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Zhao D, Yang G, Liu Q, Liu W, Weng Y, Zhao Y, Qu F, Li L, Huang Y. A photo-triggerable aptamer nanoswitch for spatiotemporal controllable siRNA delivery. NANOSCALE 2020; 12:10939-10943. [PMID: 32207496 DOI: 10.1039/d0nr00301h] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A photo-triggerable aptamer nanoswitch was proposed for spatiotemporal regulation of siRNA delivery. Recognition between AS1411 and nucleolin was effectively blocked by a photo-labile complementary oligonucleotide, which could be reactivated with photo-irradiation, resulting in efficient tumor-targeted siRNA internalization and gene silencing in vitro and in vivo.
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Affiliation(s)
- Deyao Zhao
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China. and Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Erqi, Zhengzhou 450000, China
| | - Ge Yang
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China.
| | - Qing Liu
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China. and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Wenjing Liu
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China. and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuhua Weng
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China.
| | - Yi Zhao
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China.
| | - Feng Qu
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China.
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science; School of Life Science; Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China.
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Ogura Y, Onishi A, Nishimura T, Tanida J. Optically controlled release of DNA based on nonradiative relaxation process of quenchers. BIOMEDICAL OPTICS EXPRESS 2016; 7:2142-53. [PMID: 27375933 PMCID: PMC4918571 DOI: 10.1364/boe.7.002142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/27/2016] [Accepted: 05/03/2016] [Indexed: 06/02/2023]
Abstract
Optically controlled release of a DNA strand based on a nonradiative relaxation process of black hole quenchers (BHQs), which are a sort of dark quenchers, is presented. BHQs act as efficient energy sources because they relax completely via a nonradiative process, i.e., without fluorescent emission-based energy losses. A DNA strand is modified with BHQs and the release of its complementary strand is controlled by excitation of the BHQs. Experimental results showed that up to 50% of the target strands were released, and these strands were capable of inducing subsequent reactions. The controlled release was localized on a substrate within an area of no more than 5 micrometers in diameter.
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Affiliation(s)
- Yusuke Ogura
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Atsushi Onishi
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Takahiro Nishimura
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Jun Tanida
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
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3
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Zou Y, Chen J, Zhu Z, Lu L, Huang Y, Song Y, Zhang H, Kang H, Yang CJ. Single-molecule photon-fueled DNA nanoscissors for DNA cleavage based on the regulation of substrate binding affinity by azobenzene. Chem Commun (Camb) 2013; 49:8716-8. [DOI: 10.1039/c3cc44188a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Schierling B, Dannemann N, Gabsalilow L, Wende W, Cathomen T, Pingoud A. A novel zinc-finger nuclease platform with a sequence-specific cleavage module. Nucleic Acids Res 2012; 40:2623-38. [PMID: 22135304 PMCID: PMC3315325 DOI: 10.1093/nar/gkr1112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 12/18/2022] Open
Abstract
Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration, the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs, ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at addressed sites with a >1000-fold preference over unaddressed PvuII sites in vitro as well as in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results present the ZF-PvuII platform as a valid alternative to conventional ZFNs.
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Affiliation(s)
- Benno Schierling
- Institute of Biochemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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Fonfara I, Curth U, Pingoud A, Wende W. Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases. Nucleic Acids Res 2011; 40:847-60. [PMID: 21965534 PMCID: PMC3258161 DOI: 10.1093/nar/gkr788] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding module and a non-specific DNA-cleavage module, resulting in nucleases able to cleave DNA at a unique sequence. Here a new approach for creating highly specific nucleases was pursued by fusing a catalytically inactive variant of the homing endonuclease I-SceI, as DNA binding-module, to the type IIP restriction enzyme PvuII, as cleavage module. The fusion enzymes were designed to recognize a composite site comprising the recognition site of PvuII flanked by the recognition site of I-SceI. In order to reduce activity on PvuII sites lacking the flanking I-SceI sites, the enzymes were optimized so that the binding of I-SceI to its sites positions PvuII for cleavage of the composite site. This was achieved by optimization of the linker and by introducing amino acid substitutions in PvuII which decrease its activity or disturb its dimer interface. The most specific variant showed a more than 1000-fold preference for the addressed composite site over an unaddressed PvuII site. These results indicate that using a specific restriction enzyme, such as PvuII, as cleavage module, offers an alternative to the otherwise often used catalytic domain of FokI, which by itself does not contribute to the specificity of the engineered nuclease.
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Affiliation(s)
- Ines Fonfara
- Institut für Biochemie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392, Giessen, Germany
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Pingoud A, Wende W. Generation of Novel Nucleases with Extended Specificity by Rational and Combinatorial Strategies. Chembiochem 2011; 12:1495-500. [DOI: 10.1002/cbic.201100055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Indexed: 12/12/2022]
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