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Sethi S, Zumila H, Watanabe Y, Mo J, Fujimoto K. UltraFast PhotoInduced double duplex DNA invasion into a 400-mer dsDNA target. Bioorg Med Chem Lett 2024; 98:129597. [PMID: 38154604 DOI: 10.1016/j.bmcl.2023.129597] [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] [Received: 09/10/2023] [Revised: 12/13/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Natural DNA restriction enzymes bind duplex DNA with high affinity at multiple sites; however, for some of the artificial chemical-based restriction moieties, invasion of the double-strand for efficient cleavage is an obstacle. We have previously reported photo-induced double-duplex invasion (pDDI) using 3-cyanovinylcarbazole (K)-containing probes for both the target strands that photo-crosslink with pyrimidine bases in a sequence-specific manner on both the strands, stabilizing the opened double-strand for cleavage. The drawback of the pDDI was low efficiency due to inter-probe cross-linking, solved by the inclusion of 5-cyano-uridine at -1 position on the complimentary strand with respect to K in both probes. Although this led to reduced inter-probe cross-linking, the pDDI efficiency was still low. RESULTS Here, we report that inter-probe cross-linking and intra-probe cross-linking of a single probe is also leading to reduced pDDI efficiency. We addressed this problem by designing DDI probes to inhibit both inter-probe and intra-probe cross-linking. CONCLUSION Based on the new design of pDDI probe with 5-cyano uridine led to a drastic increase in the efficiency of pDDI in (400-mer) double-stranded DNA with only 1 s of photo-irradiation.
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Affiliation(s)
- Siddhant Sethi
- Biofunctional Medical Engineering Research Area, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Hailili Zumila
- Biofunctional Medical Engineering Research Area, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Yasuha Watanabe
- Biofunctional Medical Engineering Research Area, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Junling Mo
- Biofunctional Medical Engineering Research Area, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
| | - Kenzo Fujimoto
- Biofunctional Medical Engineering Research Area, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan.
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2
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Chao D, Xu X, Miao Y, Yang L, Gao Q, Xu R, Tian Y, Zhao Y, Du Y, Han D. Covalent stabilization of DNA nanostructures on cell membranes for efficient surface receptor-mediated labeling and function regulations. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1413-5] [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]
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3
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Cadoni E, Pennati F, Muangkaew P, Elskens J, Madder A, Manicardi A. Synthesis and structure–activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown. RSC Chem Biol 2022; 3:1129-1143. [PMID: 36128507 PMCID: PMC9428673 DOI: 10.1039/d2cb00095d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
After optimization of interstrand crosslink reaction between furan-containing peptide nucleic acids and target oligonucleotides, the reversibility of the formed product is exploited for the pull-down of a sequence of interest from cell lysates.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Francesca Pennati
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, 10330 Bangkok, Thailand
| | - Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
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4
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Watanabe Y, Fujimoto K. Complete Photochemical Regulation of 8-17 DNAzyme Activity by Using Reversible DNA Photo-crosslinking. Chembiochem 2020; 21:3244-3248. [PMID: 32596920 DOI: 10.1002/cbic.202000227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/28/2020] [Indexed: 12/15/2022]
Abstract
The regulation of DNAzyme activity is an important problem for its in vivo applications. We achieved photochemical regulation of DNAzyme activity by using reversible DNA photo-crosslinking of 3-cyanovinylcarbazole (CNV K). The ODN containing CNV K photo-crosslinked to a pyrimidine base in the complementary strand after a few seconds of photoirradiation, and its photoadduct was split by photoirradiation of another wavelength. The activity of photo-crosslinked DNAzyme with CNV K was completely inhibited (OFF state). In contrast, after 312 nm irradiation, DNAzyme activity was recovered upon addition of a substrate strand (ON state). In addition, the photo-crosslinked DNAzyme is prone to enzymatic digestion by exonuclease. This photochemical OFF to ON switching with reversible DNA photo-crosslinking was regulated at the desired time and position; therefore, it might be possible to use it for in vivo application.
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Affiliation(s)
- Yasuha Watanabe
- School of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Kenzo Fujimoto
- School of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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5
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Wang Y, Zhao H, Zhou Q, Dai X, Liu K, Song D, Su H. Monitoring the Structure-Dependent Reaction Pathways of Guanine Radical Cations in Triplex DNA: Deprotonation Versus Hydration. J Phys Chem B 2019; 123:2853-2863. [PMID: 30834754 DOI: 10.1021/acs.jpcb.9b00608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exposure of DNA to one-electron oxidants leads initially to the formation of guanine radical cations (G•+), which may degrade by deprotonation or hydration and ultimately cause strand breaks or 8-oxoG lesions. As the structure is dramatically changed by binding of the third strand in the major groove of the target duplex, it makes the triplex an interesting DNA structure to be examined and compared with the duplex on the G•+ degradation pathways. Here, we report for the first time the time-resolved spectroscopy study on the G•+ reaction dynamics in triplex DNA together with the Fourier transform infrared characterization of steady-state products, from which structural effects on the reactivity of G•+ are unraveled. For an antiparallel triplex-containing GGC motif, G•+ mainly suffers from fast deprotonation (9.8 ± 0.2) × 106 s-1, featuring release of both N1-H and N2-H of G in the third strand directly into bulk water. The much faster and distinct deprotonation behavior compared to the duplex should be related to long-resident water spines in the third strand. The G•+ hydration product 8-oxoG is negligible for an antiparallel triplex; instead, the 5-HOO-(G-H) hydroperoxide formed after G•+ deprotonation is identified by its vibrational marker band. In contrast, in a parallel triplex (C+GC), the deprotonation of G•+ occurs slowly (6.0 ± 0.3) × 105 s-1 with the release of N1-H, while G•+ hydration becomes the major pathway with yields of 8-oxoG larger than in the duplex. The increased positive charge brought by the third strand makes the G radical in the parallel triplex sustain more cation character and prone for hydration. These results indicate that non-B DNA (triplex) plays an important role in DNA damage formation and provide mechanistic insights to rationalize why triplex structures might become hot spots for mutagenesis.
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Affiliation(s)
- Yinghui Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Qian Zhou
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Xiaojuan Dai
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Kunhui Liu
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Di Song
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Hongmei Su
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
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6
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Cha Y, Choi Y, Choi H, Park H, Kim JH, Jung JH. Reversible cyanovinylcarbazole-based polymer gel via photo-cross-linking reaction. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1392021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yubin Cha
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University , Jinju, Korea
| | - Yeonweon Choi
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University , Jinju, Korea
| | - Heekyoung Choi
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University , Jinju, Korea
| | - Hyesong Park
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University , Jinju, Korea
| | - Ju Hyun Kim
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University , Jinju, Korea
| | - Jong Hwa Jung
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University , Jinju, Korea
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7
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Nakamura S, Kawabata H, Fujimoto K. Double duplex invasion of DNA induced by ultrafast photo-cross-linking using 3-cyanovinylcarbazole for antigene methods. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc01746d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
New photoresponsive antigene probes containingCNVK andCNU have a high double-duplex invasion capability upon photoirradiation because of the inhibition of photo-cross-linking between the probes.
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Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| | - Hayato Kawabata
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
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8
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Carrette LLG, Gyssels E, De Laet N, Madder A. Furan oxidation based cross-linking: a new approach for the study and targeting of nucleic acid and protein interactions. Chem Commun (Camb) 2016; 52:1539-54. [PMID: 26679922 DOI: 10.1039/c5cc08766j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The coming of age story of furan oxidation cross-linking.
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Affiliation(s)
- L. L. G. Carrette
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - E. Gyssels
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - N. De Laet
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - A. Madder
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
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9
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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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10
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Gyssels E, Carrette LLG, Vercruysse E, Stevens K, Madder A. Triplex crosslinking through furan oxidation requires perturbation of the structured triple-helix. Chembiochem 2015; 16:651-8. [PMID: 25630588 DOI: 10.1002/cbic.201402602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 01/08/2023]
Abstract
Short oligonucleotides can selectively recognize duplexes by binding in the major groove thereby forming triplexes. Based on the success of our recently developed strategy for furan-based crosslinking in DNA duplexes, we here investigated for the first time the use of the furan-oxidation crosslink methodology for the covalent locking of triplex structures by an interstrand crosslink. It was shown that in a triplex context, although crosslinking yields are surprisingly low (to nonexistent) when targeting fully complementary duplexes, selective crosslinking can be achieved towards mismatched duplex sites at the interface of triplex to duplex structures. We show the promising potential of furan-containing probes for the selective detection of single-stranded regions within nucleic acids containing a variety of structural motifs.
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Affiliation(s)
- Ellen Gyssels
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Gent (Belgium)
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11
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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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