1
|
Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
Collapse
Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
2
|
Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S. Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions. ACS Sens 2023; 8:923-932. [PMID: 36740828 DOI: 10.1021/acssensors.2c02617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (ThexT) and its 2'-O-methyluridine analogue (2'-OMe-ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ThexT and 2'-OMe-ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.
Collapse
Affiliation(s)
- Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ban Kinoshita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
3
|
Liu M, Cui Y, Zhang Y, An R, Li L, Park S, Sugiyama H, Liang X. Single base-modification reports and locates Z-DNA conformation on a Z-B-chimera formed by topological constraint. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20210400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| |
Collapse
|
4
|
Hori D, Yum JH, Sugiyama H, Park S. Tropylium Derivatives as New Entrants that Sense Quadruplex Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daisuke Hori
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
5
|
Han JH, Hirashima S, Park S, Sugiyama H. Highly sensitive and selective mercury sensor based on mismatched base pairing with dioxT. Chem Commun (Camb) 2019; 55:10245-10248. [PMID: 31393473 DOI: 10.1039/c9cc05123f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A highly selective and sensitive sensor for mercury was designed based on a new fluorescent nucleobase, dioxT. Its metal-sensing ability was investigated using mismatched dioxT-T and dioxT-C base pairing. The sensor exhibited a high sensitivity (quenching efficiency, 80%, 1 : 1 binding mode) and selectivity upon the addition of mercury ions.
Collapse
Affiliation(s)
- Ji Hoon Han
- Department of Chemistry, Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | | | | | | |
Collapse
|
6
|
Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S, Sugiyama H, Kim KK. Sequence preference and structural heterogeneity of BZ junctions. Nucleic Acids Res 2019; 46:10504-10513. [PMID: 30184200 PMCID: PMC6212838 DOI: 10.1093/nar/gky784] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/20/2018] [Indexed: 12/16/2022] Open
Abstract
BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.
Collapse
Affiliation(s)
- Doyoun Kim
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Jeonghwan Hur
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Ji Hoon Han
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| |
Collapse
|
7
|
Martinez-Fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Martì J, Mori M, Mely Y, Improta R. Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine. Chemistry 2019; 25:7375-7386. [PMID: 30882930 DOI: 10.1002/chem.201900677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.
Collapse
Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias, Modúlo13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Javier Segarra Martì
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134, Napoli, Italy
| |
Collapse
|
8
|
Zhang Y, Cui Y, An R, Liang X, Li Q, Wang H, Wang H, Fan Y, Dong P, Li J, Cheng K, Wang W, Wang S, Wang G, Xue C, Komiyama M. Topologically Constrained Formation of Stable Z-DNA from Normal Sequence under Physiological Conditions. J Am Chem Soc 2019; 141:7758-7764. [PMID: 30844265 DOI: 10.1021/jacs.8b13855] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Z-DNA, a left-handed duplex, has been shown to form in vivo and regulate expression of the corresponding gene. However, its biological roles have not been satisfactorily understood, mainly because Z-DNA is easily converted to the thermodynamically favorable B-DNA. Here we present a new idea to form stable Z-DNA under normal physiological conditions and achieve detailed analysis on its fundamental features. Simply by mixing two complementary minicircles of single-stranded DNA with no chemical modification, the hybridization spontaneously induces topological constraint which twines one-half of the double-stranded DNA into stable Z-DNA. The formation of Z-conformation with high stability has been proved by using circular dichroism spectroscopy, Z-DNA-specific antibody binding assay, nuclease digestion, etc. Even at a concentration of MgCl2 as low as 0.5 mM, Z-DNA was successfully obtained, avoiding the use of high salt conditions, limited sequences, ancillary additives, or chemical modifications, criteria which have hampered Z-DNA research. The resultant Z-DNA has the potential to be used as a canonical standard sample in Z-DNA research. By using this approach, further developments of Z-DNA science and its applications become highly promising.
Collapse
Affiliation(s)
- Yaping Zhang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yixiao Cui
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Qi Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Haiting Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Hao Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yiqiao Fan
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ping Dong
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Jing Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Kai Cheng
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Weinan Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Sai Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Guoqing Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Changhu Xue
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| |
Collapse
|
9
|
Balasubramaniyam T, Ishizuka T, Xu Y. Stability and properties of Z-DNA containing artificial nucleobase 2'-O-methyl-8-methyl guanosine. Bioorg Med Chem 2018; 27:364-369. [PMID: 30545733 DOI: 10.1016/j.bmc.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
We synthesized several DNA oligonucleotides containing one or several 2'-O-methyl-8-methyl guanosine (m8Gm) and demonstrated that these oligonucleotides not only stabilize the Z-DNA with a wide range of sequences under low salt conditions but also possess high thermal stability. Using artificial nucleobase-containing oligonucleotides, we studied the interaction of the Zα domain with Z-DNA. Furthermore, we showed that the m8Gm-contained oligonucleotides allow to study the photochemical reaction of Z-DNA.
Collapse
Affiliation(s)
- Thananjeyan Balasubramaniyam
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan.
| |
Collapse
|
10
|
Han JH, Park S, Hashiya F, Sugiyama H. Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase
th
dG–tC FRET Pair. Chemistry 2018; 24:17091-17095. [DOI: 10.1002/chem.201803382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/07/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Ji Hoon Han
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Soyoung Park
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Fumitaka Hashiya
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)Kyoto University Yoshida-ushinomiyacho Sakyo-ku Kyoto 606–8501 Japan
| |
Collapse
|
11
|
2'- O-Methyl-8-methylguanosine as a Z-Form RNA Stabilizer for Structural and Functional Study of Z-RNA. Molecules 2018; 23:molecules23102572. [PMID: 30304782 PMCID: PMC6222775 DOI: 10.3390/molecules23102572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/28/2018] [Accepted: 10/07/2018] [Indexed: 11/16/2022] Open
Abstract
In contrast to Z-DNA that was stabilized and well-studied for its structure by chemical approaches, the stabilization and structural study of Z-RNA remains a challenge. In this study, we developed a Z-form RNA stabilizer m⁸Gm, and demonstrated that incorporation of m⁸Gm into RNA can markedly stabilize the Z-RNA at low salt conditions. Using the m⁸Gm-contained Z-RNA, we determined the structure of Z-RNA and investigated the interaction of protein and Z-RNA.
Collapse
|
12
|
Han JH, Yamamoto S, Park S, Sugiyama H. Development of a Vivid FRET System Based on a Highly Emissive dG-dC Analogue Pair. Chemistry 2017; 23:7607-7613. [PMID: 28411372 DOI: 10.1002/chem.201701118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 12/12/2022]
Abstract
A new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues is reported. The FRET pair consists of 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (th dG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. The distance and orientation between donor and acceptor was controlled by systematic incorporation of th dG and tC into DNA sequences to investigate the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors. In addition, this nucleic acid-based FRET pair was used to monitor DNA conformation and achieved visualization of the B-Z transition.
Collapse
Affiliation(s)
- Ji Hoon Han
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Seigi Yamamoto
- Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University,Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| |
Collapse
|
13
|
Okamura I, Park S, Hiraga R, Yamamoto S, Sugiyama H. Synthesis, Photophysical Properties, and Enzymatic Incorporation of an Emissive Thymidine Analogue. CHEM LETT 2017. [DOI: 10.1246/cl.161024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
14
|
Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|