1
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Hayashi J, Ochi Y, Senpuku K, Wada SI, Wada F, Harada-Shiba M, Urata H. Rational design of prodrug-type apoB-targeted siRNA for nuclease resistance improvement without compromising gene silencing potency. Bioorg Med Chem 2024; 104:117693. [PMID: 38552598 DOI: 10.1016/j.bmc.2024.117693] [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: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Synthetic siRNA molecules without chemical modifications are easily degraded in the body, and 2'-O-modifications are frequently introduced to enhance stability. However, such chemical modifications tend to impact the gene knockdown potency of siRNA negatively. To circumvent this problem, we previously developed a prodrug-type siRNA bearing 2'-O-methyldithiomethyl (MDTM) groups, which can be converted into unmodified siRNA under the reductive environment in cells. In this study, we developed a nuclease-resistant prodrug-type 2'-O-MDTM siRNA for deployment in future animal experiments. To rationally design siRNA modified with a minimal number of 2'-O-MDTM nucleotide residues, we identified the sites susceptible to nuclease digestion and tolerant to 2'-O-methyl (2'-OMe) modification in the antisense strand of apolipoprotein B-targeted siRNA. Subsequently, we optimized the positions where the 2'-OMe and 2'-O-MDTM groups should be incorporated. siRNA bearing the 2'-O-MDTM and 2'-OMe groups at their respective optimized positions exhibited efficient knockdown potency in vitro and enhanced stability in serum.
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Affiliation(s)
- Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Yosuke Ochi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Kota Senpuku
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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2
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Sugimoto N, Hayashi J, Funaki R, Wada SI, Wada F, Harada-Shiba M, Urata H. Prodrug-Type Phosphotriester Oligonucleotides with Linear Disulfide Promoieties Responsive to Reducing Environment. Chembiochem 2023; 24:e202300526. [PMID: 37840006 DOI: 10.1002/cbic.202300526] [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: 07/27/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/17/2023]
Abstract
Various chemical modifications have been developed to create new antisense oligonucleotides (AONs) for clinical applications. Our previously designed prodrug-type phosphotriester-modified oligonucleotide with cyclic disulfides (cyclic SS PTE ON) can be converted into unmodified ON in an intracellular-mimetic reducing environment. However, the conversion rate of the cyclic SS PTE ON was very low, and the AON with cyclic SS PTE modifications showed much weaker antisense activity than corresponding to the fully phosphorothioate-modified AON. In this study, we synthesized several types of PTE ONs containing linear disulfides (linear SS PTE ONs) and evaluated their conversion rates under reducing conditions. From the results, the structural requirements for the conversion of the synthesized linear SS PTE ONs were elucidated. Linear SS PTE ON with promising promoieties showed a nuclease resistance up to 4.8-fold compared to unmodified ON and a cellular uptake by endocytosis without any transfection reagent. In addition, although the knockdown activity of the linear SS PTE gapmer AON is weaker than that of the fully phosphorothioate-modified gapmer AON, the knockdown activity is slightly stronger than that of the cyclic SS PTE gapmer AON. These results suggest that the conversion rates may be related to the expression of the antisense activity.
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Affiliation(s)
- Norihito Sugimoto
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Ryohei Funaki
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka, 564-8565, Japan
- Present address: Liid Pharmaceuticals, Inc.21001 Open Innovation Center, National Cerebral & Cardiovascular Center, 6-1 Kishibe-shinmachi, Suita, Osaka, 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka, 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
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3
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Wang Z, Fan X, Mu G, Zhao X, Wang Q, Wang J, Tang X. Cathepsin B-activatable cyclic antisense oligonucleotides for cell-specific target gene knockdown in vitro and in vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:548-558. [PMID: 37588686 PMCID: PMC10425675 DOI: 10.1016/j.omtn.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/20/2023] [Indexed: 08/18/2023]
Abstract
Trigger-activatable antisense oligonucleotides have been widely applied to regulate gene function. Among them, caged cyclic antisense oligonucleotides (cASOs) maintain a specific topology that temporarily inhibits their interaction with target genes. By inserting linkers that respond to cell-specific endogenous stimuli, they can be powerful tools and potential therapeutic agents for specific types of cancer cells with low off-target effects on normal cells. Here, we developed enzyme-activatable cASOs by tethering two terminals of linear antisense oligonucleotides through a cathepsin B (CB) substrate peptide (Gly-Phe-Leu-Gly [GFLG]), which could be efficiently uncaged by CB. CB-activatable cASOs were used to successfully knock down two disease-related endogenous genes in CB-abundant PC-3 tumor cells at the mRNA and protein levels but had much less effect on gene knockdown in CB-deficient human umbilical vein endothelial cell (HUVECs). In addition, reduced nonspecific immunostimulation was found using cASOs compared with their linear counterparts. Further in vivo studies indicated that CB-activatable cASOs showed effective tumor inhibition in PC-3 tumor model mice through downregulation of translationally controlled tumor protein (TCTP) protein in tumors. This study applies endogenous enzyme-activatable cASOs for antitumor therapy in tumor model mice, which demonstrates a promising stimulus-responsive cASO strategy for cell-specific gene knockdown upon endogenous activation and ASO prodrug development.
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Affiliation(s)
- Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Guanqun Mu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Xiaoran Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu 210023, People’s Republic of China
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4
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Hartmann D, Chowdhry R, Smith JM, Booth MJ. Orthogonal Light-Activated DNA for Patterned Biocomputing within Synthetic Cells. J Am Chem Soc 2023; 145:9471-9480. [PMID: 37125650 PMCID: PMC10161232 DOI: 10.1021/jacs.3c02350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cell-free gene expression is a vital research tool to study biological systems in defined minimal environments and has promising applications in biotechnology. Developing methods to control DNA templates for cell-free expression will be important for precise regulation of complex biological pathways and use with synthetic cells, particularly using remote, nondamaging stimuli such as visible light. Here, we have synthesized blue light-activatable DNA parts that tightly regulate cell-free RNA and protein synthesis. We found that this blue light-activated DNA could initiate expression orthogonally to our previously generated ultraviolet (UV) light-activated DNA, which we used to generate a dual-wavelength light-controlled cell-free AND-gate. By encapsulating these orthogonal light-activated DNAs into synthetic cells, we used two overlapping patterns of blue and UV light to provide precise spatiotemporal control over the logic gate. Our blue and UV orthogonal light-activated DNAs will open the door for precise control of cell-free systems in biology and medicine.
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Affiliation(s)
- Denis Hartmann
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Jefferson M Smith
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Michael J Booth
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
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5
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Le‐Vinh B, Akkuş‐Dağdeviren ZB, Le NN, Nazir I, Bernkop‐Schnürch A. Alkaline Phosphatase: A Reliable Endogenous Partner for Drug Delivery and Diagnostics. ADVANCED THERAPEUTICS 2022. [DOI: 10.1002/adtp.202100219] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bao Le‐Vinh
- Department of Pharmaceutical Technology Institute of Pharmacy University of Innsbruck Innrain 80/82 Innsbruck 6020 Austria
- Department of Industrial Pharmacy Faculty of Pharmacy University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City 700000 Viet Nam
| | - Zeynep Burcu Akkuş‐Dağdeviren
- Department of Pharmaceutical Technology Institute of Pharmacy University of Innsbruck Innrain 80/82 Innsbruck 6020 Austria
| | - Nguyet‐Minh Nguyen Le
- Department of Pharmaceutical Technology Institute of Pharmacy University of Innsbruck Innrain 80/82 Innsbruck 6020 Austria
- Department of Industrial Pharmacy Faculty of Pharmacy University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City 700000 Viet Nam
| | - Imran Nazir
- Department of Pharmacy COMSATS University Islamabad Abbottabad Campus Abbottabad 22060 Pakistan
| | - Andreas Bernkop‐Schnürch
- Department of Pharmaceutical Technology Institute of Pharmacy University of Innsbruck Innrain 80/82 Innsbruck 6020 Austria
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6
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Zhou X, Pan Y, Yu L, Wu J, Li Z, Li H, Guan Z, Tang X, Yang Z. Feasibility of cRGD conjugation at 5'-antisense strand of siRNA by phosphodiester linkage extension. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:603-612. [PMID: 34589281 PMCID: PMC8463321 DOI: 10.1016/j.omtn.2021.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022]
Abstract
Small interfering RNAs (siRNAs) are widely studied for their highly specific gene silencing activity. However, obstacles remain to the clinical application of siRNAs. Attaching conjugates to siRNAs can improve their stability and broaden their application, and most functional conjugates of siRNAs locate at the 3'-terminus of the sense or antisense strand. In this work, we found that conjugating a group at the 5'-terminus of the antisense strand via phosphodiester was practicable, especially when the group was a flexible moiety such as an alkyl linker. When conjugating a bulky ligand, such as cRGD, the length of the 5'-phosphodiester linker between the ligand and the 5'-terminus of the antisense strand was the key in terms of RNA interference (RNAi). With a relative longer linker, the conjugates showed potency similar to siRNA. A highly efficient transfection system composed of a neutral cytidinyl lipid (DNCA) and a gemini-like cationic lipid (CLD) was employed to deliver siRNAs or their conjugates. The cRGD conjugates showed superior targeting delivery and antitumor efficacy in vivo and also selective cellular uptake in vitro. This unity of encapsulation and conjugation strategy may provide potential strategies for siRNA-based gene therapy.
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Affiliation(s)
- Xinyang Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- People’s Public Security University of China, Beijing 100038, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- National Center for Occupational Safety and Health, NHC, Beijing 102308, China
| | - Jing Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zheng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Huantong Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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7
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Riebe J, Niemeyer J. Mechanically Interlocked Molecules for Biomedical Applications. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jan Riebe
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE) University of Duisburg-Essen Universitätsstr. 7 45141 Essen Germany
| | - Jochen Niemeyer
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE) University of Duisburg-Essen Universitätsstr. 7 45141 Essen Germany
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8
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Lee YH, Yu E, Park CM. Programmable site-selective labeling of oligonucleotides based on carbene catalysis. Nat Commun 2021; 12:1681. [PMID: 33727561 PMCID: PMC7966772 DOI: 10.1038/s41467-021-21839-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/03/2021] [Indexed: 11/08/2022] Open
Abstract
Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. Here we report chemo- and regioselective modification of oligonucleotides based on rhodium(I)-carbene catalysis in a programmable fashion. Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures. Moreover, high regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex. This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates.
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Affiliation(s)
- Yang-Ha Lee
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea
| | - Eunsoo Yu
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea
| | - Cheol-Min Park
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea.
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9
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Yang L, Dmochowski IJ. Conditionally Activated ("Caged") Oligonucleotides. Molecules 2021; 26:1481. [PMID: 33803234 PMCID: PMC7963183 DOI: 10.3390/molecules26051481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/09/2023] Open
Abstract
Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Affiliation(s)
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA;
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10
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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11
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Kishimoto Y, Nakagawa O, Fujii A, Yoshioka K, Nagata T, Yokota T, Hari Y, Obika S. 2',4'-BNA/LNA with 9-(2-Aminoethoxy)-1,3-diaza-2-oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance*. Chemistry 2021; 27:2427-2438. [PMID: 33280173 PMCID: PMC7898338 DOI: 10.1002/chem.202003982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 11/28/2022]
Abstract
Artificial nucleic acids are widely used in various technologies, such as nucleic acid therapeutics and DNA nanotechnologies requiring excellent duplex-forming abilities and enhanced nuclease resistance. 2'-O,4'-C-Methylene-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA) with 1,3-diaza-2-oxophenoxazine (BNAP (BH )) was previously reported. Herein, a novel BH analogue, 2',4'-BNA/LNA with 9-(2-aminoethoxy)-1,3-diaza-2-oxophenoxazine (G-clamp), named BNAP-AEO (BAEO ), was designed. The BAEO nucleoside was successfully synthesized and incorporated into oligodeoxynucleotides (ODNs). ODNs containing BAEO possessed up to 104 -, 152-, and 11-fold higher binding affinities for complementary (c) RNA than those of ODNs containing 2'-deoxycytidine (C), 2',4'-BNA/LNA with 5-methylcytosine (L), or 2'-deoxyribonucleoside with G-clamp (PAEO ), respectively. Moreover, duplexes formed by ODN bearing BAEO with cDNA and cRNA were thermally stable, even under molecular crowding conditions induced by the addition of polyethylene glycol. Furthermore, ODN bearing BAEO was more resistant to 3'-exonuclease than ODNs with phosphorothioate linkages.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Kotaro Yoshioka
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Tetsuya Nagata
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Takanori Yokota
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
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12
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Chen C, Wang Z, Jing N, Chen W, Tang X. Photomodulation of Caged RNA Oligonucleotide Functions in Living Systems. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Changmai Chen
- School of Pharmacy Fujian Medical University No.1 Xuefu N Rd, University Town Fuzhou 350122 China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Wei Chen
- School of Pharmacy Fujian Medical University No.1 Xuefu N Rd, University Town Fuzhou 350122 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
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13
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Cheng L, Ma D, Lu L, Ouyang D, Xi Z. Building Customizable Multisite‐Targeting c‐Myc shRNA Array into Branch‐PCR‐Constructed DNA Nanovectors for Enhanced Tumor Cell Suppression. ChemistrySelect 2020. [DOI: 10.1002/slct.202002609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Longhuai Cheng
- Department of Chemical Biology State Key Laboratory of Elemento-Organic Chemistry National Engineering Research Center of Pesticide (Tianjin) College of Chemistry Nankai University Weijin Road 94 Tianjin 300071 P. R. China
| | - Dejun Ma
- Department of Chemical Biology State Key Laboratory of Elemento-Organic Chemistry National Engineering Research Center of Pesticide (Tianjin) College of Chemistry Nankai University Weijin Road 94 Tianjin 300071 P. R. China
| | - Liqing Lu
- Department of Chemical Biology State Key Laboratory of Elemento-Organic Chemistry National Engineering Research Center of Pesticide (Tianjin) College of Chemistry Nankai University Weijin Road 94 Tianjin 300071 P. R. China
| | - Di Ouyang
- Department of Chemical Biology State Key Laboratory of Elemento-Organic Chemistry National Engineering Research Center of Pesticide (Tianjin) College of Chemistry Nankai University Weijin Road 94 Tianjin 300071 P. R. China
| | - Zhen Xi
- Department of Chemical Biology State Key Laboratory of Elemento-Organic Chemistry National Engineering Research Center of Pesticide (Tianjin) College of Chemistry Nankai University Weijin Road 94 Tianjin 300071 P. R. China
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14
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Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
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Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
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15
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Kimura Y, Shu Z, Ito M, Abe N, Nakamoto K, Tomoike F, Shuto S, Ito Y, Abe H. Intracellular build-up RNAi with single-strand circular RNAs as siRNA precursors. Chem Commun (Camb) 2020; 56:466-469. [DOI: 10.1039/c9cc04872c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein report a new approach for RNA interference, so-called “build-up RNAi” approach, where single-strand circular RNAs with a photocleavable unit or disulfide moiety were used as siRNA precursors.
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Affiliation(s)
- Yasuaki Kimura
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Zhaoma Shu
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Mika Ito
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Kita-12, Nishi-6, Kita-ku
- Sapporo 060-0812
- Japan
| | - Naoko Abe
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Kosuke Nakamoto
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Kita-12, Nishi-6, Kita-ku
- Sapporo 060-0812
- Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
- Wako-Shi
- Japan
| | - Hiroshi Abe
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
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16
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Banno A, Higashi S, Shibata A, Ikeda M. A stimuli-responsive DNAzyme displaying Boolean logic-gate responses. Chem Commun (Camb) 2019; 55:1959-1962. [PMID: 30681683 DOI: 10.1039/c8cc09345h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introducing a desired stimuli-responsive function into catalytically active biomacromolecules is potentially useful in developing molecular tools for various bio-applications. In this paper, we discuss the development of a stimuli-responsive DNAzyme (catalytic deoxyribozyme) capable of displaying Boolean logic-gate responses.
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Affiliation(s)
- Ayaka Banno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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17
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Markwart JC, Wurm FR. The 2-acetylthioethyl ester group: A versatile protective group for P-OH-groups. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Gymnotic delivery and gene silencing activity of reduction-responsive siRNAs bearing lipophilic disulfide-containing modifications at 2'-position. Bioorg Med Chem 2018; 26:4635-4643. [PMID: 30121212 DOI: 10.1016/j.bmc.2018.07.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/09/2018] [Accepted: 07/19/2018] [Indexed: 12/25/2022]
Abstract
Modified oligoribonucleotides used as siRNAs bearing biolabile disulfide-containing groups at some 2'-positions were synthesized following a post-synthesis transformation of solid-supported 2'-O-acetylthiomethyl RNA, previously described. Thus, the reduction-responsive and lipophilic benzyldithiomethyl (BnSSM) modification was introduced at different locations into siRNAs targeting the Ewing sarcoma EWS-Fli1 protein. Thermal stability, serum stability and response to glutathione treatment of modified siRNAs were thoroughly investigated. Among 17 modified siRNAs, significant gene silencing activities were demonstrated for the 8 most stable siRNAs in serum (half-life > 1 h) when using a transfection reagent. Of special interest, two naked 2'-O-BnSSM siRNAs transfection exhibited a remarkable gene silencing activity after 24 h incubation. These inhibitions are consistent with an efficient gymnotic delivery demonstrated by the presence of the corresponding fluorescent siRNAs within cells.
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19
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Yu L, Liang D, Chen C, Tang X. Caged siRNAs with Single cRGD Modification for Photoregulation of Exogenous and Endogenous Gene Expression in Cells and Mice. Biomacromolecules 2018; 19:2526-2534. [DOI: 10.1021/acs.biomac.8b00159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University, No. 38, Xueyuan Rd, Beijing 100191, China
| | - Duanwei Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University, No. 38, Xueyuan Rd, Beijing 100191, China
| | - Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University, No. 38, Xueyuan Rd, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University, No. 38, Xueyuan Rd, Beijing 100191, China
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20
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Yu L, Jing N, Yang Z, Zhang L, Tang X. Caged siRNAs with single folic acid modification of antisense RNA for photomodulation of exogenous and endogenous gene expression in cells. Org Biomol Chem 2018; 16:7029-7035. [DOI: 10.1039/c8ob01952e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Photoregulating gene expression using folic acid modified caged siRNA through complex formation of folic acid/folate receptor.
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Affiliation(s)
- Lijia Yu
- National Center of Occupational Safety and Health
- State Administration of Work Safety
- Beijing 102308
- China
- State key Laboratory of Natural and Biomimetic Drugs
| | - Nannan Jing
- State key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine
- Peking University
- Beijing 100191
- China
| | - Zhenjun Yang
- State key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine
- Peking University
- Beijing 100191
- China
| | - Lihe Zhang
- State key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine
- Peking University
- Beijing 100191
- China
| | - Xinjing Tang
- State key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine
- Peking University
- Beijing 100191
- China
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