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Tateishi-Karimata H, Kawauchi K, Takahashi S, Sugimoto N. Development of a Pseudocellular System to Quantify Specific Interactions Determining the G-Quadruplex Function in Cells. J Am Chem Soc 2024; 146:8005-8015. [PMID: 38498910 DOI: 10.1021/jacs.3c11160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Intracellular chemical microenvironments, including ion concentrations and molecular crowding, play pivotal roles in cell behaviors, such as proliferation, differentiation, and cell death via regulation of gene expression. However, there is no method for quantitative analysis of intracellular environments due to their complexity. Here, we have developed a system for highlighting the environment inside of the cell (SHELL). SHELL is a pseudocellular system, wherein small molecules are removed from the cell and a crowded intracellular environment is maintained. SHELL offers two prominent advantages: (1) It allows for precise quantitative biochemical analysis of a specific factor, and (2) it enables the study of any cell, thereby facilitating the study of target molecule effects in various cellular environments. Here, we used SHELL to study G-quadruplex formation, an event that implicated cancer. We show that G-quadruplexes are more stable in SHELL compared with in vitro conditions. Although malignant transformation perturbs cellular K+ concentrations, environments in SHELL act as buffers against G-quadruplex destabilization at lower K+ concentrations. Notably, the buffering effect was most pronounced in SHELL derived from nonaggressive cancer cells. Stable G-quadruplexes form due to the binding of the G-quadruplex with K+ in different cancer cells. Furthermore, the observed pattern of G-quadruplex-induced transcriptional inhibition in SHELL is consistent with that in living cells at different cancer stages. Our results indicate that ion binding to G-quadruplexes regulates gene expression during pathogenesis.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Keiko Kawauchi
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Endoh T, Sugimoto N. Signaling Aptamer Optimization through Selection Using RNA-Capturing Microsphere Particles. Anal Chem 2020; 92:7955-7963. [PMID: 32363852 DOI: 10.1021/acs.analchem.0c01338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An RNA signaling aptamer is composed of two units: a sensing aptamer that binds the input target molecule and a working aptamer that binds the output target molecule to result in a detectable signal. A conformational change of the signaling aptamer that induces an allosteric interaction with the output target molecule in response to the input target molecule depends on a junction region, which connects the two aptamer units. Efficient and effective optimization of the junction region remains a technical challenge. In this study, we demonstrate a simple strategy for optimizing the junction region through functional RNA selection using RNA-capturing microsphere particles. From approximately 0.2 million sequence variants, a signaling aptamer that enabled intracellular detection of S-adenosyl methionine with a high signal-to-noise ratio, which is approximately 2-fold higher relative fluorescence increment compared to the previously reported signaling aptamer, was obtained after single round of selection. The technology demonstrated here can be used to select RNA sequences that carry out specific functions in response to particular stimuli.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
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Jia X, Guo M, Han Q, Tian Y, Yuan Y, Wang Z, Qian Y, Wang W. Synergetic Tumor Probes for Facilitating Therapeutic Delivery by Combined-Functionalized Peptide Ligands. Anal Chem 2020; 92:5650-5655. [DOI: 10.1021/acs.analchem.0c00440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiangqian Jia
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 10084, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, P. R. China
| | - Mingmei Guo
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Qiuju Han
- College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, P. R. China
| | - Yuwei Tian
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Yafei Yuan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zihua Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, P. R. China
| | - Yixia Qian
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, P. R. China
| | - Weizhi Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
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Kuwahara M, Fujita H, Kataoka Y, Nakajima Y, Yamada M, Sugimoto N. In situ condensation of an anti-cancer drug into fibrin gel enabling effective inhibition of tumor cell growth. Chem Commun (Camb) 2019; 55:11679-11682. [PMID: 31524892 DOI: 10.1039/c9cc06418d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We show herein the highly effective inhibition of tumor cell growth using a gel consisting of a fibrin polymer formed with the in situ condensation of a camptothecin (CPT) derivative as an anti-cancer drug, which is efficiently conveyed with a carrier aptamer from a solution to the gel in a phenomenon, called selective oligonucleotide entrapment in fibrin polymers (SOEF).
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Hiroto Fujita
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Yuka Kataoka
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Yasuyo Nakajima
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Graduate School of Medicine, Gunma University, 3-39-15 Showa-machi, Maebashi, 371-8511, Japan
| | - Masanobu Yamada
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Graduate School of Medicine, Gunma University, 3-39-15 Showa-machi, Maebashi, 371-8511, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan
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Abstract
Riboswitches are RNA elements that recognize diverse chemical and biomolecular inputs, and transduce this recognition process to genetic, fluorescent, and other engineered outputs using RNA conformational changes. These systems are pervasive in cellular biology and are a promising biotechnology with applications in genetic regulation and biosensing. Here, we derive a simple expression bounding the activation ratio-the proportion of RNA in the active vs. inactive states-for both ON and OFF riboswitches that operate near thermodynamic equilibrium: 1+[I]/KdI, where [I] is the input ligand concentration and KdI is the intrinsic dissociation constant of the aptamer module toward the input ligand. A survey of published studies of natural and synthetic riboswitches confirms that the vast majority of empirically measured activation ratios have remained well below this thermodynamic limit. A few natural and synthetic riboswitches achieve activation ratios close to the limit, and these molecules highlight important principles for achieving high riboswitch performance. For several applications, including "light-up" fluorescent sensors and chemically-controlled CRISPR/Cas complexes, the thermodynamic limit has not yet been achieved, suggesting that current tools are operating at suboptimal efficiencies. Future riboswitch studies will benefit from comparing observed activation ratios to this simple expression for the optimal activation ratio. We present experimental and computational suggestions for how to make these quantitative comparisons and suggest new molecular mechanisms that may allow non-equilibrium riboswitches to surpass the derived limit.
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Affiliation(s)
| | - Michelle Wu
- Program in Biomedical Informatics, Stanford University, Stanford, CA, United States
| | - Michael Gotrik
- Department of Biochemistry, Stanford University, Stanford, CA, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, United States; Department of Physics, Stanford University, Stanford, CA, United States.
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Endoh T, Ohyama T, Sugimoto N. RNA-Capturing Microsphere Particles (R-CAMPs) for Optimization of Functional Aptamers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805062. [PMID: 30773785 DOI: 10.1002/smll.201805062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/23/2019] [Indexed: 06/09/2023]
Abstract
RNA aptamers are useful building blocks for constructing functional nucleic acid-based nanoarchitectures. The abilities of aptamers to recognize specific ligands have also been utilized for various biotechnological applications. Solution conditions, which can differ depending on the application, impact the affinity of the aptamers, and thus it is important to optimize the aptamers for the solution conditions to be employed. To simplify the aptamer optimization process, an efficient method that enables re-selection of an aptamer from a partially randomized library is developed. The process relies on RNA-capturing microsphere particles (R-CAMPs): each particle displays different clones of identical DNA and RNA sequences. Using a fluorescence-activated cell sorter, the R-CAMPs that are linked to functional aptamers are sorted. It is demonstrated that after a single round of reselection, several functional aptamers, including the wild-type, are selected from a library of 16 384 sequences. The selection using R-CAMPs is further performed under the solution containing high concentration of ethylene glycol, suggesting applicability in various conditions to optimize an aptamer for a particular application. As any type of RNA clone can be displayed on the microspheres, the technology demonstrated here will be useful for the selection of RNAs based on diverse functions.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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