanical Engineering at the Georgia Institute of Technology, Atlanta, GA 30332, United States of America
| | - M J Weissburg
- School of Biological Sciences at the Georgia Institute of Technology, Atlanta, GA 30332, United States of America
| | - B Bras
- George W. Woodruff School of Mechanical Engineering at the Georgia Institute of Technology, Atlanta, GA 30332, United States of America
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10
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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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11
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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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12
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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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13
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:93. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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14
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Sednev MV, Liaqat A, Höbartner C. High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq). J Am Chem Soc 2022; 144:2090-2094. [PMID: 35081311 DOI: 10.1021/jacs.1c12489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states.
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Affiliation(s)
- Maksim V Sednev
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Anam Liaqat
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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15
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Liaqat A, Sednev MV, Höbartner C. In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications. Methods Mol Biol 2022; 2533:167-179. [PMID: 35796988 PMCID: PMC9761555 DOI: 10.1007/978-1-0716-2501-9_10] [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: 06/15/2023]
Abstract
Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N 6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.
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Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Maksim V Sednev
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany.
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16
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Gao Y, Zhang S, Wu C, Li Q, Shen Z, Lu Y, Wu ZS. Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice. ACS NANO 2021; 15:19211-19224. [PMID: 34854292 DOI: 10.1021/acsnano.1c04260] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.
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Affiliation(s)
- Yansha Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde 415000, China
| | - Chengwei Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Qian Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
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17
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Zhao D, Chang D, Zhang Q, Chang Y, Liu B, Sun C, Li Z, Dong C, Liu M, Li Y. Rapid and Specific Imaging of Extracellular Signaling Molecule Adenosine Triphosphate with a Self-Phosphorylating DNAzyme. J Am Chem Soc 2021; 143:15084-15090. [PMID: 34415153 DOI: 10.1021/jacs.1c04925] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is a central extracellular signaling agent involved in various physiological and pathological processes. However, precise measurements of the temporal and spatial components of ATP dynamics are lacking due primarily to the limitations of available methods for ATP detection. Here, we report on the first effort to design a self-phosphorylating DNAzyme (SPDz) sensor for fluorescence imaging of ATP. In response to ATP, SPDz sensors exhibit subsecond response kinetics, extremely high specificity, and micromolar affinities. In particular, we demonstrate cell-surface-anchored SPDz sensors for fluorescence imaging of both stress-induced endogenous ATP release in astrocytes and mechanical stimulation-evoked ATP release at the single-cell level. We also validated their utility for visualizing the rapid dynamic properties of ATP signaling upon electrical stimulation in astrocytes. Thus, SPDz sensors are robust tools for monitoring ATP signaling underlying diverse cellular processes.
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Affiliation(s)
- Dan Zhao
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Bo Liu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Changsen Sun
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Zhonping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Chuan Dong
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
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18
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Chang D, Zakaria S, Esmaeili Samani S, Chang Y, Filipe CDM, Soleymani L, Brennan JD, Liu M, Li Y. Functional Nucleic Acids for Pathogenic Bacteria Detection. Acc Chem Res 2021; 54:3540-3549. [PMID: 34478272 DOI: 10.1021/acs.accounts.1c00355] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pathogens have long presented a significant threat to human lives, and hence the rapid detection of infectious pathogens is vital for improving human health. Current detection methods lack the means to detect infectious pathogens in a simple, rapid, and reliable manner at the time and point of need. Functional nucleic acids (FNAs) have the potential to overcome these limitations by acting as key components for point-of-care (POC) biosensors due to their distinctive advantages that include high binding affinities and specificities, excellent chemical stability, ease of synthesis and modification, and compatibility with a variety of signal-amplification and signal-transduction mechanisms.This Account summarizes the work completed in our groups toward developing FNA-based biosensors for detecting bacteria. In vitro selection has led to the isolation of many RNA-cleaving fluorogenic DNAzymes (RFDs) and DNA aptamers that can recognize infectious pathogens, including Escherichia coli, Clostridium difficile, Helicobacter pylori, and Legionella pneumophila. In most cases, a "many-against-many" approach was employed using a DNA library against a crude cellular mixture of an infectious pathogen containing diverse biomarkers as the target to isolate RFDs, with combined counter and positive selections ensuring high specificity toward the desired target. This procedure allows for the isolation of pathogen-specific FNAs without first identifying a suitable biomarker. Multiple target-specific DNA aptamers, including anti-glutamate dehydrogenase (GDH) circular aptamers, anti-degraded toxin B aptamers, and anti-RNase HII aptamers, have also been isolated for the detection of bacteria such as Clostridium difficile. The isolated FNAs have been integrated into fluorescent, colorimetric, and electrochemical biosensors using various signal transduction mechanisms. Both simple-to-use paper-based analytical devices and hand-held electrical devices with integrated FNAs have been developed for POC applications. In addition, signal-amplification strategies, including DNA catenane enabled rolling circle amplification (RCA), DNAzyme feedback RCA, and an all-DNA amplification system using a four-way junction and catalytic hairpin assembly (CHA), have been designed and applied to these systems to further increase their detection sensitivity. The use of these FNA-based biosensors to detect pathogens directly in clinical samples, such as urine, blood, and stool, has now been demonstrated with an outstanding sensitivity of as low as 10 cells per milliliter, highlighting the tremendous potential of using FNA-based sensors in clinical applications. We further describe strategies to overcome the challenges of using FNA-based biosensors in clinical applications, including strategies to improve the stability of FNAs in biological samples and prevent their nonspecific degradation from nucleases and strategies to deal with issues such as signal loss caused by nonspecific binding and biofouling. Finally, the remaining roadblocks for employing FNA-based biosensors in clinical applications are discussed.
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Affiliation(s)
| | | | | | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | | | | | | | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
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19
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Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
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Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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20
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Lyu M, Kong L, Yang Z, Wu Y, McGhee CE, Lu Y. PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity. J Am Chem Soc 2021; 143:9724-9728. [PMID: 34156847 DOI: 10.1021/jacs.1c03129] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, we herein report peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.
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21
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Cortés-Guajardo C, Rojas-Hernández F, Paillao-Bustos R, Cepeda-Plaza M. Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme. Org Biomol Chem 2021; 19:5395-5402. [PMID: 34047747 DOI: 10.1039/d1ob00366f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for its function, is the most studied catalytic DNA in terms of its mechanism. By the end of 2017, a report of the crystal structure of the enzyme-substrate complex in the presence of Pb2+ probed some of the previous findings and opened new questions, especially around the participation of the metal ion in the catalytic mechanism and the promiscuity exhibited by the enzyme in terms of the metal cofactor required for catalysis. In this article we explore the role of the divalent metal ion in the mechanism of the 8-17 DNAzyme as a general acid, by measuring the influence of pH over the activity of a slower variant of the enzyme in the presence of Pb2+. We replaced G14, which has been identified as a general base in the mechanism of the enzyme, by the unnatural analog 2-aminopurine, with a lower pKa value of the N1 group. With this approach, we obtained a bell-shaped pH-rate profile with experimental pKa values of 5.4 and 7.0. Comparing these results with previous pH-rate profiles in the presence of Mg2+, our findings suggest the stabilization of the 5'-O leaving group by the hydrated metal ion acting as a general acid, in addition to the activation of the 2'-OH nucleophile by the general base G14.
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22
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Xu X, Xiao L, Gu C, Shang J, Xiang Y. Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells. ACS OMEGA 2021; 6:13153-13160. [PMID: 34056465 PMCID: PMC8158819 DOI: 10.1021/acsomega.1c00976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 05/09/2023]
Abstract
RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn2+-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.
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23
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Liu Y, Liu Z, Liu R, Wang K, Shi H, Huang J. A MnO 2 nanosheet-mediated photo-controlled DNAzyme for intracellular miRNA cleavage to suppress cell growth. Analyst 2021; 146:3391-3398. [PMID: 33876148 DOI: 10.1039/d1an00406a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Certain miRNAs, called oncomiRs, play a causal role in the onset and maintenance of cancer when overexpressed, thus, representing a potential new class of targets for therapeutic intervention. RNA-cleaving DNAzymes, mainly aimed at mRNA, have shown potential as therapeutic agents for various diseases. However, it's rarely reported that a DNAzyme was used for intracellular miRNA cleavage to suppress cell growth. Herein, we have developed a MnO2 nanosheet-mediated photo-controlled DNAzyme (NPD) for intracellular miRNA cleavage to suppress cell growth. MnO2 nanosheets adsorb photocaged DNAzymes, protect them from enzymatic digestion, and efficiently deliver them into cells. In the presence of intracellular glutathione (GSH), MnO2 nanosheets are reduced to Mn2+ ions, which serve as cofactors of the 8-17 DNAzyme for miRNA cleavage. Once the DNAzyme is activated by light, it can cyclically cleave endogenous miR-21 inside cells, which would suppress cancer cell migration and invasion, and finally induce cancer cell apoptosis.
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Affiliation(s)
- Yehua Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
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24
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25
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Saran R, Huang Z, Liu J. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Yao T, Przybyla JJ, Yeh P, Woodard AM, Nilsson HJ, Brandsen BM, Silverman SK. DNAzymes for amine and peptide lysine acylation. Org Biomol Chem 2021; 19:171-181. [PMID: 33150349 PMCID: PMC7790989 DOI: 10.1039/d0ob02015j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However, finding DNAzymes for peptide lysine acylation is a substantial challenge. By using suitably reactive aryl ester acyl donors as the electrophiles, here we used in vitro selection to identify DNAzymes that acylate amines, including lysine side chains of DNA-anchored peptides. Some of the DNAzymes can transfer a small glutaryl group to an amino group. These results expand the scope of DNAzyme catalysis and suggest the future broader applicability of DNAzymes for sequence-selective lysine acylation of peptide and protein substrates.
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Affiliation(s)
- Tianjiong Yao
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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27
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Goodman E, Zhou C, Cargnello M. Design of Organic/Inorganic Hybrid Catalysts for Energy and Environmental Applications. ACS CENTRAL SCIENCE 2020; 6:1916-1937. [PMID: 33274270 PMCID: PMC7706093 DOI: 10.1021/acscentsci.0c01046] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Indexed: 05/31/2023]
Abstract
Controlling selectivity between competing reaction pathways is crucial in catalysis. Several approaches have been proposed to achieve this goal in traditional heterogeneous catalysts including tuning nanoparticle size, varying alloy composition, and controlling supporting material. A less explored and promising research area to control reaction selectivity is via the use of hybrid organic/inorganic catalysts. These materials contain inorganic components which serve as sites for chemical reactions and organic components which either provide diffusional control or directly participate in the formation of active site motifs. Despite the appealing potential of these hybrid materials to increase reaction selectivity, there are significant challenges to the rational design of such hybrid nanostructures. Structural and mechanistic characterization of these materials play a key role in understanding and, therefore, designing these organic/inorganic hybrid catalysts. This Outlook highlights the design of hybrid organic/inorganic catalysts with a brief overview of four different classes of materials and discusses the practical catalytic properties and opportunities emerging from such designs in the area of energy and environmental transformations. Key structural and mechanistic characterization studies are identified to provide fundamental insight into the atomic structure and catalytic behavior of hybrid organic/inorganic catalysts. Exemplary works are used to show how specific active site motifs allow for remarkable changes in the reaction selectivity. Finally, to demonstrate the potential of hybrid catalyst materials, we suggest a characterization-based approach toward the design of biomimetic hybrid organic/inorganic materials for a specific application in the energy and environmental research space: the conversion of methane into methanol.
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28
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Bi Y, Du X, He P, Wang C, Liu C, Guo W. Smart Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film Actuators Exhibiting Programmable Responsive and Reversible Macroscopic Shape Deformations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906998. [PMID: 32985098 DOI: 10.1002/smll.201906998] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 07/13/2020] [Indexed: 06/11/2023]
Abstract
As a crucial instinct for the survival of organisms, adaptive smart deformation has been well shown via profusely astounding examples within biological morphogenesis in nature, which inspired the construction of biomimetic shape-morphing materials with controlled actuating behaviors. Herein, the construction of nature-inspired bilayer hydrogel film actuators, composed of a polyacrylamide hydrogel passive layer and a polyacrylamide-DNA hybrid hydrogel active layer, which exhibited programmable stimuli-responsive and reversible macroscopic shape deformations directed by the sequence of DNA crosslinking units in the active layer, is reported. As a proof-of-concept, the introduction of DNA i-motif based crosslinking structures into the active layer, which can undergo pH-stimulated formation and dissociation of crosslinking between polymers and therefore change the crosslinking density of the active layer, lead to the redistribution of the internal stresses within the bilayer structure, and result in the pH-stimulated shape deformations. By programming the sequence of DNA units in the active layer, a Ag+ /Cysteamine-stimulated bilayer DNA hybrid hydrogel film actuator is further constructed and exhibits excellent actuation behaviors. Thanks to the micrometer-scale thickness of the films, these actuators exhibit a high degree of macroscopic and reversible shape deformations at high speed, which may find use in future smart biosensing and biomedical applications.
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Affiliation(s)
- Yanhui Bi
- College of Chemistry, Research Centre for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, P. R. China
| | - Xiaoxue Du
- College of Chemistry, Research Centre for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, P. R. China
| | - Pingping He
- College of Chemistry, Research Centre for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, P. R. China
| | - Chunyan Wang
- College of Chemistry, Research Centre for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, P. R. China
| | - Chang Liu
- College of Chemistry, Research Centre for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, P. R. China
| | - Weiwei Guo
- College of Chemistry, Research Centre for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, P. R. China
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29
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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30
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Scheitl CPM, Lange S, Höbartner C. New Deoxyribozymes for the Native Ligation of RNA. Molecules 2020; 25:molecules25163650. [PMID: 32796587 PMCID: PMC7465978 DOI: 10.3390/molecules25163650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022] Open
Abstract
Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalyzing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 5'-adenylated RNA (5'-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four new DNAzymes were identified by in vitro selection from an N40 random DNA library and were shown to catalyze the intermolecular linear RNA-RNA ligation via the formation of a native 3'-5'-phosphodiester linkage. The catalytic activity is distinct from previously described RNA-ligating deoxyribozymes. Kinetic analyses revealed the optimal incubation conditions for high ligation yields and demonstrated a broad RNA substrate scope. Together with the smooth synthetic accessibility of 5'-adenylated RNAs, the new DNA enzymes are promising tools for the protein-free synthesis of long RNAs, for example containing precious modified nucleotides or fluorescent labels for biochemical and biophysical investigations.
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Affiliation(s)
- Carolin P. M. Scheitl
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
| | - Sandra Lange
- Agricultural Center, BASF SE, Speyerer Str 2, 67117 Limburgerhof, Germany;
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
- Correspondence:
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31
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Peeters B, Safdar S, Daems D, Goos P, Spasic D, Lammertyn J. Solid-Phase PCR-Amplified DNAzyme Activity for Real-Time FO-SPR Detection of the MCR-2 Gene. Anal Chem 2020; 92:10783-10791. [PMID: 32638586 DOI: 10.1021/acs.analchem.0c02241] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The polymerase chain reaction (PCR) has been the gold standard molecular analysis technique for decades and has seen quite some evolution in terms of reaction components, methodology, and readout mechanisms. Nucleic acid enzymes (NAzymes) have been used to further exploit the applications of PCR, but so far the work was limited to the colorimetric G-quadruplex or fluorescent substrate cleaving NAzymes. In this study, a solid-phase, fiber optic surface plasmon resonance (FO-SPR) technique is presented as an alternative readout for PCR utilizing NAzymes. First, the surface cleavage activity of DNAzyme-extended amplicons (DNAzyme-amps) is established, followed by optimization of the PCR conditions, which are required for compatibility with the FO-SPR system. Next, by integrating the complement of a 10-23 DNAzyme into the primer pair, PCR-amplified DNAzyme-amps were generated, tested, and validated on qPCR for the detection of the antimicrobial resistance gene MCR-2. Once validated, this primer concept was developed as a one-step assay, driven by PCR-amplified DNAzymes, for FO-SPR-based sensitive and specific detection. Using gold nanoparticle labeled RNA-DNA hybrid strands as substrate for the DNAzyme, PCR-amplified DNAzyme-amps generated in the presence of MCR-2 gene were monitored in real-time, which resulted in an experimental limit of detection of 4 × 105 copy numbers or 6.6 fM. In addition, the DNAzyme-based FO-PCR assay was able to discriminate between the MCR-1 and MCR-2 genes, to further prove the specificity of this assay. Henceforth, this DNAzyme-based fiber optic PCR assay provides a universally applicable, real-time system for the detection of virtually any target NA, in a specific and sensitive manner.
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Affiliation(s)
- Bernd Peeters
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Devin Daems
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Peter Goos
- Department of Biosystems, Biostatistics Group, KU Leuven, Kasteelpark Arenberg 30, Leuven B-3001, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
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32
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Zhou Z, Brennan JD, Li Y. A Multi‐component All‐DNA Biosensing System Controlled by a DNAzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Zhixue Zhou
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences 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 4O3 Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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33
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Zhou Z, Brennan JD, Li Y. A Multi‐component All‐DNA Biosensing System Controlled by a DNAzyme. Angew Chem Int Ed Engl 2020; 59:10401-10405. [PMID: 32207868 DOI: 10.1002/anie.202002019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Zhixue Zhou
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences 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 4O3 Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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34
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Nucleic acid-cleaving catalytic DNA for sensing and therapeutics. Talanta 2020; 211:120709. [PMID: 32070594 DOI: 10.1016/j.talanta.2019.120709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022]
Abstract
DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.
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35
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36
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Liu Y, Lai P, Wang J, Xing X, Xu L. A superior G-quadruplex DNAzyme through functionalized modification of the hemin cofactor. Chem Commun (Camb) 2020; 56:2427-2430. [DOI: 10.1039/c9cc09729e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical modifications of the hemin structure through introducing new functionalities are proposed to enhance the catalytic efficiency of the hemin/G-quadruplex DNAzyme.
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Affiliation(s)
- Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou
- China
| | - Peidong Lai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou
- China
| | - Jingru Wang
- Department of Biotechnology
- College of Life Science and Technology
- Jinan University
- Guangzhou
- China
| | - Xiwen Xing
- Department of Biotechnology
- College of Life Science and Technology
- Jinan University
- Guangzhou
- China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou
- China
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37
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Samani SE, Chang D, McConnell EM, Rothenbroker M, Filipe CDM, Li Y. Highly Sensitive RNA-Cleaving DNAzyme Sensors from Surface-to-Surface Product Enrichment. Chembiochem 2019; 21:632-637. [PMID: 31544309 DOI: 10.1002/cbic.201900575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 12/13/2022]
Abstract
The engineering of easy-to-use biosensors with ultra-low detection sensitivity remains a major challenge. Herein, we report a simple approach for creating such sensors through the use of an RNA-cleaving DNAzyme (RcD) and a strategy designed to concentrate its cleavage product significantly. The assay uses micron-sized beads loaded with a target-responsive RcD and a paper strip containing a microzone covered with a DNA oligonucleotide capable of capturing the cleavage product of the RcD through Watson-Crick hybridization. Placing the beads and the paper strip in a target-containing test sample allows the bead-bound RcD molecules to undergo target-induced RNA cleavage, releasing a DNA fragment that is captured by the paper strip. This strategy, though simple, is very effective in achieving high levels of detection sensitivity, being able to enrich the concentration of the cleavage product by three orders of magnitude. It is also compatible with both fluorescence-based and colorimetric reporting mechanisms. This work provides a simple platform for developing ultrasensitive biosensors that take advantage of the widely available RcDs as molecular recognition elements.
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Affiliation(s)
- Sahar Esmaeili Samani
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Meghan Rothenbroker
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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38
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Nedorezova DD, Fakhardo AF, Molden TA, Kolpashchikov DM. Deoxyribozyme‐Based DNA Machines for Cancer Therapy. Chembiochem 2019; 21:607-611. [DOI: 10.1002/cbic.201900525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Solution Chemistry of Advanced Materials and TechnologiesITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Anna F. Fakhardo
- Laboratory of Solution Chemistry of Advanced Materials and TechnologiesITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Tatiana A. Molden
- Chemistry DepartmentUniversity of Central Florida Orlando FL 32816-2366 USA
| | - Dmitry M. Kolpashchikov
- Chemistry DepartmentUniversity of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical SciencesUniversity of Central Florida Orlando FL 32816 USA
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39
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Hanpanich O, Miyaguchi H, Huang H, Shimada N, Maruyama A. Cationic copolymer-chaperoned short-armed 10-23 DNAzymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:156-169. [PMID: 31608816 DOI: 10.1080/15257770.2019.1675168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The cationic copolymer poly(L-lysine)-graft-dextran (PLL-g-Dex) has nucleic acid chaperone-like activity. The copolymer facilitates both DNA hybridization and strand exchange reactions. For these reasons, DNA-based enzyme (DNAzyme) activity is enhanced in the presence of copolymer. In this study, we evaluated activities of DNAzymes with substrate-binding arms (S-arms) of various lengths. The copolymer promoted DNAzyme reactivity and turnover efficacy, and, depending on S-arm length, maximally accelerated the reaction rate by 250-fold compared to the rate in the absence of copolymer. The copolymer permitted up to six nucleotides truncation of the S-arms having initial length of 10 and 11 nucleotides without loss of catalytic efficiency, enable tuning of the optimal temperature ranging from 30 to 55 °C. The approach might be useful for the development of DNAzyme systems targeting short or highly structured RNAs as well for improvement of DNAzyme-based nanomachines and biosensors.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitonari Miyaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - He Huang
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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40
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Hanpanich O, Oyanagi T, Shimada N, Maruyama A. Cationic copolymer-chaperoned DNAzyme sensor for microRNA detection. Biomaterials 2019; 225:119535. [PMID: 31614289 DOI: 10.1016/j.biomaterials.2019.119535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 02/08/2023]
Abstract
Multi-component nucleic acid enzymes (MNAzymes) are allosteric deoxyribozymes that are activated upon binding of a specific nucleic acid effector. MNAzyme activity is limited due to an insufficient assembly of the MNAzyme and its turnover. In this work, we describe the successful improvement of MNAzyme reactivity and selectivity by addition of cationic copolymers, which exhibit nucleic acid chaperone-like activity. The copolymer allowed a 210-fold increase in signal activity and a 95-fold increase in the signal-to-background selectivity of MNAzymes constructed for microRNA (miRNA) detection. The selectivity of the MNAzyme for homologous miRNAs was demonstrated in a multiplex format in which isothermal reactions of two different MNAzymes were performed. In addition, the copolymer permitted miRNA detections even in the presence of a ribonuclease which is ubiquitous in environments, indicating the protective effect of the copolymer against ribonucleases.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Tomoya Oyanagi
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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41
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McGoldrick LK, Weiss EA, Halámek J. Symmetric-Key Encryption Based on Bioaffinity Interactions. ACS Synth Biol 2019; 8:1655-1662. [PMID: 31287664 DOI: 10.1021/acssynbio.9b00164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The research presented here shows a bridge between biochemistry and cryptography. Enzyme-based assays were used in a new methodology linked to ciphers and cipher systems. Three separate enzyme assays, alkaline phosphatase (ALP) (E.C. 3.1.3.1), lysozyme (E.C. 3.2.1.17), and horseradish peroxidase (HRP) (E.C. 1.11.1.7), were used to create a cipher key in order to encrypt a message. By choosing certain parameters for one's experiment that are performed in the same way as a person receiving the message, correct encryption and decryption keys would be produced, resulting in a correct encryption and decryption of a message. It is imperative that both parties perform the same experiment under the same conditions in order to correctly interpret the message. Bioaffinity-based assays, in particular enzymatic assays, provide a specific, yet flexible mechanism to use for the encryption of messages. Because of the nature of this process there are a multitude of sets of parameters that may be chosen, each of which would result in a different key being produced, heightening the security and the robustness of the method. This paper shows that by using this concept of forming encryption keys using a bioaffinity-based approach, one is able to properly encrypt and decrypt a message, which could be viable for other biochemically based techniques.
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Affiliation(s)
- Leif K. McGoldrick
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Elizabeth A. Weiss
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Jan Halámek
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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42
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Feng M, Gu C, Sun Y, Zhang S, Tong A, Xiang Y. Enhancing Catalytic Activity of Uranyl-Dependent DNAzyme by Flexible Linker Insertion for More Sensitive Detection of Uranyl Ion. Anal Chem 2019; 91:6608-6615. [PMID: 31016961 DOI: 10.1021/acs.analchem.9b00490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The uranyl-dependent DNAzyme 39E cleaves its nucleic acid substrate in the presence of uranyl ion (UO22+). It has been widely utilized in many sensor designs for selective and sensitive detection of UO22+ in the environment and inside live cells. In this work, by inserting a flexible linker (C3 Spacer) into one critical site (A20) of the 39E catalytic core, we successfully enhanced the original catalytic activity of 39E up to 8.1-fold at low UO22+ concentrations. Applying such a modified DNAzyme (39E-A20-C3) in a label-free fluorescent sensor for UO22+ detection achieved more than 1 order of magnitude sensitivity enhancement over using native 39E, with the UO22+ detection limit improved from 2.6 nM (0.63 ppb) to 0.19 nM (0.047 ppb), while the high selectivity to UO22+ over other metal ions was fully preserved. The method was also successfully applied for the detection of UO22+-spiked environmental water samples to demonstrate its practical usefulness.
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Affiliation(s)
- Mengli Feng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Chunmei Gu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Yanping Sun
- School of Chemistry and Biological Engineering , University of Science and Technology Beijing , Beijing 100083 , People's Republic of China
| | - Shuyuan Zhang
- School of Chemistry and Biological Engineering , University of Science and Technology Beijing , Beijing 100083 , People's Republic of China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
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43
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Nedorezova DD, Fakhardo AF, Nemirich DV, Bryushkova EA, Kolpashchikov DM. Towards DNA Nanomachines for Cancer Treatment: Achieving Selective and Efficient Cleavage of Folded RNA. Angew Chem Int Ed Engl 2019; 58:4654-4658. [PMID: 30693619 DOI: 10.1002/anie.201900829] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Indexed: 11/10/2022]
Abstract
Despite decades of effort, gene therapy (GT) has failed to deliver clinically significant anticancer treatment, owing in part to low selectivity, low efficiency, and poor accessibility of folded RNA targets. Herein, we propose to solve these common problems of GT agents by using a DNA nanotechnology approach. We designed a deoxyribozyme-based DNA machine that can i) recognize the sequence of a cancer biomarker with high selectivity, ii) tightly bind a structured fragment of a housekeeping gene mRNA, and iii) cleave it with efficiency greater than that of a traditional DZ-based cleaving agent. An important advantage of the DNA nanomachine over other gene therapy approaches (antisense, siRNA, and CRISPR/cas) is its ability to cleave a housekeeping gene mRNA after being activated by a cancer marker RNA, which can potentially increase the efficiency of anticancer gene therapy. The DNA machine could become a prototype platform for a new type of anticancer GT agent.
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Affiliation(s)
- Daria D Nedorezova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
| | - Anna F Fakhardo
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
| | - Daria V Nemirich
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina A Bryushkova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation.,Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
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44
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Nedorezova DD, Fakhardo AF, Nemirich DV, Bryushkova EA, Kolpashchikov DM. Towards DNA Nanomachines for Cancer Treatment: Achieving Selective and Efficient Cleavage of Folded RNA. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900829] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Anna F. Fakhardo
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Daria V. Nemirich
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Ekaterina A. Bryushkova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
- Chemistry Department University of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando FL 32816 USA
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45
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Electrochemical analysis of 8-hydroxy-2'-deoxyguanosine with enhanced sensitivity based on exonuclease-mediated functional nucleic acid. Talanta 2019; 199:324-328. [PMID: 30952266 DOI: 10.1016/j.talanta.2019.02.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/16/2019] [Accepted: 02/21/2019] [Indexed: 01/27/2023]
Abstract
In this work, an electrochemical method for sensitive analysis of 8-hydroxy-2'-deoxyguanosine, a key biomarker that is widely used to study oxidative injury-related diseases, is proposed based on exonuclease-mediated functional nucleic acid. In the design, exonuclease can not only distinguish the existence of target, but also suppress the background noise, thus the sensitivity can be enhanced. Moreover, DNAzyme designed in the functional nucleic acid can further improve the sensitivity of the analysis during signal generation process. Therefore, exonuclease-mediated functional nucleic acid may ensure high sensitivity of the assay. Further studies reveal that the detection of 8-hydroxy-2'-deoxyguanosine can be achieved with a linearity from 0.01 nM to 7.0 μM and a detection limit of 6.82 pM. The new method has also been successfully applied to the determination of 8-OHdG in urine with good results, indicating its great potential for practical use.
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Shomali Z, Kompany-Zareh M, Omidikia N. Fluorescence Based Investigation of Temperature-Dependent Pb 2+-Specific 8-17E DNAzyme Catalytic Sensor. J Fluoresc 2019; 29:335-342. [PMID: 30778897 DOI: 10.1007/s10895-019-02346-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/14/2019] [Indexed: 12/13/2022]
Abstract
The 8-17E DNAzyme is a temperature-dependent DNA metalloenzyme catalyzing RNA trans esterification in the presence of Pb2+ metal ions. Labeling the stems of the substrate and DNAzyme with the Cy3 and Cy5 respectively, the considered DNAzyme was studied by the fluorescence spectroscopy. The temperature-dependent variability of the Pb2+-specific 8-17E DNAzyme catalytic sensor was investigated trough a number of successive temperature fluctuations from 4 to 25 °C to obtain information. Investigating underlined biochemical system reveals that in this sensor, free single strands Enzyme (Cy5-E) and Substrate (Cy3-S) have higher fluorescence intensities than hybridized forms, suggesting that the fluorophores are in a contact quenched. Increasing the temperature has three effects: 1) Fluorescence intensities for the free fluorophores were reduced, 2) stability of the hybridized form was reduced and cleavage of substrate in presence of Pb2+was occurred, and 3) conformation of ES hybridized form was changed (before cleavage). As a result of conformation changes in ES, S was more affected than E in the ES. Pb2+ ion shows quenching effect on both fluorophores and in the absence of N2(g) purge the effect was more considerable. A main goal that we had in mind was to find if significantly lower concentrations of Pb2+ and ES, compared to previous reports, can generate any observable cleavage in substrate. Analysis of the cleavage reaction for 50 nM ES indicates that S is cleaved at 25 °C in presence of N2(g) and 0.5 μM Pb2+, while in same condition no apparent change occurs in the 4 or 10 °C. The rapid, sensitive and low cost strategy presented here can be applicable to study temperature-dependent behavior of other nucleic acid-based biosensors.
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Affiliation(s)
- Zohreh Shomali
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Mohsen Kompany-Zareh
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran. .,Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, NS, B3H 4R2, Canada.
| | - Nematollah Omidikia
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, 98135-674, Iran
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Lichtor PA, Chen Z, Elowe NH, Chen JC, Liu DR. Side chain determinants of biopolymer function during selection and replication. Nat Chem Biol 2019; 15:419-426. [PMID: 30742124 PMCID: PMC6430648 DOI: 10.1038/s41589-019-0229-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The chemical functionalities within biopolymers determine their physical properties and biological activities. The relationship between the side-chains available to a biopolymer population and the potential functions of the resulting polymers, however, has proven difficult to study experimentally. Using seven sets of chemically diverse charged, polar, and nonpolar side-chains, we performed cycles of artificial translation, in vitro selections for binding to either PCSK9 or IL-6 protein, and replication on libraries of random side-chain-functionalized nucleic acid polymers. Polymer sequence convergence, bulk population target binding, affinity of individual polymers, and head-to-head competition among post-selection libraries collectively indicate that polymer libraries with nonpolar side-chains outperformed libraries lacking these side-chains. The presence of nonpolar groups, resembling functionality present in proteins but missing from natural nucleic acids, thus may be strong determinants of binding activity. This factor may contribute to the apparent evolutionary advantage of proteins over their nucleic acid precursors for some molecular recognition tasks.
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Affiliation(s)
- Phillip A Lichtor
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Zhen Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nadine H Elowe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan C Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Chen J, Zhang Y, Cheng M, Guo Y, Šponer J, Monchaud D, Mergny JL, Ju H, Zhou J. How Proximal Nucleobases Regulate the Catalytic Activity of G-Quadruplex/Hemin DNAzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03811] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingying Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiri Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC Dijon 21078, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, 33600 Pessac, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Xu Q, Zhang Y, Xiang D, Li CC, Zhang CY. A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules. Anal Chim Acta 2018; 1043:81-88. [PMID: 30392672 DOI: 10.1016/j.aca.2018.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022]
Abstract
We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.
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Affiliation(s)
- Qinfeng Xu
- College of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Dongxue Xiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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Manochehry S, McConnell EM, Tram KQ, Macri J, Li Y. Colorimetric Detection of Uranyl Using a Litmus Test. Front Chem 2018; 6:332. [PMID: 30140672 PMCID: PMC6095041 DOI: 10.3389/fchem.2018.00332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/16/2018] [Indexed: 01/10/2023] Open
Abstract
Ingestion of water containing toxic contaminants above levels deemed safe for human consumption can occur unknowingly since numerous common contaminants in drinking water are colorless and odorless. Uranyl is particularly problematic as it has been found at dangerous levels in sources of drinking water. Detection of this heavy metal-ion species in drinking water currently requires sending a sample to a laboratory where trained personnel use equipment to perform the analysis and turn-around times can be long. A pH-responsive colorimetric biosensor was developed to enable detection of uranyl in water which coupled the uranyl-specific 39E DNAzyme as a recognition element, and an enzyme capable of producing a pH change as the reporter element. The rapid colorimetric assay presented herein can detect uranyl in lake and well water at concentrations relevant for environmental monitoring, as demonstrated by the detection of uranyl at levels below the limits set for drinking water by major regulatory agencies including the World Health Organization (30 μg/L). This simple and inexpensive DNAzyme-based assay enabled equipment-free visual detection of 15 μg/L uranyl, using both solution-based and paper-based pH-dependent visualization strategies.
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Affiliation(s)
- Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Erin M. McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Kha Q. Tram
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
| | - Joseph Macri
- Department of Pathology and Molecular Medicine, McMaster UniversityHamilton, ON, Canada
- Hamilton Regional Laboratory Medicine ProgramHamilton, ON, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
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