1
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Goshisht MK, Tripathi N, Patra GK, Chaskar M. Organelle-targeting ratiometric fluorescent probes: design principles, detection mechanisms, bio-applications, and challenges. Chem Sci 2023; 14:5842-5871. [PMID: 37293660 PMCID: PMC10246671 DOI: 10.1039/d3sc01036h] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
Biological species, including reactive oxygen species (ROS), reactive sulfur species (RSS), reactive nitrogen species (RNS), F-, Pd2+, Cu2+, Hg2+, and others, are crucial for the healthy functioning of cells in living organisms. However, their aberrant concentration can result in various serious diseases. Therefore, it is essential to monitor biological species in cellular organelles such as the cell membrane, mitochondria, lysosome, endoplasmic reticulum, Golgi apparatus, and nucleus. Among various fluorescent probes for species detection within the organelles, ratiometric fluorescent probes have drawn special attention as a potential way to get beyond the drawbacks of intensity-based probes. This method depends on measuring the intensity change of two emission bands (caused by an analyte), which produces an efficient internal referencing that increases the detection's sensitivity. This review article discusses the literature publications (from 2015 to 2022) on organelle-targeting ratiometric fluorescent probes, the general strategies, the detecting mechanisms, the broad scope, and the challenges currently faced by fluorescent probes.
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Affiliation(s)
- Manoj Kumar Goshisht
- Department of Chemistry, Natural and Applied Sciences, University of Wisconsin-Green Bay 2420 Nicolet Drive Green Bay WI 54311-7001 USA
- Department of Chemistry, Government Naveen College Tokapal Bastar Chhattisgarh 494442 India
| | - Neetu Tripathi
- Department of Chemistry, Guru Nanak Dev University Amritsar Punjab 143005 India
| | - Goutam Kumar Patra
- Department of Chemistry, Faculty of Physical Sciences Guru Ghasidas Vishwavidyalaya Bilaspur Chhattisgarh 495009 India
| | - Manohar Chaskar
- Department of Technology, Savitribai Phule Pune University Ganeshkhind Pune 411007 India
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2
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Nagatsugi F, Onizuka K. Selective Chemical Modification to the Higher-Order Structures of Nucleic Acids. CHEM REC 2023; 23:e202200194. [PMID: 36111635 DOI: 10.1002/tcr.202200194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Indexed: 11/06/2022]
Abstract
DNA and RNA can adopt a variety of stable higher-order structural motifs, including G-quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher-order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher-order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher-order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher-order structures of nucleic acids is also underway. In this personal account, we focus on the following higher-order structures of nucleic acids, double-stranded DNA containing the abasic site, T-T/U-U mismatch structure, and G-quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.
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Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
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3
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Chen Y, Onizuka K, Hazemi ME, Nagatsugi F. Reactivity Modulation of Reactive OFF–ON Type G-Quadruplex Alkylating Agents. Bioconjug Chem 2022; 33:2097-2102. [DOI: 10.1021/acs.bioconjchem.2c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yutong Chen
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Madoka E. Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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4
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Onizuka K, Yamano Y, Abdelhady AM, Nagatsugi F. Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids. Org Biomol Chem 2022; 20:4699-4708. [PMID: 35622064 DOI: 10.1039/d2ob00551d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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5
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Onizuka K, Ganbold E, Ma Y, Sasaki S, Hazemi ME, Chen Y, Sato N, Ozawa M, Nagasawa K, Nagatsugi F. Selective alkylation of parallel G-quadruplex structure. Org Biomol Chem 2021; 19:2891-2894. [PMID: 33570069 DOI: 10.1039/d0ob02365e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The selective alkylation of nucleic acids is important for a medicinal approach and biological study. We now report a novel selective alkylation of the parallel G-quadruplex structure using the conjugate of the macrocyclic hexaoxazole L2G2-6OTD-1M1PA and vinyl-quinazolinone-S(O)Me (6OTD-VQ-S(O)Me).
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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6
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Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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7
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Onizuka K, Hazemi ME, Sato N, Tsuji GI, Ishikawa S, Ozawa M, Tanno K, Yamada K, Nagatsugi F. Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids. Nucleic Acids Res 2020; 47:6578-6589. [PMID: 31188442 PMCID: PMC6649768 DOI: 10.1093/nar/gkz512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/15/2019] [Accepted: 05/30/2019] [Indexed: 01/02/2023] Open
Abstract
Higher-ordered structure motifs of nucleic acids, such as the G-quadruplex (G-4), mismatched and bulge structures, are significant research targets because these structures are involved in genetic control and diseases. Selective alkylation of these higher-order structures is challenging due to the chemical instability of the alkylating agent and side-reactions with the single- or double-strand DNA and RNA. We now report the reactive OFF-ON type alkylating agents, vinyl-quinazolinone (VQ) precursors with a sulfoxide, thiophenyl or thiomethyl group for the OFF-ON control of the vinyl reactivity. The stable VQ precursors conjugated with aminoacridine, which bind to the G-4 DNA, selectively reacted with a T base on the G-4 DNA in contrast to the single- and double-strand DNA. Additionally, the VQ precursor reacted with the T or U base in the AP-site, G-4 RNA and T-T mismatch structures. These VQ precursors would be a new candidate for the T or U specific alkylation in the higher-ordered structures of nucleic acids.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Madoka E Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Gen-Ichiro Tsuji
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Shunya Ishikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kousuke Tanno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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8
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Datta D. A convenient route to synthesize N2-(isobutyryl)-9-(carboxymethyl)guanine for aeg-PNA backbone. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:530-541. [PMID: 31588835 DOI: 10.1080/15257770.2019.1666139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Synthesis of exclusive N2-(isobutyryl)-9-(carboxymethyl)guanine, an important moiety for peptide nucleic acid synthesis has been reported through a high-yielding reaction scheme starting from 6-chloro-2-amino purine. Crystal structures of two intermediates confirmed the formation of N9-regioisomer. This new synthetic route can potentially replace the conventional tedious method with moderate overall yield.
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Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry, Chemical Biology Unit, Indian Institute of Science Education and Research, Pune, India
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9
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Onizuka K, Usami A, Yamaoki Y, Kobayashi T, Hazemi ME, Chikuni T, Sato N, Sasaki K, Katahira M, Nagatsugi F. Selective alkylation of T-T mismatched DNA using vinyldiaminotriazine-acridine conjugate. Nucleic Acids Res 2019; 46:1059-1068. [PMID: 29309639 PMCID: PMC5814796 DOI: 10.1093/nar/gkx1278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022] Open
Abstract
The alkylation of the specific higher-order nucleic acid structures is of great significance in order to control its function and gene expression. In this report, we have described the T–T mismatch selective alkylation with a vinyldiaminotriazine (VDAT)–acridine conjugate. The alkylation selectively proceeded at the N3 position of thymidine on the T–T mismatch. Interestingly, the alkylated thymidine induced base flipping of the complementary base in the duplex. In a model experiment for the alkylation of the CTG repeats DNA which causes myotonic dystrophy type 1 (DM1), the observed reaction rate for one alkylation increased in proportion to the number of T–T mismatches. In addition, we showed that primer extension reactions with DNA polymerase and transcription with RNA polymerase were stopped by the alkylation. The alkylation of the repeat DNA will efficiently work for the inhibition of replication and transcription reactions. These functions of the VDAT–acridine conjugate would be useful as a new biochemical tool for the study of CTG repeats and may provide a new strategy for the molecular therapy of DM1.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Akira Usami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yudai Yamaoki
- 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
| | - Tomohito Kobayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Madoka E Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Tomoko Chikuni
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kaname Sasaki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, 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
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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10
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Hazemi ME, Onizuka K, Kobayashi T, Usami A, Sato N, Nagatsugi F. Vinyldiaminotriazine-acridine conjugate as G-quadruplex alkylating agent. Bioorg Med Chem 2018; 26:3551-3558. [PMID: 29807700 DOI: 10.1016/j.bmc.2018.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/18/2018] [Accepted: 05/19/2018] [Indexed: 10/16/2022]
Abstract
Higher-order structures of nucleic acids have become widely noted for their biological consequences and the discovery of an alkylating small molecule for these structures has been of interest due to its therapeutic potential. We previously developed the vinyldiaminotriazine (VDAT)-acridine conjugate as a T-T mismatch alkylating agent. In this report, we focused on the finding of the alkylation to the G-quadruplex (G4) DNA with VDAT-acridine conjugates. The VDAT-acridine conjugates exhibited a considerable alkylation ability to G4 under mild conditions. Moreover, the investigation of properties with the alkylated G4 revealed that alkylation by this conjugate significantly increased the stability of the G4 structure. This study provides a starting point in the further development of selective G4 alkylating small molecules.
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Affiliation(s)
- Madoka E Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Tomohito Kobayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Akira Usami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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11
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Sato N, Takahashi S, Tateishi-Karimata H, Hazemi ME, Chikuni T, Onizuka K, Sugimoto N, Nagatsugi F. Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA. Org Biomol Chem 2018; 16:1436-1441. [PMID: 29412214 DOI: 10.1039/c7ob03179c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The G-quadruplex structure has been found in biologically significant regions of the genomic DNA, including the telomere and promoter regions, and is known to play an important role in a number of biological processes. In this paper, we report the development of alkylating probes for the G-quadruplex structure and evaluation of the properties of the modified G-quadruplex structure.
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Affiliation(s)
- Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, 980-8577, Japan.
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12
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Hoechst-naphthalimide dyad with dual emissions as specific and ratiometric sensor for nucleus DNA damage. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.07.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017; 45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
| | - Stefanie Geigle
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
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14
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Affiliation(s)
- Masato Ikeda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193
| | - Marina Kabumoto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
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15
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Akisawa T, Yamada K, Nagatsugi F. Synthesis of peptide nucleic acids (PNA) with a crosslinking agent to RNA and effective inhibition of dicer. Bioorg Med Chem Lett 2016; 26:5902-5906. [PMID: 27838183 DOI: 10.1016/j.bmcl.2016.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/29/2016] [Accepted: 11/01/2016] [Indexed: 12/18/2022]
Abstract
Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. In this study, we have synthesized PNAs incorporating 2-amino-6-vinylpurine (AVP) for the covalent targeting of single-stranded DNA and RNA, and evaluated their reactivities for these targets. PNA containing AVP at the N-terminal position showed a high reactivity to uracil in RNA and thymine in DNA at the complementary site with AVP. In addition, the crosslinking reactions to pre-miR122 with PNA containing AVP increased the inhibition effect for the Dicer processing of pre-miR122 in vitro.
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Affiliation(s)
- Takuya Akisawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
| | - Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan.
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16
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Nagatsugi F. Development of the Strategy for Chemical Modifications to Nucleic Acids. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
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