1
|
Chen K, Zhu L, Li J, Zhang Y, Yu Y, Wang X, Wei W, Huang K, Xu W. High-content tailoring strategy to improve the multifunctionality of functional nucleic acids. Biosens Bioelectron 2024; 261:116494. [PMID: 38901394 DOI: 10.1016/j.bios.2024.116494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.
Collapse
Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yongxia Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wei Wei
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| |
Collapse
|
2
|
Levina AS, Repkova MN, Netesova NA, Ternovoi VA, Mazurkov OY, Filippova EI, Mazurkova NA, Zarytova VF. Substantial Antiviral Potential of Deoxyribozymes Fixed on Anatase Nanoparticles Against Influenza A Viruses in vitro and in vivo. J Pharm Sci 2024; 113:1202-1208. [PMID: 37879408 DOI: 10.1016/j.xphs.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
Influenza A viruses (IAV) are a high threat to humanity because of a lack of proper effective antiviral drugs and resistance of viruses to existing vaccines. We describe the sufficient anti-IAV effect of Ans/PL-Dz nanocomposites that contain deoxyribozymes (Dz) immobilized on anatase TiO2 nanoparticles (Ans) through polylysine linker (PL). The Dz-containing nanocomposites appear to be more efficient than the Ans/PL-ODN nanocomposites that contain common oligodeoxyribonucleotides (ODN) targeted to the same RNA regions of the viral genome. The simultaneous use of nanocomposites that contain Dz and ODN, which are targeted to different sites of viral RNA provides a higher overall effect than the independent action of each of them (synergism). The inhibition of IAV with the proposed nanocomposites was shown to be effective, sequence-specific, and dose-dependent. The most efficient Ans/PL-Dz nanocomposite exhibited a high antiviral effect in vivo on mice models. The efficiency of IAV inhibition with this nanocomposite in vitro and in vivo is higher than that for the approved antiflu drug oseltamivir. The results open the prospect of creating a unique antiviral agent suitable for IAV suppression.
Collapse
Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian branch of RAS, pr. Lavrent'eva 8, Novosibirsk 630090, Russia.
| | - Marina N Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian branch of RAS, pr. Lavrent'eva 8, Novosibirsk 630090, Russia
| | - Nina A Netesova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region 630559, Russia
| | - Vladimir A Ternovoi
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region 630559, Russia
| | - Oleg Yu Mazurkov
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region 630559, Russia
| | - Ekaterina I Filippova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region 630559, Russia
| | - Natalia A Mazurkova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region 630559, Russia
| | - Valentina F Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian branch of RAS, pr. Lavrent'eva 8, Novosibirsk 630090, Russia
| |
Collapse
|
3
|
Polydopamine assembled stable core-shell nanoworms-DNAzyme probe for selective detection of Pb2+ and in living cells imaging. Talanta 2023. [DOI: 10.1016/j.talanta.2022.123984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
4
|
Cao X, Chen C, Zhu Q. Biosensors based on functional nucleic acids and isothermal amplification techniques. Talanta 2023; 253:123977. [PMID: 36201957 DOI: 10.1016/j.talanta.2022.123977] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.
Collapse
Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| |
Collapse
|
5
|
Ling P, Cheng S, Wang L, Sun X, Gao X, Gao F. Electrochemically classifying DNA structure based on the small molecule-DNA recognition. Bioelectrochemistry 2022; 147:108193. [PMID: 35753199 DOI: 10.1016/j.bioelechem.2022.108193] [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: 04/05/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
Abstract
Herein, we reported the differential binding ability of aminoglycosides to DNA structures using electrochemical method through principal component analysis (PCA) to classify different DNA secondary structures and understand the link between secondary structure and DNA conformation. In these analyses, the DNA with different secondary structure motifs: bulge, internal loop, hairpin loop and stem loop were designed. The aminoglycosides as receptors were modified on the surface of electrode. In the presence of DNA, the DNA will be absorbed on the surface of electrode via the recognition of DNA and aminoglycosides, resulting in the electrochemical signal observed in [Fe(CN)6]3-/4-. Furthermore, the DNA structures labeled with 2-aminopurine (2-AP) at the structural motif of interest were also employed to study the binding affinity between aminoglycosides and different DNA motifs. The PCA suggested that this method may achieve nucleotide-specific classification of two independent secondary structure motifs, and the structure and sequence of DNA and the size and structure of small molecule could affect the binding ability of the aminoglycosides and DNA. This approach presents a new approach to classify DNA structure and offers ideas for designing targeted drugs small molecule compounds for wound dressing and drug delivery.
Collapse
Affiliation(s)
- Pinghua Ling
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China.
| | - Shan Cheng
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Linyu Wang
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Xinyu Sun
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Xianping Gao
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Feng Gao
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China.
| |
Collapse
|
6
|
Zn 2+-dependent DNAzymes that cleave all combinations of ribonucleotides. Commun Biol 2021; 4:221. [PMID: 33594202 PMCID: PMC7886857 DOI: 10.1038/s42003-021-01738-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 11/14/2020] [Indexed: 11/08/2022] Open
Abstract
Although several DNAzymes are known, their utility is limited by a narrow range of substrate specificity. Here, we report the isolation of two zinc-dependent DNAzymes, ZincDz1 and ZincDz2, which exhibit compact catalytic core sequences with highly versatile hydrolysis activity. They were selected through in vitro selection followed by deep sequencing analysis. Despite their sequence similarity, each DNAzyme showed different Zn2+-concentration and pH-dependent reaction profiles, and cleaved the target RNA sequences at different sites. Using various substrate RNA sequences, we found that the cleavage sequence specificity of ZincDz2 and its highly active mutant ZincDz2-v2 to be 5'-rN↓rNrPu-3'. Furthermore, we demonstrated that the designed ZincDz2 could cut microRNA miR-155 at three different sites. These DNAzymes could be useful in a broad range of applications in the fields of medicine and biotechnology.
Collapse
|
7
|
Hu L, Fu X, Kong G, Yin Y, Meng HM, Ke G, Zhang XB. DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging. J Mater Chem B 2020; 8:9449-9465. [DOI: 10.1039/d0tb01750g] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.
Collapse
Affiliation(s)
- Ling Hu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiaoyi Fu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Gezhi Kong
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Yao Yin
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Hong-Min Meng
- College of Chemistry
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiao-Bing Zhang
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| |
Collapse
|
8
|
Xiong M, Yang Z, Lake RJ, Li J, Hong S, Fan H, Zhang X, Lu Y. DNAzyme‐Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019; 132:1907-1912. [DOI: 10.1002/ange.201912514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory (MBL)State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringCollaborative Innovation Center for Chemistry and Molecular MedicineHunan University Changsha 410082 P. R. China
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Zhenglin Yang
- Department of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Ryan J. Lake
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Junjie Li
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Shanni Hong
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Huanhuan Fan
- Molecular Science and Biomedicine Laboratory (MBL)State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringCollaborative Innovation Center for Chemistry and Molecular MedicineHunan University Changsha 410082 P. R. China
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Xiao‐Bing Zhang
- Molecular Science and Biomedicine Laboratory (MBL)State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringCollaborative Innovation Center for Chemistry and Molecular MedicineHunan University Changsha 410082 P. R. China
| | - Yi Lu
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| |
Collapse
|
9
|
Xiong M, Yang Z, Lake RJ, Li J, Hong S, Fan H, Zhang XB, Lu Y. DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019; 59:1891-1896. [PMID: 31746514 DOI: 10.1002/anie.201912514] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 12/21/2022]
Abstract
Genetically encoded fluorescent proteins (FPs) have been used for metal ion detection. However, their applications are restricted to a limited number of metal ions owing to the lack of available metal-binding proteins or peptides that can be fused to FPs and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. We report herein the use of Mg2+ -specific 10-23 or Zn2+ -specific 8-17 RNA-cleaving DNAzymes to regulate the expression of FPs as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green FP (GFP), by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red FP (RFP), is not affected. The Mg2+ or Zn2+ in HeLa cells can be detected using both confocal imaging and flow cytometry. Since a wide variety of metal-specific DNAzymes can be obtained, this method can likely be applied to imaging many other metal ions, expanding the range of the current genetically encoded fluorescent protein-based sensors.
Collapse
Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zhenglin Yang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ryan J Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Junjie Li
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shanni Hong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huanhuan Fan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
10
|
Li W, Chen S, Xu D, Wen Q, Yang T, Liu J. A DNA as a Substrate and an Enzyme: Direct Profiling of Methyltransferase Activity by Cytosine Methylation of a DNAzyme. Chemistry 2018; 24:14500-14505. [DOI: 10.1002/chem.201802822] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Wang Li
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
- Department of Chemistry, Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Siyi Chen
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Dong Xu
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Qian Wen
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Tao Yang
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Juewen Liu
- Department of Chemistry, Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| |
Collapse
|
11
|
Wang Y, Liu E, Lam CH, Perrin DM. A densely modified M 2+-independent DNAzyme that cleaves RNA efficiently with multiple catalytic turnover. Chem Sci 2018; 9:1813-1821. [PMID: 29675226 PMCID: PMC5890787 DOI: 10.1039/c7sc04491g] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/04/2018] [Indexed: 12/12/2022] Open
Abstract
Sequence-specific cleavage of RNA targets in the absence of a divalent metal cation (M2+) has been a long-standing goal in bioorganic chemistry. Herein, we report the in vitro selection of novel RNA cleaving DNAzymes that are selected using 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) along with dGTP. These modified dNTPs provide key functionalities reminiscent of the active sites of ribonucleases, notably RNase A. Of several such M2+-free DNAymes, DNAzyme 7-38-32 cleaves a 19 nt all-RNA substrate with multiple-turnover, under simulated physiological conditions wherein only 0.5 mM Mg2+ was present, attaining values of kcat of 1.06 min-1 and a KM of 1.37 μM corresponding to a catalytic efficiency of ∼106 M-1 min-1. Therefore, Dz7-38-32 represents a promising candidate towards the development of therapeutically efficient DNAzymes.
Collapse
Affiliation(s)
- Yajun Wang
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - Erkai Liu
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - Curtis H Lam
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - David M Perrin
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| |
Collapse
|
12
|
Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
Collapse
Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
| |
Collapse
|
13
|
Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
14
|
Wang W, Satyavolu NSR, Wu Z, Zhang JR, Zhu JJ, Lu Y. Near-Infrared Photothermally Activated DNAzyme-Gold Nanoshells for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2017; 56:6798-6802. [PMID: 28471018 PMCID: PMC5861726 DOI: 10.1002/anie.201701325] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/30/2017] [Indexed: 12/31/2022]
Abstract
DNAzymes have enjoyed success as metal ion sensors outside cells. Their susceptibility to metal-dependent cleavage during delivery into cells has limited their intracellular applications. To overcome this limitation, a near-infrared (NIR) photothermal activation method is presented for controlling DNAzyme activity in living cells. The system consists of a three-stranded DNAzyme precursor (TSDP), the hybridization of which prevents the DNAzyme from being active. After conjugating the TSDP onto gold nanoshells and upon NIR illumination, the increased temperature dehybridizes the TSDP to release the active DNAzyme, which then carries out metal-ion-dependent cleavage, resulting in releasing the cleaved product containing a fluorophore. Using this construct, detecting Zn2+ in living HeLa cells is demonstrated. This method has expanded the DNAzyme versatility for detecting metal ions in biological systems under NIR light that exhibits lower phototoxicity and higher tissue penetration ability.
Collapse
Affiliation(s)
- Wenjing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, P.R. China
| | | | - Zhenkun Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, P.R. China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, P.R. China
- School of Chemistry and Life Science, Nanjing University, Jinling College, Nanjing, Jiangsu, 210089, P.R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, P.R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
15
|
Wang W, Satyavolu NSR, Wu Z, Zhang JR, Zhu JJ, Lu Y. Near-Infrared Photothermally Activated DNAzyme-Gold Nanoshells for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701325] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wenjing Wang
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- State Key Laboratory of Analytical for Life Science; School of Chemistry & Chemical Engineering; Nanjing University; Nanjing Jiangsu 210093 P.R. China
| | | | - Zhenkun Wu
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- State Key Laboratory of Chemo/BioSensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha Hunan 410082 P.R. China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical for Life Science; School of Chemistry & Chemical Engineering; Nanjing University; Nanjing Jiangsu 210093 P.R. China
- School of Chemistry and Life Science; Nanjing University, Jinling College; Nanjing Jiangsu 210089 P.R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science; School of Chemistry & Chemical Engineering; Nanjing University; Nanjing Jiangsu 210093 P.R. China
| | - Yi Lu
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| |
Collapse
|
16
|
Abstract
DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.
Collapse
|
17
|
Zhou W, Saran R, Huang PJJ, Ding J, Liu J. An Exceptionally Selective DNA Cooperatively Binding Two Ca2+Ions. Chembiochem 2017; 18:518-522. [PMID: 28087991 DOI: 10.1002/cbic.201600708] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Runjhun Saran
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
| | - Juewen Liu
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| |
Collapse
|
18
|
Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases. Sci Rep 2016; 6:38612. [PMID: 27924926 PMCID: PMC5141509 DOI: 10.1038/srep38612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/10/2016] [Indexed: 01/21/2023] Open
Abstract
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates. We also showed that the sequence specificities of Mini-III RNases are not reflected by different binding affinities for cognate and non-cognate sequences, suggesting that target selection occurs predominantly at the cleavage step. We were able to identify two structural elements, the α4 helix and α5b-α6 loop that were involved in target selection. Characterization of the sequence specificity of the eight Mini-III RNases may provide a basis for better understanding RNA substrate recognition by Mini-III RNases and adopting these enzymes and their engineered derivatives as tools for RNA research.
Collapse
|
19
|
Hwang K, Hosseinzadeh P, Lu Y. Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes. Inorganica Chim Acta 2016; 452:12-24. [PMID: 27695134 DOI: 10.1016/j.ica.2016.04.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review summarizes research into the metal-binding properties of catalytic DNAzymes, towards the goal of understanding the structural properties leading to metal ion specificity. Progress made and insight gained from a range of biochemical and biophysical techniques are covered, and promising directions for future investigations are discussed.
Collapse
Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parisa Hosseinzadeh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| |
Collapse
|
20
|
Behera AK, Schlund KJ, Mason AJ, Alila KO, Han M, Grout RL, Baum DA. Enhanced deoxyribozyme-catalyzed RNA ligation in the presence of organic cosolvents. Biopolymers 2016; 99:382-91. [PMID: 23529690 DOI: 10.1002/bip.22191] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/16/2012] [Accepted: 11/26/2012] [Indexed: 02/06/2023]
Abstract
Deoxyribozyme and aptamer selections are typically conducted in aqueous buffer solutions. Using nonaqueous cosolvents in selection experiments will help expand the activity of deoxyribozymes with non-oligonucleotide substrates and will allow identification of new aptamers for nonprotein targets. We undertook in vitro selections utilizing a small amount of methanol in the reaction to keep the herbicides alachlor and atrazine in solution with the goal of identifying deoxyribozymes that require these herbicides for activity. The resulting deoxyribozymes successfully catalyze RNA ligation, but do not require alachlor or atrazine. Surprisingly, some of these deoxyribozymes displayed better catalytic activity in the presence of methanol over just aqueous buffer. We investigated several organic cosolvents to see if this enhancement was limited to methanol and found that other cosolvents, including ethanol, DMSO, and DMF, supported activity; in some cases, greater enhancement was observed. On the basis of these results, we tested two other previously identified RNA-ligating deoxyribozymes to assess their tolerance of cosolvents and determined that different deoxyribozymes showed different responses to the cosolvents. Our results demonstrate that deoxyribozymes can tolerate and, in some cases, display enhanced activity in alternative solvent conditions. These findings will facilitate the development of responsive deoxyribozyme systems utilizing components with limited water solubility.
Collapse
Affiliation(s)
- Anit K Behera
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, MO, 63103
| | | | | | | | | | | | | |
Collapse
|
21
|
Kasprowicz A, Stokowa-Sołtys K, Wrzesiński J, Jeżowska-Bojczuk M, Ciesiołka J. In vitro selection of deoxyribozymes active with Cd(2+) ions resulting in variants of DNAzyme 8-17. Dalton Trans 2016; 44:8138-49. [PMID: 25836771 DOI: 10.1039/c5dt00187k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In vitro selection was performed to search for RNA-cleaving DNAzymes catalytically active with Cd(2+) ions from the oligonucleotide combinatorial library with a 23-nucleotide random region. All the selected, catalytically active variants turned out to belong to the 8-17 type DNAzyme. Three DNAzymes were prepared in shortened, cis-acting versions which were subjected to a detailed study of the kinetic properties and metal ion preferences. Although the selection protocol was designed for Cd(2+)-dependent DNAzymes, the variants showed broader metal ion specificity. They preferred Cd(2+) but were also active with Mn(2+) and Zn(2+), suggesting that binding of the catalytic ion does not require an extremely specific coordination pattern. The unexpected decrease of the catalytic activity of the variants along with the temperature increase suggested that some changes occurred in their structures or the rate-limiting step of the reaction was changed. Two elements of the catalytic core of DNAzyme 1/VIIWS, the nucleotide at position 12 and the three-base-pair hairpin motif, were mutated. The presence of a purine residue at position 12 was crucial for the catalytic activity but the changes at that position had a relatively small influence on the metal ion preferences of this variant. The middle base pair of the three-base-pair hairpin was changed from A-T to C-G interaction. The catalytic activity of the mutated variant was increased with Zn(2+), decreased with Mn(2+), and was not changed in the presence of Cd(2+) ions. Clearly, this base pair was important for defining the metal ion preferences of the DNAzyme 1/VIIWS.
Collapse
Affiliation(s)
- Aleksandra Kasprowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
| | | | | | | | | |
Collapse
|
22
|
Räz MH, Hollenstein M. Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8-17 and 10-23. MOLECULAR BIOSYSTEMS 2016; 11:1454-61. [PMID: 25854917 DOI: 10.1039/c5mb00102a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNAzymes (Dz) 8-17 and 10-23 are two widely studied and well-characterized RNA-cleaving DNA catalysts. In an effort to further improve the understanding of the fragile interactions and dynamics of the enzymatic mechanism, this study examines the catalytic efficiency of minimally modified DNAzymes. Five single mutants of Dz8-17 and Dz10-23 were prepared by replacing the adenine residues in the corresponding catalytic cores with 3-deazaadenine units. Kinetic assays were used to assess the effect on the catalytic activity and thereby identify the importance of hydrogen bonding that arises from the N3 atoms. The results suggest that modifications at A15 and A15.0 of Dz8-17 have a significant influence and show a reduction in catalytic activity. Modification at each location in Dz10-23 results in a decrease of the observed rate constants, with A12 appearing to be the most affected with a reduction of ∼80% of kobs and ∼25% of the maximal cleavage rate compared to the wild-type DNAzyme. On the other hand, modification of A12 in Dz8-17 showed an ∼130% increase in kobs, thus unraveling a new potential site for the introduction of chemical modifications. A pH-profile analysis showed that the chemical cleavage step is rate-determining, regardless of the presence and/or location of the mutation. These findings point towards the importance of the N3-nitrogens of certain adenine nucleotides located within the catalytic cores of the DNAzymes for efficient catalytic activity and further suggest that they might directly partake in maintaining the appropriate tertiary structure. Therefore, it appears that minor groove interactions constitute an important feature of DNAzymes as well as ribozymes.
Collapse
Affiliation(s)
- Michael H Räz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | | |
Collapse
|
23
|
Huang PJJ, Liu J. Two Pb2+-specific DNAzymes with opposite trends in split-site-dependent activity. Chem Commun (Camb) 2014; 50:4442-4. [PMID: 24643441 DOI: 10.1039/c4cc00864b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By splitting the catalytic core of DNAzymes into two halves, two Pb(2+)-specific DNAzymes retain partial activity, while they show opposite trends of activity as a function of the split site, revealing important nucleotides for catalysis and metal binding.
Collapse
Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | | |
Collapse
|
24
|
Evdokimov AA, Mazurkova NA, Malygin EG, Zarytova VF, Levina AS, Repkova MN, Zagrebelnyi SN, Netesova NA. Design of deoxyribozymes for inhibition of influenza a virus reproduction. Mol Biol 2013. [DOI: 10.1134/s0026893312060040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
25
|
Xiang Y, Wu P, Tan LH, Lu Y. DNAzyme-functionalized gold nanoparticles for biosensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:93-120. [PMID: 24026635 DOI: 10.1007/10_2013_242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.
Collapse
Affiliation(s)
- Yu Xiang
- Department of Chemistry and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | | | | |
Collapse
|
26
|
Xiang Y, Wang Z, Xing H, Lu Y. Expanding DNAzyme Functionality through Enzyme Cascades with Applications in Single Nucleotide Repair and Tunable DNA-Directed Assembly of Nanomaterials. Chem Sci 2013; 4:398-404. [PMID: 23264874 PMCID: PMC3524592 DOI: 10.1039/c2sc20763j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many biological functions require two or more enzymes working together in cascades. While many examples of protein and RNA enzyme cascades are known, few enzyme cascades containing solely DNAzymes have been reported. Herein we demonstrate the combination of an 8-17 DNAzyme with RNA cleavage activity and an E47 DNAzyme with DNA ligation activity to achieve a new function of single ribonucleotide repair in DNA while maintaining the integrity of the original DNA sequence, which is difficult for a single DNAzyme to achieve. In addition, this method is applied to modify the sequences of DNA strands immobilized on the surface of nanoparticles to control the DNA-directed assembly selectively and sequentially. Such an approach can be applied to other DNAzymes with different activities to expand the functions of DNAzymes and the scope of their applications.
Collapse
Affiliation(s)
- Yu Xiang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zidong Wang
- Department of Material Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hang Xing
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Material Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
27
|
RNA-Cleaving DNA Enzymes and Their Potential Therapeutic Applications as Antibacterial and Antiviral Agents. FROM NUCLEIC ACIDS SEQUENCES TO MOLECULAR MEDICINE 2012. [PMCID: PMC7119987 DOI: 10.1007/978-3-642-27426-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA catalysts are synthetic single-stranded DNA molecules that have been identified by in vitro selection from random sequence DNA pools. The most prominent representatives of DNA catalysts (also known as DNA enzymes, deoxyribozymes, or DNAzymes) catalyze the site-specific cleavage of RNA substrates. Two distinct groups of RNA-cleaving DNA enzymes are the 10-23 and 8-17 enzymes. A typical RNA-cleaving DNA enzyme consists of a catalytic core and two short binding arms which form Watson–Crick base pairs with the RNA targets. RNA cleavage is usually achieved with the assistance of metal ions such as Mg2+, Ca2+, Mn2+, Pb2+, or Zn2+, but several chemically modified DNA enzymes can cleave RNA in the absence of divalent metal ions. A number of studies have shown the use of 10-23 DNA enzymes for modest downregulation of therapeutically relevant RNA targets in cultured cells and in whole mammals. Here we focus on mechanistic aspects of RNA-cleaving DNA enzymes and their potential to silence therapeutically appealing viral and bacterial gene targets. We also discuss delivery options and challenges involved in DNA enzyme-based therapeutic strategies.
Collapse
|
28
|
Lan T, Lu Y. Metal Ion-Dependent DNAzymes and Their Applications as Biosensors. Met Ions Life Sci 2012; 10:217-48. [DOI: 10.1007/978-94-007-2172-2_8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
29
|
Grimpe B. Deoxyribozymes and bioinformatics: complementary tools to investigate axon regeneration. Cell Tissue Res 2011; 349:181-200. [PMID: 22190188 PMCID: PMC7087747 DOI: 10.1007/s00441-011-1291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/17/2011] [Indexed: 11/28/2022]
Abstract
For over 100 years, scientists have tried to understand the mechanisms that lead to the axonal growth seen during development or the lack thereof during regeneration failure after spinal cord injury (SCI). Deoxyribozyme technology as a potential therapeutic to treat SCIs or other insults to the brain, combined with a bioinformatics approach to comprehend the complex protein-protein interactions that occur after such trauma, is the focus of this review. The reader will be provided with information on the selection process of deoxyribozymes and their catalytic sequences, on the mechanism of target digestion, on modifications, on cellular uptake and on therapeutic applications and deoxyribozymes are compared with ribozymes, siRNAs and antisense technology. This gives the reader the necessary knowledge to decide which technology is adequate for the problem at hand and to design a relevant agent. Bioinformatics helps to identify not only key players in the complex processes that occur after SCI but also novel or less-well investigated molecules against which new knockdown agents can be generated. These two tools used synergistically should facilitate the pursuit of a treatment for insults to the central nervous system.
Collapse
Affiliation(s)
- Barbara Grimpe
- Applied Neurobiology, Department of Neurology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany.
| |
Collapse
|
30
|
Lam JCF, Kwan SO, Li Y. Characterization of non-8-17 sequences uncovers structurally diverse RNA-cleaving deoxyribozymes. MOLECULAR BIOSYSTEMS 2011; 7:2139-46. [PMID: 21523306 DOI: 10.1039/c1mb05034f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA-cleaving deoxyribozymes (DNAzymes) can be isolated from random-sequence DNA pools via the process of in vitro selection. However, small and simple catalytic motifs, such as the 8-17 DNAzyme, are commonly observed in sequence space, presenting a challenge in discovering large and complex DNAzymes. In an effort to investigate underrepresented molecular species derived from in vitro selection, in this study we sought to characterize non-8-17 sequences obtained from a previous in vitro selection experiment wherein the 8-17 deoxyribozyme was the dominant motif. We examined 9 sequence families from 21 motifs by characterizing their structural and functional features. We discovered 9 novel deoxyribozyme classes with large catalytic domains (>40 nucleotides) utilizing three-way or four-way junction structural frameworks. Kinetic studies revealed that these deoxyribozymes exhibit moderate to excellent catalytic rates (k(obs) from 0.003 to 1 min(-1)), compared to other known RNA-cleaving DNAzymes. Although chemical probing experiments, site-directed mutational analyses, and metal cofactor dependency tests suggest unique catalytic cores for each deoxyribozyme, common dinucleotide junction selectivity was observed between DNAzymes with similar secondary structural features. Together, our findings indicate that larger, structurally more complex, and diverse catalytic motifs are able to survive the process of in vitro selection despite a sequence space dominated by smaller and structurally simpler catalysts.
Collapse
Affiliation(s)
- Jeffrey C F Lam
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada
| | | | | |
Collapse
|
31
|
Wang B, Cao L, Chiuman W, Li Y, Xi Z. Probing the function of nucleotides in the catalytic cores of the 8-17 and 10-23 DNAzymes by abasic nucleotide and C3 spacer substitutions. Biochemistry 2010; 49:7553-62. [PMID: 20698496 DOI: 10.1021/bi100304b] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
8-17 and 10-23 are the two most comprehensively studied RNA-cleaving DNAzymes to date and have the ability to carry out sequence-specific cleavage of both all-RNA or chimeric RNA/DNA substrates. Mutagenesis studies of 8-17 and 10-23 DNAzymes using alternative natural nucleotides to substitute a given nucleotide in the DNAzyme sequence have found that both DNAzymes are able to tolerate a variety of alterations at many sequence locations. Chemical modification studies employing nucleotides containing nonnatural nucleobases have led to findings that some specific entities of selected nucleobases are irreplaceable by other functional groups. In this work, we set out to carry out a mutagenesis study on both 8-17 and 10-23 by substituting individual nucleotides in their catalytic cores with a baseless (abasic) nucleotide or a baseless/sugarless nucleotide containing only acyclic C3 spacer. We observed that the substitution with an abasic nucleotide or C3 spacer at many locations within the catalytic core of both 8-17 and 10-23 was still able to support a significant level of catalytic activity of each DNAzyme, suggesting that both DNAzymes have considerable structural plasticity to maintain their catalytic functions. We also observed that almost all nucleobases in the catalytic core of each DNAzyme appeared to make either an absolutely essential contribution to the function of each DNAzyme or exhibit a "chaperone-like" activity that is important for the optimal function of each DNAzyme; in contrast, only one sugar ring in 8-17 and four in 10-23 were inferred to make some contribution to the optimal function of the relevant DNAzyme. Finally, our study also raised a possibility that the 10-23 DNAzyme might be a special structural variant of the larger 8-17 DNAzyme family.
Collapse
Affiliation(s)
- Bin Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, Tianjin, 300071, China
| | | | | | | | | |
Collapse
|
32
|
McManus SA, Li Y. The structural diversity of deoxyribozymes. Molecules 2010; 15:6269-84. [PMID: 20877222 PMCID: PMC6257715 DOI: 10.3390/molecules15096269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/23/2010] [Accepted: 09/02/2010] [Indexed: 11/16/2022] Open
Abstract
When not constrained to long double-helical arrangements, DNA is capable of forming structural arrangements that enable specific sequences to perform functions such as binding and catalysis under defined conditions. Through a process called in vitro selection, numerous catalytic DNAs, known as deoxyribozymes or DNAzymes, have been isolated. Many of these molecules have the potential to act as therapeutic agents and diagnostic tools. As such, a better understanding of the structural arrangements present in these functional DNAs will aid further efforts in the development and optimization of these useful molecules. Structural characterization of several deoxyribozymes through mutagenesis, in vitro re-selection, chemical probing and circular dichroism has revealed many distinct and elaborate structural classes. Deoxyribozymes have been found to contain diverse structural elements including helical junctions, pseudoknots, triplexes, and guanine quadruplexes. Some of these studies have further shown the repeated isolation of similar structural motifs in independent selection experiments for the same type of chemical reaction, suggesting that some structural motifs are well suited for catalyzing a specific chemical reaction. To investigate the extent of structural diversity possible in deoxyribozymes, a group of kinase deoxyribozymes have been extensively characterized. Such studies have discovered some interesting structural features of these DNAzymes while revealing some novel DNA structures.
Collapse
Affiliation(s)
- Simon A. McManus
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; E-Mail:
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; E-Mail:
- Department of Chemistry and Chemical Biology, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-905-528-9140 ext. 22462
| |
Collapse
|
33
|
Lee CS, Mui TP, Silverman SK. Improved deoxyribozymes for synthesis of covalently branched DNA and RNA. Nucleic Acids Res 2010; 39:269-79. [PMID: 20739352 PMCID: PMC3017605 DOI: 10.1093/nar/gkq753] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A covalently branched nucleic acid can be synthesized by joining the 2′-hydroxyl of the branch-site ribonucleotide of a DNA or RNA strand to the activated 5′-phosphorus of a separate DNA or RNA strand. We have previously used deoxyribozymes to synthesize several types of branched nucleic acids for experiments in biotechnology and biochemistry. Here, we report in vitro selection experiments to identify improved deoxyribozymes for synthesis of branched DNA and RNA. Each of the new deoxyribozymes requires Mn2+ as a cofactor, rather than Mg2+ as used by our previous branch-forming deoxyribozymes, and each has an initially random region of 40 rather than 22 or fewer combined nucleotides. The deoxyribozymes all function by forming a three-helix-junction (3HJ) complex with their two oligonucleotide substrates. For synthesis of branched DNA, the best new deoxyribozyme, 8LV13, has kobs on the order of 0.1 min−1, which is about two orders of magnitude faster than our previously identified 15HA9 deoxyribozyme. 8LV13 also functions at closer-to-neutral pH than does 15HA9 (pH 7.5 versus 9.0) and has useful tolerance for many DNA substrate sequences. For synthesis of branched RNA, two new deoxyribozymes, 8LX1 and 8LX6, were identified with broad sequence tolerances and substantial activity at pH 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA. These experiments provide new, and in key aspects improved, practical catalysts for preparation of synthetic branched DNA and RNA.
Collapse
Affiliation(s)
- Christine S Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | |
Collapse
|
34
|
Lam JCF, Li Y. Influence of Cleavage Site on Global Folding of an RNA-Cleaving DNAzyme. Chembiochem 2010; 11:1710-9. [DOI: 10.1002/cbic.201000144] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
35
|
Lam JCF, Withers JB, Li Y. A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction. J Mol Biol 2010; 400:689-701. [PMID: 20630470 DOI: 10.1016/j.jmb.2010.05.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 04/19/2010] [Accepted: 05/19/2010] [Indexed: 11/29/2022]
Abstract
Several RNA-cleaving deoxyribozymes (DNAzymes) have been reported for efficient cleavage of purine-containing junctions, but none is able to efficiently cleave pyrimidine-pyrimidine (Pyr-Pyr) junctions. We hypothesize that a stronger Pyr-Pyr cleavage activity requires larger DNAzymes with complex structures that are difficult to isolate directly from a DNA library; one possible way to obtain such DNAzymes is to optimize DNA sequences with weak activities. To test this, we carried out an in vitro selection study to derive DNAzymes capable of cleaving an rC-T junction in a chimeric DNA/RNA substrate from DNA libraries constructed through chemical mutagenesis of five previous DNAzymes with a k(obs) of approximately 0.001 min-1 for the rC-T junction. After several rounds of selective amplification, DNAzyme descendants with a k(obs) of approximately 0.1 min-1 were obtained from a DNAzyme pool. The most efficient motif, denoted "CT10-3.29," was found to have a catalytic core of approximately 50 nt, larger than other known RNA-cleaving DNAzymes, and its secondary structure contains five short duplexes confined by a four-way junction. Several variants of CT10-3.29 exhibit a k(obs) of 0.3-1.4 min-1 against the rC-T junction. CT10-3.29 also shows strong activity (k(obs)>0.1 min-1) for rU-A and rU-T junctions, medium activity (>0.01 min-1) for rC-A and rA-T junctions, and weak activity (>0.001 min-1) for rA-A, rG-T, and rG-A junctions. Interestingly, a single-point mutation within the catalytic core of CT10-3.29 altered the pattern of junction specificity with a significantly decreased ability to cleave rC-T and rC-A junctions and a substantially increased ability to cleave rA-A, rA-T, rG-A, rG-T, rU-A, and rU-T junctions. This observation illustrates the intricacy and plasticity of this RNA-cleaving DNAzyme in dinucleotide junction selectivity. The current study shows that it is feasible to derive efficient DNAzymes for a difficult chemical task and reveals that DNAzymes require more complex structural solutions for such a task.
Collapse
Affiliation(s)
- Jeffrey C F Lam
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada L8N 3Z5
| | | | | |
Collapse
|
36
|
Schlosser K, Li Y. A Versatile Endoribonuclease Mimic Made of DNA: Characteristics and Applications of the 8-17 RNA-Cleaving DNAzyme. Chembiochem 2010; 11:866-79. [DOI: 10.1002/cbic.200900786] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
37
|
Liu Y, Sen D. Local Rather than Global Folding Enables the Lead-dependent Activity of the 8-17 Deoxyribozyme: Evidence from Contact Photo-crosslinking. J Mol Biol 2010; 395:234-41. [DOI: 10.1016/j.jmb.2009.11.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 10/28/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
|
38
|
Abstract
BACKGROUND Although catalytic RNA enzymes (CRzs) are naturally occurring in many organisms, their DNA counterparts (CDzs) were developed by in vitro selection/evolution from random sequence libraries. OBJECTIVE To provide a brief overview of how CDzs have been selected in vitro, and of their properties and functions, as well as their possible future utility. METHODS We concentrated on examples of 'direct' selection of CDzs. Many CDzs have been used in biological settings, for example downregulation of target mRNAs, while many more recent applications use CDzs in biosensor and nanotechnology settings. CONCLUSIONS Although much work has concentrated on using CDzs for regulating gene expression, their potential as nucleic acid medicines has diminished substantially, supplanted by simple antisense oligonucleotides and, more recently, by small interfering RNAs (siRNAs). It seems unlikely that CDzs will have clinical utility. In contrast, they are likely to have significant potential in the sensor/nanotechnology arena.
Collapse
Affiliation(s)
- Weihua Pan
- Department of Pathology, Pennsylvania State University, Gittlen Cancer Research Foundation, Hershey Medical Center, Hershey, PA 17033, USA
| | | |
Collapse
|
39
|
Schlosser K, Gu J, Lam JCF, Li Y. In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions. Nucleic Acids Res 2008; 36:4768-77. [PMID: 18644842 PMCID: PMC2504313 DOI: 10.1093/nar/gkn396] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Herein, we sought new or improved endoribonucleases based on catalytic DNA molecules known as deoxyribozymes. The current repertoire of RNA-cleaving deoxyribozymes can cleave nearly all of the 16 possible dinucleotide junctions with rates of at least 0.1/min, with the exception of pyrimidine–pyrimidine (pyr–pyr) junctions, which are cleaved 1–3 orders of magnitude slower. We conducted four separate in vitro selection experiments to target each pyr–pyr dinucleotide combination (i.e. CC, UC, CT and UT) within a chimeric RNA/DNA substrate. We used a library of DNA molecules containing only 20 random-sequence nucleotides, so that all possible sequence permutations could be sampled in each experiment. From a total of 245 clones, we identified 22 different sequence families, of which 21 represented novel deoxyribozyme motifs. The fastest deoxyribozymes exhibited kobs values (single-turnover, intermolecular format) of 0.12/min, 0.04/min, 0.13/min and 0.15/min against CC, UC, CT and UT junctions, respectively. These values represent a 6- to 8-fold improvement for CC and UC junctions, and a 1000- to 1600-fold improvement for CT and UT junctions, compared to the best rates reported previously under identical reaction conditions. The same deoxyribozymes exhibited ∼1000-fold lower activity against all RNA substrates, but could potentially be improved through further in vitro evolution and engineering.
Collapse
Affiliation(s)
- Kenny Schlosser
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | | | | | | |
Collapse
|
40
|
Schlosser K, Gu J, Sule L, Li Y. Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res 2008; 36:1472-81. [PMID: 18203744 PMCID: PMC2275145 DOI: 10.1093/nar/gkm1175] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many sequence variations of the 8–17 RNA-cleaving deoxyribozyme have been isolated through in vitro selection. In an effort to understand how these sequence variations affect cleavage site selectivity, we systematically mutated the catalytic core of 8–17 and measured the cleavage activity of each mutant deoxyribozyme against all 16 possible chimeric (RNA/DNA) dinucleotide junctions. We observed sequence-function relationships that suggest how the following non-conserved positions in the catalytic core influence selectivity at the dinucleotide (5′ rN18-N1.1 3′) cleavage site: (i) positions 2.1 and 12 represent a primary determinant of the selectivity at the 3′ position (N1.1) of the cleavage site; (ii) positions 15 and 15.0 represent a primary determinant of the selectivity at the 5′ position (rN18) of the cleavage site and (iii) the sequence of the 3-bp intramolecular stem has relatively little influence on cleavage site selectivity. Furthermore, we report for the first time that 8–17 variants have the collective ability to cleave all dinucleotide junctions with rate enhancements of at least 1000-fold over background. Three optimal 8–17 variants, identified from ∼75 different sequences that were examined, can collectively cleave 10 of 16 junctions with useful rates of ≥0.1 min−1, and exhibit an overall hierarchy of reactivity towards groups of related junctions according to the order NG > NA > NC > NT.
Collapse
Affiliation(s)
- Kenny Schlosser
- Department of Biochemistry and Biomedical Sciences and Department of Chemistry, McMaster University, Hamilton, Ontario, Canada
| | | | | | | |
Collapse
|
41
|
Hengesbach M, Meusburger M, Lyko F, Helm M. Use of DNAzymes for site-specific analysis of ribonucleotide modifications. RNA (NEW YORK, N.Y.) 2008; 14:180-187. [PMID: 17998290 PMCID: PMC2151034 DOI: 10.1261/rna.742708] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 09/15/2007] [Indexed: 05/25/2023]
Abstract
Post-transcriptional ribonucleotide modifications are widespread and abundant processes that have not been analyzed adequately due to the lack of appropriate detection methods. Here, two methods for the analysis of modified nucleotides in RNA are presented that are based on the quantitative and site-specific DNAzyme-mediated cleavage of the target RNA at or near the site of modification. Quantitative RNA cleavage is achieved by cycling the DNAzyme and its RNA substrate through repeated periods of heating and cooling. In a first approach, DNAzyme-directed cleavage directly 5' of the residue in question allows radioactive labeling of the newly freed 5'-OH. After complete enzymatic hydrolysis, the modification status can be assessed by two-dimensional thin layer chromatography. In a second approach, oligoribonucleotide fragments comprising the modification site are excised from the full-length RNA in an endonucleolytic fashion, using a tandem DNAzyme. The excised fragment is isolated by electrophoresis and submitted to further conventional analysis. These results establish DNAzymes as valuable tools for the site-specific and highly sensitive detection of ribonucleotide modifications.
Collapse
Affiliation(s)
- Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany
| | | | | | | |
Collapse
|
42
|
Lee NK, Koh HR, Han KY, Kim SK. Folding of 8-17 Deoxyribozyme Studied by Three-Color Alternating-Laser Excitation of Single Molecules. J Am Chem Soc 2007; 129:15526-34. [DOI: 10.1021/ja0725145] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nam Ki Lee
- Contribution from the School of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Hye Ran Koh
- Contribution from the School of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Kyu Young Han
- Contribution from the School of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Seong Keun Kim
- Contribution from the School of Chemistry, Seoul National University, Seoul 151-747, Korea
| |
Collapse
|
43
|
Ali MM, Kandadai SA, Li Y. Characterization of pH3DZ1 — An RNA-cleaving deoxyribozyme with optimal activity at pH 3. CAN J CHEM 2007. [DOI: 10.1139/v07-017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We previously described a cis-acting RNA-cleaving deoxyribozyme known as pH3DZ1 that exhibits optimal catalytic activity at pH 3.0 (Zhongjie Liu, Shirley H. Mei, John D. Brennan, and Yingfu Li. J. Am. Chem. Soc. 125, 7539 (2003)). This DNA catalyst was made of a 99-nucleotide (nt) catalytic domain covalently linked to a 23-nt DNA–RNA chimeric substrate containing a single ribonucleotide as the cleavage site. In the present work, we conducted an extensive sequence examination of this deoxyribozyme via nucleotide truncation and reselection experiments, with a goal to minimize its size and identify the nucleotides that are crucial to its catalytic function. A trans-acting deoxyribozyme that can process an external substrate was also successfully designed. Stretches of 30 and 17 nucleotides from the 5′ and 3′ ends of the trans catalyst, respectively, were found to be completely dispensable; in contrast, few nucleotides could be deleted internally without producing a detrimental effect. The reselection experiment led to the discovery of 7 and 5 absolutely conserved nucleotides located at the 5′ and 3′ ends of the minimized catalyst, respectively, separated by a 31-nt element in which 14 highly conserved nucleotides were scattered among 17 variable nucleotides. The shortened deoxyribozyme and the original catalyst showed a similar pH profile with the optimal activity at pH 3; however, the minimized deoxyribozyme still exhibited strong catalytic activity at pH 2.5, while the full-length catalyst was barely active at this pH. Finally, it was found that this deoxyribozyme generated two cleavage fragments, one with 2′,3′-cyclic phosphate and the other with 5′-OH.Key words: DNA, deoxyribozyme, RNA cleavage, in vitro selection, catalysis.
Collapse
|
44
|
De Paula D, Bentley MVLB, Mahato RI. Hydrophobization and bioconjugation for enhanced siRNA delivery and targeting. RNA (NEW YORK, N.Y.) 2007; 13:431-56. [PMID: 17329355 PMCID: PMC1831859 DOI: 10.1261/rna.459807] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved process by which double-stranded small interfering RNA (siRNA) induces sequence-specific, post-transcriptional gene silencing. Unlike other mRNA targeting strategies, RNAi takes advantage of the physiological gene silencing machinery. The potential use of siRNA as therapeutic agents has attracted great attention as a novel approach for treating severe and chronic diseases. RNAi can be achieved by either delivery of chemically synthesized siRNAs or endogenous expression of small hairpin RNA, siRNA, and microRNA (miRNA). However, the relatively high dose of siRNA required for gene silencing limits its therapeutic applications. This review discusses several strategies to improve therapeutic efficacy as well as to abrogate off-target effects and immunostimulation caused by siRNAs. There is an in-depth discussion on various issues related to the (1) mechanisms of RNAi, (2) methods of siRNA production, (3) barriers to RNAi-based therapies, (4) biodistribution, (5) design of siRNA molecules, (6) chemical modification and bioconjugation, (7) complex formation with lipids and polymers, (8) encapsulation into lipid particles, and (9) target specificity for enhanced therapeutic effectiveness.
Collapse
Affiliation(s)
- Daniel De Paula
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | | | | |
Collapse
|
45
|
McManus SA, Li Y. Multiple occurrences of an efficient self-phosphorylating deoxyribozyme motif. Biochemistry 2007; 46:2198-204. [PMID: 17263557 DOI: 10.1021/bi061613c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic and structural characteristics of two new self-phosphorylating deoxyribozymes (referred to as deoxyribozyme kinases), denoted "Dk3" and "Dk4", are compared to those of Dk2, a previously reported deoxyribozyme kinase. All three deoxyribozymes not only utilize GTP as the source of activated phosphate and Mn(II) as the divalent metal cofactor but also share a common secondary structure with significant sequence variations. Multiple Watson-Crick helices are identified within the secondary structure, and these helical interactions confine three extremely conserved sequence elements of 8, 5, and 14 nucleotides in length, presumably for the formation of the catalytic core for GTP binding and the self-phosphorylating reaction. The locations of the conserved regions suggest that these three deoxyribozymes arose independently from in vitro selection. The existence of three sequence variants of the same deoxyribozyme from the same in vitro selection experiment implies that these catalytic DNAs may represent the simplest structural solution for the DNA self-phosphorylation reaction when GTP is used as the substrate.
Collapse
Affiliation(s)
- Simon A McManus
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Canada L8N 3Z5
| | | |
Collapse
|
46
|
Zhu X, Li T, Dang Y, Feng Y, Huang P. A novel in vitro transcription method for producing siRNAs without specific sequence requirements. Mol Biotechnol 2007; 31:187-92. [PMID: 16230768 DOI: 10.1385/mb:31:3:187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
RNA interference is a powerful genetic approach for silencing of target genes in which 21-23 nucleotide small interfering RNAs (siRNAs) work as sequence-specific RNA interference (RNAi) mediators. Production of siRNAs by in vitro transcription is a useful method that it is simple, effective, and inexpensive. Commonly used in vitro transcription promoters use guanine as the transcription start nucleotide. This method is, therefore, restricted to generating siRNAs with target sequences of 5'-NNGN17C. Here we report a modified in vitro transcription method, in which pre-siRNAs containing the 5' overhanging single-stranded leader sequence are first synthesized, then a DNA oligonucleotide complementary to the leader sequence is added to form a RNA-DNA hybrid, which is removed using RNase H to obtain desired siRNAs. Using siRNAs prepared with this method, we successfully inhibited the expression of both exogenous and endogenous genes.
Collapse
Affiliation(s)
- Xudong Zhu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, 20 Fengtai Dongdajie Street, Beijing, 100071, China.
| | | | | | | | | |
Collapse
|
47
|
Leung EKY, Sen D. Electron Hole Flow Patterns through the RNA-Cleaving 8-17 Deoxyribozyme Yield Unusual Information about Its Structure and Folding. ACTA ACUST UNITED AC 2007; 14:41-51. [PMID: 17254951 DOI: 10.1016/j.chembiol.2006.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 10/31/2006] [Accepted: 11/06/2006] [Indexed: 11/21/2022]
Abstract
DNA double helices have been shown to conduct electron holes over significant distances. Here, we report on the hole flow patterns within a more intricately folded DNA complex, the 8-17 deoxyribozyme bound to a DNA pseudosubstrate, incorporating three helical elements and two catalytically relevant loops. The observed hole flow patterns within the complex permitted a quantitative assessment of the stacking preferences of the three constituent helices and provided evidence for significant transitions within the complex's global geometry. The patterns further suggested varying levels of solvent exposure of the complex's constituent parts, and revealed that a catalytically relevant cytosine within the folded complex exists in an unusual structural/electronic environment. Our data suggest that the study of charge flow may provide novel perspectives on the structure and folding of intricately folded DNAs and RNAs.
Collapse
Affiliation(s)
- Edward K Y Leung
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | | |
Collapse
|
48
|
Vlassov AV, Ilves H, Johnston BH. Inhibition of hepatitis C IRES-mediated gene expression by 8–17 deoxyribozymes in human tissue culture cells. DOKL BIOCHEM BIOPHYS 2006; 410:257-9. [PMID: 17286096 DOI: 10.1134/s1607672906050012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, pr Akademika Lavrent'eva 8, Novosibirsk, 630090 Russia
| | | | | |
Collapse
|
49
|
Schlosser K, Lam JC, Li Y. Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection. Nucleic Acids Res 2006; 34:2445-54. [PMID: 16682452 PMCID: PMC1458524 DOI: 10.1093/nar/gkl276] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We previously conducted an in vitro selection experiment for RNA-cleaving deoxyribozymes, using a combinatorial DNA library containing 80 random nucleotides. Ultimately, 110 different sequence classes were isolated, but the vast majority contained a short14-15 nt catalytic DNA motif commonly known as 8-17. Herein, we report extensive truncation experiments conducted on multiple sequence classes to confirm the suspected catalytic role played by 8-17 and to determine the effect of excess sequence elements on the activity of this motif and the outcome of selection. Although we observed beneficial, detrimental and neutral consequences for activity, the magnitude of the effect rarely exceeded 2-fold. These deoxyribozymes appear to have survived increasing selection pressure despite the presence of additional sequence elements, rather than because of them. A new deoxyribozyme with comparable activity, called G15-30, was approximately 2.5-fold larger and experienced a approximately 4-fold greater inhibitory effect from excess sequence elements than the average 8-17 motif. Our results suggest that 8-17 may be less susceptible to the potential inhibitory effects of excess arbitrary sequence than larger motifs, which represents a previously unappreciated selective advantage that may contribute to its widespread recurrence.
Collapse
Affiliation(s)
| | | | - Yingfu Li
- To whom correspondence should be addressed. Tel: 1 905 5259140; Fax: 1 905 522 9033;
| |
Collapse
|
50
|
Fluiter K, Frieden M, Vreijling J, Koch T, Baas F. Evaluation of LNA-modified DNAzymes targeting a single nucleotide polymorphism in the large subunit of RNA polymerase II. Oligonucleotides 2006; 15:246-54. [PMID: 16396619 DOI: 10.1089/oli.2005.15.246] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Allele-specific inhibition (ASI) is a new strategy to treat cancer through a vulnerability created by the loss of large segments of chromosomal material by loss of heterozygosity (LOH). Using antisense approaches, it is possible to target single nucleotide polymorphisms (SNP) in the remaining allele of an essential gene in the tumor, thus killing the tumor while the heterozygous patient survives at the expense of the other nontargeted allele lost by the tumor. In this study, the feasibility of using locked nucleic acid (LNA)-modified DNAzymes (LNAzymes) of the 10-23 motif as allele-specific drugs was investigated. We demonstrate that incorporation of LNA into 10-23 motif DNAzymes increases their efficacy in mRNA degradation and that, in a cell-free system, the 10-23 motif LNAzyme can adequately discriminate and recognize an SNP in the large subunit of RNA polymerase II (POLR2A), an essential gene frequently involved in LOH in cancer cells. However, the LNAzymes, optimized under in vitro conditions, are not always efficient in cleaving their RNA target in cell culture, and the efficiency of RNA cleavage in cell culture is cell type dependent. The cleavage rate of the LNAzyme is also much slower than RNase H-recruiting DNA phosphorothioate antisense oligonucleotides. Moreover, compared with DNA phosphorothioates, the ability of the LNAzymes to differentially knock down two POLR2A alleles in cultured cancer cells is limited.
Collapse
Affiliation(s)
- Kees Fluiter
- Department of Neurogenetics, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands.
| | | | | | | | | |
Collapse
|