1
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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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2
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Abdelhady AM, Onizuka K, Ishida K, Yajima S, Mano E, Nagatsugi F. Rapid Alkene-Alkene Photo-Cross-Linking on the Base-Flipping-Out Field in Duplex DNA. J Org Chem 2022; 87:2267-2276. [PMID: 34978198 DOI: 10.1021/acs.joc.1c01498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specific chemical reactions by enzymes acting on a nucleobase are realized by flipping the target base out of the helix. Similarly, artificial oligodeoxynucleotides (ODNs) can also induce the base flipping and a specific chemical reaction. We now report an easily prepared and unique structure-providing photo-cross-linking reaction by taking advantage of the base-flipping-out field formed by alkene-type base-flipping-inducing artificial bases. Two 3-arylethenyl-5-methyl-2-pyridone nucleosides with the Ph or An group were synthesized and incorporated into the ODNs. We found that the two Ph derivatives provided the cross-linked product in a high yield only by a 10 s photoirradiation when their alkenes overlap each other in the duplex DNA. The highly efficient reaction enabled forming a cross-linked product even when using the duplex with a low Tm value.
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Affiliation(s)
- 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, Cairo 11884, Egypt
| | - 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
| | - Kei Ishida
- 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
| | - Sayaka Yajima
- 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
| | - Eriko Mano
- 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.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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3
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Kikuta K, Taniguchi Y, Sasaki S. Study of the Inducible Cross-Linking Reaction to mRNA and the Effect on the Translation. Chem Pharm Bull (Tokyo) 2019; 67:877-883. [PMID: 31366836 DOI: 10.1248/cpb.c19-00337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 4-vinylpyrimidin-2-one nucleoside (T-vinyl) forms a cross-link with the RNA containing uracil at the complementary site at a high reaction rate. To obtain the stable T-vinyl derivative so that its reactivity is protected until it access to the target site, several derivatives were investigated, and the 2-thiopyridinyl- and 2-thiopyrimidinyl T-vinyl derivatives were determined to be good candidates. The 2-thiopyrimidinyl T-vinyl derivative was found to more efficiently cross-link with mRNA albeit having a better stability than the 2-thiopyridinyl T-vinyl derivative. The investigation using the luciferase (Luc) mRNA, the synthetic mRNA and non-cellular translation system revealed that the translation is terminated at the end of the cross-linked duplex between the mRNA and the oligoribonucleotide (ORN). Thus, the 2-thiopyrimidinyl T-vinyl derivative has successfully demonstrated both a good stability and high efficiency for the cross-linking reaction, and expanded its applicability in biological applications.
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Affiliation(s)
- Kenji Kikuta
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
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4
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Nakamura S, Uehara H, Hasegawa T, Fujimoto K. Phototriggered Sequence-specific DNA Transportation into Liposomes Using Ultrafast DNA Photocrosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.170835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Harunobu Uehara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Takashi Hasegawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
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5
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Nakamura S, Kawabata H, Fujimoto K. Sequence-Specific DNA Photosplitting of Crosslinked DNAs Containing the 3-Cyanovinylcarbazole Nucleoside by Using DNA Strand Displacement. Chembiochem 2016; 17:1499-503. [PMID: 27357523 DOI: 10.1002/cbic.201600236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/30/2022]
Abstract
An oligodeoxynucleotide (ODN) containing the ultrafast reversible 3-cyanovinylcarbazole ((CNV) K) photo-crosslinker was photo-crosslinked to a complementary strand upon exposure to 366 nm irradiation and photosplit by use of 312 nm irradiation. In this paper we report that the photoreaction of (CNV) K on irradiation at 366 nm involves a photostationary state and that its reaction can be controlled by temperature. Guided by this new insight, we proposed and have now demonstrated previously unknown photosplitting of (CNV) K aided by DNA strand displacement as an alternative to heating. The photo-crosslinked double-stranded DNA (dsDNA) underwent >80 % photosplitting aided by DNA strand displacement on irradiation at 366 nm without heating. In this photosplitting based on DNA strand displacement, the relative thermal stability of the invader strand with respect to the template strands plays an important role, and an invader strand/template strand system that is more stable than the passenger strand/template strand system induces photosplitting without heating. This new strand-displacement-aided photosplitting occurred in a sequence-specific manner through irradiation at 366 nm in the presence of an invader strand.
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Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan
| | - Hayato Kawabata
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan.
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6
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Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chemistry 2016; 22:10533-8. [DOI: 10.1002/chem.201602006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- PRESTO (Japan) Science and Technology Agency; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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7
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Doi T, Kashida H, Asanuma H. Efficiency of [2 + 2] photodimerization of various stilbene derivatives within the DNA duplex scaffold. Org Biomol Chem 2016; 13:4430-7. [PMID: 25689316 DOI: 10.1039/c4ob02520b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A DNA duplex was used as a scaffold to evaluate the intrinsic reactivity of [2 + 2] photodimerization between stilbene derivatives; the duplex pre-organizes the substrates avoiding the need for an association step. Unmodified stilbenes were first introduced at base-pairing positions on complementary DNA strands. The duplex was then irradiated with 340 nm UV light. HPLC analyses revealed that [2 + 2] photodimerization proceeded rapidly without side reactions. Thus, it was confirmed that the DNA duplex could be used as an ideal scaffold for [2 + 2] photodimerization of stilbenes. Next, we examined homo-photodimerization abilities of various stilbene derivatives. Homo-photodimerization of p-cyanostilbene, p-methylstilbazolium, and p-stilbazole occurred efficiently, whereas homo-photodimerization of p-dimethylaminostilbene and p-nitrostilbene did not proceed at all, probably because the reaction was quenched by dimethylamino and nitro groups. Time-dependent density functional theory calculations revealed that excitation energy was correlated with quantum yield. We further investigated hetero-photodimerization. These reactions were made possible by the use of two complementary oligodeoxyribonucleotides tethering different stilbene derivatives. Reactivities in hetero-photodimerization were highly dependent on the combination of derivatives. A high correlation was observed between the quantum yields and energy gaps of HOMO and LUMO between reactive derivatives. Unexpectedly, nitrostilbene, which was non-reactive in homo-photodimerization, cross-reacted with p-methylstilbazolium and p-stilbazole, both of which had close HOMO or LUMO with nitrostilbene. Evaluation of the intrinsic reactivity of homo- and hetero-photodimerization of stilbene derivatives was made possible by the use of DNA as a scaffold.
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Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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8
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Sugihara Y, Nakata Y, Yamayoshi A, Murakami A, Kobori A. Cross-Linking Antisense Oligodeoxyribonucleotides with a Photoresponsive α-Chloroaldehyde Moiety for RNA Point Mutations. J Org Chem 2016; 81:981-6. [PMID: 26788869 DOI: 10.1021/acs.joc.5b02573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because point mutations in GTPase-coding genes have been reported to be responsible for the transformation of cells, anticancer reagents that react effectively and sequence selectively with target RNAs having a point mutation are highly desired. In this study, we developed novel photo-cross-linking oligodeoxyribonucleotides ((pro)PCA-ODNs) that had a caged α-chloroaldehyde group conjugated to a 2-methylpropanediyl backbone ((pro)PCA) in the middle of the strand. A kinetic study of the deprotection reaction of (pro)PCA-ODN revealed that the bis(2-nitrobenzyl)acetal group was completely deprotected within 1 min. Photo-cross-linking studies of (pro)PCA-ODNs with complementary oligoribonucleotides (ORNs) revealed that (pro)PCA-ODNs reacts efficiently and selectively with the target ORNs that have an adenosine or cytidine residue at a frontal position of the (pro)PCA residue without adverse effects of bases adjacent to the mutation site.
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Affiliation(s)
- Yuta Sugihara
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology , Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuki Nakata
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology , Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Asako Yamayoshi
- The Hakubi Center for Advanced Research, Kyoto University , Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Akira Murakami
- Kyoto Pharmaceutical University , Misasagi-Shichonocho 1, Yamashina-ku, Kyoto 607-8412, Japan
| | - Akio Kobori
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology , Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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9
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Sakamoto T, Ooe M, Fujimoto K. Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3-Cyanovinylcarbazole Nucleoside. Bioconjug Chem 2015; 26:1475-8. [PMID: 26190032 DOI: 10.1021/acs.bioconjchem.5b00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside ((CNV)K), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s(-1)) is comparable to that of (CNV)K toward T paired with A (k = 3.5 s(-1)). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Minako Ooe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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10
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Stadler JM, Stafforst T. Pyrene chromophores for the photoreversal of psoralen interstrand crosslinks. Org Biomol Chem 2015; 12:5260-6. [PMID: 24922335 DOI: 10.1039/c4ob00603h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Applying psoralen interstrand crosslinks for the photoactivation of nucleic acids is a new concept. To find chromophores that can efficiently stimulate crosslink repair we screened several pyrenes and appended them to peptide nucleic acids for their site-selective addressing. Even though pyrenes conjugated to uracil revealed desirable spectroscopic properties they were not effective in crosslink reversal. In contrast, bare pyrenes are well suitable for crosslink repair with 350 nm light showing an uncaging efficiency similar to classical photocaging groups.
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Affiliation(s)
- Jens M Stadler
- Interfaculty Institute of Biochemistry, Auf der Morgenstelle 15. and University of Tübingen, 72076 Tübingen, Germany.
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11
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Sakamoto T, Tanaka Y, Fujimoto K. DNA photo-cross-linking using 3-cyanovinylcarbazole modified oligonucleotide with threoninol linker. Org Lett 2015; 17:936-9. [PMID: 25654759 DOI: 10.1021/acs.orglett.5b00035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
3-Cyanovinylcarbazole modified D-threoninol ((CNV)D) was incorporated in oligodeoxyribonucleotide and tested for a photo-cross-linking reaction with complementary oligodeoxyribonucleotide. The photoreactivity was 1.8- to 8-fold greater than that of 3-cyanovinylcarbazole modified deoxyribose ((CNV)K) previously reported. From the results of melting analysis and circular dichroism spectroscopy of the duplexes, the relatively flexible structure of (CNV)D compared with (CNV)K might be advantageous for [2 + 2] photocycloaddition between the cyanovinyl group on the (CNV)D and pyrimidine base in the complementary strand.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, ‡Research Center for Bio-architecture, Japan Advanced Institute of Science and Technology , 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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12
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Kusano S, Haruyama T, Ishiyama S, Hagihara S, Nagatsugi F. Development of the crosslinking reactions to RNA triggered by oxidation. Chem Commun (Camb) 2014; 50:3951-4. [DOI: 10.1039/c3cc49463b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this paper, we have reported a novel oxidation triggered crosslinking nucleobase ATVP (1) and demonstrated that the oxidized form ASVP (2) showed a very fast and selective crosslinking reaction to cytosine in RNA.
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Affiliation(s)
- Shuhei Kusano
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Takuya Haruyama
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Shogo Ishiyama
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
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13
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Sakamoto T, Shigeno A, Ohtaki Y, Fujimoto K. Photo-regulation of constitutive gene expression in living cells by using ultrafast photo-cross-linking oligonucleotides. Biomater Sci 2014; 2:1154-1157. [DOI: 10.1039/c4bm00117f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We clearly demonstrated that photoreactive AS-ODNs having CNVK act as effective photo-regulators of constitutive GFP gene expression in living cells with only 10 s of 366 nm irradiation.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
| | - Atsuo Shigeno
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
| | - Yuichi Ohtaki
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
| | - Kenzo Fujimoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
- Research Center for Bio-Architecture
- Japan Advanced Institute of Science and Technology
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14
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Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T. Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping. J Am Chem Soc 2013; 135:16161-7. [DOI: 10.1021/ja406965f] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Tadashi Tsukaguchi
- Faculty
of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
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15
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Fujimoto K, Kishi S, Sakamoto T. Geometric Effect on the Photocrosslinking Reaction between 3-Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex. Photochem Photobiol 2013; 89:1095-9. [DOI: 10.1111/php.12118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/16/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Satomi Kishi
- School of Materials Science; Japan Advanced Institute of Science and Technology; Nomi-shi; Japan
| | - Takashi Sakamoto
- School of Materials Science; Japan Advanced Institute of Science and Technology; Nomi-shi; Japan
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16
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Vieregg J, Nelson HM, Stoltz BM, Pierce NA. Selective nucleic acid capture with shielded covalent probes. J Am Chem Soc 2013; 135:9691-9. [PMID: 23745667 PMCID: PMC3703666 DOI: 10.1021/ja4009216] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Indexed: 11/29/2022]
Abstract
Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2-3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1-2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo).
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Affiliation(s)
- Jeffrey
R. Vieregg
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Hosea M. Nelson
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Brian M. Stoltz
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Niles A. Pierce
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
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17
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Fujimoto K, Yoshinaga H, Yoshio Y, Sakamoto T. Quick and reversible photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside in a DNA triplex. Org Biomol Chem 2013; 11:5065-8. [DOI: 10.1039/c3ob40915e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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