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Chen S, Ma J, Xiao Y, Zhou D, He P, Chen Y, Zheng X, Lin H, Qiu F, Yuan Y, Zhong J, Li X, Pan X, Fang Z, Wang C. RNA Interference against ATP as a Gene Therapy Approach for Prostate Cancer. Mol Pharm 2023; 20:5214-5225. [PMID: 37733628 DOI: 10.1021/acs.molpharmaceut.3c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Chemotherapeutic agents targeting energy metabolism have not achieved satisfactory results in different types of tumors. Herein, we developed an RNA interference (RNAi) method against adenosine triphosphate (ATP) by constructing an interfering plasmid-expressing ATP-binding RNA aptamer, which notably inhibited the growth of prostate cancer cells through diminishing the availability of cytoplasmic ATP and impairing the homeostasis of energy metabolism, and both glycolysis and oxidative phosphorylation were suppressed after RNAi treatment. Further identifying the mechanism underlying the effects of ATP aptamer, we surprisingly found that it markedly reduced the activity of membrane ionic channels and membrane potential which led to the dysfunction of mitochondria, such as the decrease of mitochondrial number, reduction in the respiration rate, and decline of mitochondrial membrane potential and ATP production. Meanwhile, the shortage of ATP impeded the formation of lamellipodia that are essential for the movement of cells, consequently resulting in a significant reduction of cell migration. Both the downregulation of the phosphorylation of AMP-activated protein kinase (AMPK) and endoplasmic reticulum kinase (ERK) and diminishing of lamellipodium formation led to cell apoptosis as well as the inhibition of angiogenesis and invasion. In conclusion, as the first RNAi modality targeting the blocking of ATP consumption, the present method can disturb the respiratory chain and ATP pool, which provides a novel regime for tumor therapies..
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Affiliation(s)
- Shuangya Chen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Jisheng Ma
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Yunbei Xiao
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Dongyan Zhou
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Ping He
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Yajing Chen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Xiaolu Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
- Pharmaceutical Department, Jinhua Central Hospital, Jinhua, Zhejiang 321000, China
| | - Hui Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Feng Qiu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Yuying Yuan
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Jiaben Zhong
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaokun Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Xuebo Pan
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
| | - Zhiyuan Fang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Cong Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325030, China
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Lighting up ATP in cells and tissues using a simple aptamer-based fluorescent probe. Mikrochim Acta 2021; 188:352. [PMID: 34554325 PMCID: PMC8459148 DOI: 10.1007/s00604-021-05012-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/28/2021] [Indexed: 01/02/2023]
Abstract
Extracellular ATP as a purinergic signaling molecule, together with ATP receptor, are playing an important role in tumor growth, therapy resistance, and host immunity suppression. Meanwhile ATP is a crucial indicator for cellular energy status and viability, thus a vital variable for tissue regeneration and in vitro tissue engineering. Most recent studies on COVID-19 virus suggest infection caused ATP deficit and release as a major characterization at the early stage of the disease and major causes for disease complications. Thus, imaging ATP molecule in both cellular and extracellular contexts has many applications in biology, engineering, and clinics. A sensitive and selective fluorescence “signal-on” probe for ATP detection was constructed, based on the base recognition between a black hole quencher (BHQ)-labeled aptamer oligonucleotide and a fluorophore (Cy5)-labeled reporter flare. The probe was able to detect ATP in solution with single digit µM detection limit. With the assistance of lipofectamine, this probe efficiently entered and shined in the model cells U2OS within 3 h. Further application of the probe in specific scenery, cardio-tissue engineering, was also tested where the ATP aptamer complex was able to sense cellular ATP status in a semi-quantitative manner, representing a novel approach for selection of functional cardiomyocytes for tissue engineering. At last a slight change in probe configuration in which a flexible intermolecular A14 linker was introduced granted regeneration capability. These data support the application of this probe in multiple circumstances where ATP measurement or imaging is on demand.
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RNA-Peptide Conjugation through an Efficient Covalent Bond Formation. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10248920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many methods for modification of an oligonucleotide with a peptide have been developed to apply for the therapeutic and diagnostic applications or for the assembly of nanostructure. We have developed a method for the construction of receptor-based fluorescent sensors and catalysts using the ribonucleopeptide (RNP) as a scaffold. Formation of a covalent linkage between the RNA and the peptide subunit of RNP improved its stability, thereby expanding the application of functional RNPs. A representative method was applied for the formation of Schiff base or dihydroxy-morpholino linkage between a dialdehyde group at the 3′-end of sugar-oxidized RNA and a hydrazide group introduced at the C-terminal of a peptide subunit through a flexible peptide linker. In this report, we investigated effects of the solution pH and contribution of the RNA and peptide subunits to the conjugation reaction by using RNA and peptide mutants. The reaction yield reached 90% at a wide range of solution pH with reaction within 3 h. The efficient reaction was mainly supported by the electrostatic interaction between the RNA subunit and the cationic peptide subunit of the RNP scaffold. Formation of the RNP complex was verified to efficiently promote the reaction for construction of the RNA-peptide conjugate.
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Nakano S, Konishi H, Morii T. Receptor-based fluorescent sensors constructed from ribonucleopeptide. Methods Enzymol 2020; 641:183-223. [PMID: 32713523 DOI: 10.1016/bs.mie.2020.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor-based fluorescent sensors are the representative tool for quantitative detection of target ligands. The high substrate-selectivity originated from biomacromolecule receptor is one of the advantages of this tool, but a laborious trial and error is usually required to construct sensors showing satisfactory fluorescence intensity changes without diminishing the function of parent receptor. Ribonucleopeptide (RNP) provides a scaffold of fluorescent sensors to improve such issues. RNP receptors for the ligand of interest are constructed by applying in vitro selection for RNA-derived RNP library. Simple modification of the N-terminal of peptide in RNP by an appropriate fluorophore converts the RNP receptor into the fluorescent sensor with retaining the affinity and selectivity for the substrate. In this chapter, we introduce the protocols for construction of fluorescent RNP sensors through selection from a library of fluorophore-modified RNP complex or by a structure-based modular design. Furthermore, we describe the application of covalently linked RNP sensors for simultaneous detection of multiple ligands.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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5
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Yan Y, Deng C. Recent advances in nanomaterials for sample pre-treatment in phosphoproteomics research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115655] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Nakano S, Shimizu M, Dinh H, Morii T. Highly selective dual sensing of ATP and ADP using fluorescent ribonucleopeptide sensors. Chem Commun (Camb) 2019; 55:1611-1614. [PMID: 30657140 DOI: 10.1039/c8cc09934k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Highly selective fluorescent sensors for ATP and ADP were constructed from RNA aptamers by applying a modular design of a ribonucleopeptide scaffold. These sensors allow facile and quantitative detection of ATP and ADP simultaneously in a solution and enable monitoring of the time-course changes of ATP and ADP concentrations in an enzymatic reaction.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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Morii T. A Bioorganic Chemistry Approach to Understanding Molecular Recognition in Protein–Nucleic Acid Complexes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011
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Park Y, Nim-Anussornkul D, Vilaivan T, Morii T, Kim BH. Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon. Bioorg Med Chem Lett 2017; 28:77-80. [PMID: 29248297 DOI: 10.1016/j.bmcl.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/23/2017] [Accepted: 12/05/2017] [Indexed: 01/02/2023]
Abstract
We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP. The fluorescence emission intensity increased upon formation of a RNA-based QF-MAB·ATP complex.
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Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | | | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
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Nakano S, Tamura T, Das RK, Nakata E, Chang YT, Morii T. A Diversity-Oriented Library of Fluorophore-Modified Receptors Constructed from a Chemical Library of Synthetic Fluorophores. Chembiochem 2017; 18:2212-2216. [PMID: 28879678 DOI: 10.1002/cbic.201700403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/16/2022]
Abstract
The practical application of biosensors can be determined by evaluating the sensing ability of fluorophore-modified derivatives of a receptor with appropriate recognition characteristics for target molecules. One of the key determinants for successfully obtaining a useful biosensor is wide variation in the fluorophores attached to a given receptor. Thus, using a larger fluorophore-modified receptor library provides a higher probability of obtaining a practically useful biosensor. However, no effective method has yet been developed for constructing such a diverse library of fluorophore-modified receptors. Herein, we report a method for constructing fluorophore-modified receptors by using a chemical library of synthetic fluorophores with a thiol-reactive group. This library was converted into a library of fluorophore-modified adenosine-binding ribonucleopeptide (RNP) receptors by introducing the fluorophores to the Rev peptide of the RNP complex by alkylation of the thiol group. This method enabled the construction of 263 fluorophore-modified ATP-binding RNP receptors and allowed the selection of suitable receptor-based fluorescent sensors that target ATP.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Raj Kumar Das
- Bharat Petroleum Corporation Ltd., Corporate R&D Centre, Plot No. 2 A, Udyog Kendra, Surajpur Industrial Area, Greater Noida, 201 306, India
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Young-Tae Chang
- Department of Chemistry and MedChem Program of Life Sciences, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
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Tamura T, Nakano S, Nakata E, Morii T. Construction of a library of structurally diverse ribonucleopeptides with catalytic groups. Bioorg Med Chem 2017; 25:1881-1888. [PMID: 28223024 DOI: 10.1016/j.bmc.2017.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 01/20/2023]
Abstract
Functional screening of structurally diverse libraries consisting of proteins or nucleic acids is an effective method to obtain receptors or aptamers with unique molecular recognition characteristics. However, further modification of these selected receptors to exert a newly desired function is still a challenging task. We have constructed a library of structurally diverse ribonucleopeptides (RNPs) that are modified with a catalytic group, in which the catalytic group aligns with various orientations against the ATP binding pocket of RNA subunit. As a proof-of-principle, the screening of the constructed RNP library for the catalytic reaction of ester hydrolysis was successfully carried out. The size of both the substrate-binding RNA library and the catalytic group modified peptide library are independently expandable, and thus, the size of RNPs library could be enlarged by a combination of these two subunits. We anticipate that the library of functionalized and structurally diverse RNPs would be expanded for various other catalytic reactions.
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Affiliation(s)
- Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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11
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Yoneda R, Suzuki S, Mashima T, Kondo K, Nagata T, Katahira M, Kurokawa R. The binding specificity of Translocated in LipoSarcoma/FUsed in Sarcoma with lncRNA transcribed from the promoter region of cyclin D1. Cell Biosci 2016; 6:4. [PMID: 26816614 PMCID: PMC4727290 DOI: 10.1186/s13578-016-0068-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/07/2016] [Indexed: 11/10/2022] Open
Abstract
Background Translocated in LipoSarcoma (TLS, also known as FUsed in Sarcoma) is an RNA/DNA binding protein whose mutation cause amyotrophic lateral sclerosis. In previous study, we demonstrated that TLS binds to long noncoding RNA, promoter-associated ncRNA-D (pncRNA-D), transcribed from the 5′ upstream region of cyclin D1 (CCND1), and inhibits the expression of CCND1. Results In order to elucidate the binding specificity between TLS and pncRNA-D, we divided pncRNA-D into seven fragments and examined the binding with full-length TLS, TLS–RGG2–zinc finger–RGG3, and TLS–RGG3 by RNA pull down assay. As a result, TLS was able to bind to all the seven fragments, but the fragments containing reported recognition motifs (GGUG and GGU) tend to bind more solidly. The full-length TLS and TLS–RGG2–zinc finger–RGG3 showed a similar interaction with pncRNA-D, but the binding specificity of TLS–RGG3 was lower compared to the full-length TLS and TLS–RGG2–zinc finger–RGG3. Mutation in GGUG and GGU motifs dramatically decreased the binding, and unexpectedly, we could only detect weak interaction with the RNA sequence with stem loop structure. Conclusion The binding of TLS and pncRNA-D was affected by the presence of GGUG and GGU sequences, and the C terminal domains of TLS function in the interaction with pncRNA-D. Electronic supplementary material The online version of this article (doi:10.1186/s13578-016-0068-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryoma Yoneda
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241 Japan
| | - Shiho Suzuki
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241 Japan
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan ; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan ; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan ; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011 Japan
| | - Riki Kurokawa
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241 Japan
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12
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de la Escosura A, Briones C, Ruiz-Mirazo K. The systems perspective at the crossroads between chemistry and biology. J Theor Biol 2015; 381:11-22. [DOI: 10.1016/j.jtbi.2015.04.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/26/2015] [Indexed: 01/21/2023]
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Vollmer S, Richert C. Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands. Org Biomol Chem 2015; 13:5734-42. [PMID: 25902412 DOI: 10.1039/c5ob00508f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.
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Affiliation(s)
- S Vollmer
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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Abstract
Incorporation of a 5-methyl-2-thiocytosine base to the parallel homopyrimidine region of a triplex DNA receptor enabled selective molecular recognition of an inosine ligand.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry and Environmental Science
- New Jersey Institute of Technology
- Newark
- USA
| | - Peter C. Tlatelpa
- Department of Chemistry and Environmental Science
- New Jersey Institute of Technology
- Newark
- USA
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Kröner C, Göckel A, Liu W, Richert C. Binding cofactors with triplex-based DNA motifs. Chemistry 2013; 19:15879-87. [PMID: 24194407 DOI: 10.1002/chem.201303098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Indexed: 12/28/2022]
Abstract
Cofactors are pivotal compounds for the cell and many biotechnological processes. It is therefore interesting to ask how well cofactors can be bound by oligonucleotides designed not to convert but to store and release these biomolecules. Here we show that triplex-based DNA binding motifs can be used to bind nucleotides and cofactors, including NADH, FAD, SAM, acetyl CoA, and tetrahydrofolate (THF). Dissociation constants between 0.1 μM for SAM and 35 μM for THF were measured. A two-nucleotide gap still binds NADH. The selectivity for one ligand over the others can be changed by changing the sequence of the binding pocket. For example, a mismatch placed in one of the two triplets adjacent to the base-pairing site changes the selectivity, favoring the binding of FAD over that of ATP. Further, changing one of the two thymines of an A-binding motif to cytosine gives significant affinity for G, whereas changing the other does not. Immobilization of DNA motifs gives beads that store NADH. Exploratory experiments show that the beads release the cofactor upon warming to body temperature.
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Affiliation(s)
- Christoph Kröner
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Zhang M, Ma WJ, He CT, Jiang L, Lu TB. Highly selective recognition and fluorescence imaging of adenosine polyphosphates in aqueous solution. Inorg Chem 2013; 52:4873-9. [PMID: 23560560 DOI: 10.1021/ic302435g] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The design and synthesis of chemosensors for the recognition of a certain nucleoside polyphosphate among various structurally similar nucleoside polyphosphates remain a fundamental challenge. Herein, we report the new fluorescent chemosensor [Zn2L](ClO4)4 (1; L = (3,6,10,13,17,20,24,27-octaaza-1,15(2,6)-dipyridina-8,22(9,10)-dianthracenacyclooctacosaphane), which can selectively recognize adenosine polyphosphates (ATP and ADP) among various nucleoside polyphosphates, with a large fluorescence enhancement (Fmax/F0 = 70 and 80 for ATP and ADP, respectively) and strong binding affinity (K = 3.1 × 10(11) M(-1) for [Zn2HL(H-1ATP)2](-), 2.8 × 10(11) M(-1) for [Zn2L(H-1ATP)2](2-), and 1.5 × 10(13) M(-1) for [Zn2L(H-1ADP)2](2-)) in aqueous solution at physiological pH 7.40. The structure of [Zn2L](P2O7) (2) was investigated, which shows that μ2-pyrophosphate anions alternately link [Zn2L](4+) cations to generate a 1D coordination polymer. The results of (31)P NMR studies and DFT calculations reveal that the two Zn(II) ions in 1 can interact with ATP/ADP anions through coordination interactions between Zn(II) and the polyphosphate groups, and two anthracene moieties in 1 can interact with adenine groups from two ATP or ADP anions through stacking interactions to form a sandwichlike structure. These multiple recognition interactions between 1 and ATP/ADP enhance the affinity and selectivity of 1 toward ATP/ADP. Due to its highly selective and sensitive ability to detect adenosine polyphosphates, 1 was successfully applied to fluorescence imaging for ATP and ADP in living cells, demonstrating the potential utility of 1 as a fluorescent chemosensor for detecting ATP and ADP.
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Affiliation(s)
- Mei Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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Annoni C, Nakata E, Tamura T, Liew FF, Nakano S, Gelmi ML, Morii T. Construction of ratiometric fluorescent sensors by ribonucleopeptides. Org Biomol Chem 2013; 10:8767-9. [PMID: 23069733 DOI: 10.1039/c2ob26722e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ratiometric fluorescent sensors were constructed from RNA aptamers by generating modular ribonucleopeptide complexes. Fluorescent ribonucleopeptides containing fluorophore seminaphthorhodafluor tethered to their peptide subunit revealed a dual emission property, which permitted a ratiometric fluorescent measurement of a substrate-binding event. The strategy successfully afforded ratiometric fluorescent sensors for biologically active small ligands, tetracycline, dopamine and streptomycin.
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Affiliation(s)
- Chiara Annoni
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Sezione Chimica Generale Organica A. Marchesini, Universita` degli Studi di Milano, via Venezian 21, 20133 Milan, Italy
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Nakano S, Fukuda M, Tamura T, Sakaguchi R, Nakata E, Morii T. Simultaneous detection of ATP and GTP by covalently linked fluorescent ribonucleopeptide sensors. J Am Chem Soc 2013; 135:3465-73. [PMID: 23373863 DOI: 10.1021/ja3097652] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A noncovalent RNA complex embedding an aptamer function and a fluorophore-labeled peptide affords a fluorescent ribonucleopeptide (RNP) framework for constructing fluorescent sensors. By taking an advantage of the noncovalent properties of the RNP complex, the ligand-binding and fluorescence characteristics of the fluorescent RNP can be independently tuned by taking advantage of the nature of the RNA and peptide subunits, respectively. Fluorescent sensors tailored for given measurement conditions, such as a detection wavelength and a detection concentration range for a ligand of interest can be easily identified by screening of fluorescent RNP libraries. The noncovalent configuration of a RNP becomes a disadvantage when the sensor is to be utilized at very low concentrations or when multiple sensors are applied to the same solution. Here, we report a strategy to convert a fluorescent RNP sensor in the noncovalent configuration into a covalently linked stable fluorescent RNP sensor. This covalently linked fluorescent RNP sensor enabled ligand detection at a low sensor concentration, even in cell extracts. Furthermore, application of both ATP and GTP sensors enabled simultaneous detection of ATP and GTP by monitoring each wavelength corresponding to the respective sensor. Importantly, when a fluorescein-modified ATP sensor and a pyrene-modified GTP sensor were co-incubated in the same solution, the ATP sensor responded at 535 nm only to changes in the concentration of ATP, whereas the GTP sensor detected GTP at 390 nm without any effect on the ATP sensor. Finally, simultaneous monitoring by these sensors enabled real-time measurement of adenosine deaminase enzyme reactions.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Wang RE, Zhang Y, Cai J, Cai W, Gao T. Aptamer-based fluorescent biosensors. Curr Med Chem 2012; 18:4175-84. [PMID: 21838688 DOI: 10.2174/092986711797189637] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 01/24/2023]
Abstract
Selected from random pools of DNA or RNA molecules through systematic evolution of ligands by exponential enrichment (SELEX), aptamers can bind to target molecules with high affinity and specificity, which makes them ideal recognition elements in the development of biosensors. To date, aptamer-based biosensors have used a wide variety of detection techniques, which are briefly summarized in this article. The focus of this review is on the development of aptamer-based fluorescent biosensors, with emphasis on their design as well as properties such as sensitivity and specificity. These biosensors can be broadly divided into two categories: those using fluorescently-labeled aptamers and others that employ label-free aptamers. Within each category, they can be further divided into "signal-on" and "signal-off" sensors. A number of these aptamer-based fluorescent biosensors have shown promising results in biological samples such as urine and serum, suggesting their potential applications in biomedical research and disease diagnostics.
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Affiliation(s)
- R E Wang
- Department of Chemistry, Washington University in St. Louis, MO, USA
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21
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Zhang L, Zhao Q, Liang Z, Yang K, Sun L, Zhang L, Zhang Y. Synthesis of adenosine functionalized metal immobilized magnetic nanoparticles for highly selective and sensitive enrichment of phosphopeptides. Chem Commun (Camb) 2012; 48:6274-6. [DOI: 10.1039/c2cc31641b] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Liew FF, Hayashi H, Nakano S, Nakata E, Morii T. A ribonucleopeptide module for effective conversion of an RNA aptamer to a fluorescent sensor. Bioorg Med Chem 2011; 19:5771-5. [PMID: 21906952 DOI: 10.1016/j.bmc.2011.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
Ribonucleopeptide (RNP) is a new class of scaffold for modular fluorescent sensors. We report here a short RNA motif that induces an efficient communication between the structural changes associated with the ligand-binding event of RNA aptamer and an optical response of a fluorescent RNP module. An optimized short RNA motif was used as a communication module for the rational design of modular RNP sensors. A modular combination of a GTP-binding RNA aptamer, the short RNA motif and the fluorophore-labeled RNP module afforded a fluorescent GTP sensor that retain the ligand-binding affinity of the parent aptamer.
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Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Liew FF, Hasegawa T, Fukuda M, Nakata E, Morii T. Construction of dopamine sensors by using fluorescent ribonucleopeptide complexes. Bioorg Med Chem 2011; 19:4473-81. [PMID: 21742507 DOI: 10.1016/j.bmc.2011.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/18/2022]
Abstract
A facile strategy of stepwise molding of a ribonucleopeptide (RNP) complex affords fluorescent RNP sensors with selective dopamine recognition. In vitro selection of a RNA-derived RNP library, a complex of the Rev peptide and its binding site Rev Responsive Element (RRE) RNA appended with random nucleotides in variable lengths, afforded RNP receptors specific for dopamine. The modular structure of the RNP receptor enables conversion of dopamine-binding RNP receptors to fluorescent dopamine sensors. Application of conditional selection schemes, such as the variation of salt concentrations and application of a counter-selection step by using a competitor ligand norepinephrine resulted in isolation of RNP receptors with defined dopamine-binding characteristics. Increasing the salt condition at the in vitro selection stage afforded RNP receptors with higher dopamine affinity, while addition of norepinephrine in the in vitro selection milieu at the counter-selection step reinforced the selectivity of RNP receptors to dopamine against norepinephrine. Thermodynamic analyses and circular dichroismic studies of the dopamine-RNP complexes suggest that the dopamine-binding RNP with higher selectivity against norepinephrine forms a pre-organized binding pocket and that the dopamine-binding RNP with higher affinity binds dopamine through the induced-fit mechanism. These results indicate that the selection condition controls the ligand-binding mechanism of RNP receptors.
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Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
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Nakano S, Nakata E, Morii T. Facile conversion of RNA aptamers to modular fluorescent sensors with tunable detection wavelengths. Bioorg Med Chem Lett 2011; 21:4503-6. [PMID: 21719284 DOI: 10.1016/j.bmcl.2011.05.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 05/28/2011] [Accepted: 05/31/2011] [Indexed: 11/26/2022]
Abstract
A GTP aptamer was converted to a modular fluorescent GTP sensor by conjugation of RRE (Rev responsive element) RNA and successive complex formation with a fluorophore-modified Rev peptide. Structural changes associated with substrate binding in the RNA aptamer were successfully transduced into changes in fluorescence intensity because of the modular structure of ribonucleopeptides. A simple modular strategy involving conjugation of a fluorophore-modified ribonucleopeptide to the stem region of an RNA aptamer deduced from secondary structural information helps produce fluorescent sensors, which allow tuning of excitation and detection wavelengths through the replacement of the fluorophore at the N-terminal of the Rev peptide.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
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