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Shemesh Y, Yavin E. PNA-Rose Bengal Conjugates as Efficient DNA Photomodulators. Bioconjug Chem 2015; 26:1916-22. [PMID: 26263421 DOI: 10.1021/acs.bioconjchem.5b00406] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Selective photoinduced modulation of DNA may provide a powerful therapeutic tool allowing spatial and temporal control of the photochemical reaction. We have explored the photoreactivity of peptide nucleic acid (PNA) conjugates that were conjugated to a highly potent photosensitizer, Rose Bengal (RB). In addition, a short PEGylated peptide (K-PEG8-K) was conjugated to the C-terminus of the PNA to improve its water solubility. A short irradiation (visible light) of PNA conjugates with a synthetic DNA resulted in highly efficient photomodulation of the DNA as evidenced by polyacrylamide gel electrophoresis (PAGE). In addition, a PNA-RB conjugate replacing K-PEG8-K with four l-glutamic acids (E4) was found to be photoinactive. Irradiation of active PNA-RB conjugates with synthetic DNA in D20 augments the photoactivity; supporting the involvement of singlet oxygen. PAGE, HPLC, and MALDI-TOF analyses indicate that PNA-DNA photo-cross-linking is a significant pathway in the observed photoreactivity. Selective photo-cross-linking of such PNA-RB conjugates may be a novel approach to selective photodynamic therapy (sPDT) as such molecules would be sequence-specific, cell-permeable, and photoactivated in the visible region.
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Affiliation(s)
- Yossi Shemesh
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
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2
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Kobori A, Yamayoshi A, Murakami A. Synthesis of Oligonucleotides Containing 4,5',8-Trimethylpsoralen at the 2'-O Position and Their Cross-Linking Properties with RNAs. ACTA ACUST UNITED AC 2014; 58:5.15.1-15. [PMID: 25199638 DOI: 10.1002/0471142700.nc0515s58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
4,5',8-Trimethylpsoralen-conjugated oligonucleotides have been used in the study of photo-cross-linking with target oligonucleotides and in the field of the photodynamic therapy. This unit describes synthetic procedures for oligonucleotides using 2'-O-methylphosphoramidite units and an adenosine phosphoramidite unit containing a 4,5',8-trimethylpsoralen derivative attached at the 2' position of an adenosine sugar moiety via an ethoxymethylene linkage. Procedures for obtaining the photo-cross-linking efficiency of 2'-O-methyloligonucleotides containing a 4,5',8-trimethylpsoralen derivative with a target oligonucleotide under UV irradiation conditions are also described, together with the procedure for preparation of (32)P-radiolabeled RNA.
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Affiliation(s)
- Akio Kobori
- Kyoto Institute of Technology, Graduate School of Science and Technology, Department of Biomolecular Engineering, Matsugasaki, Sakyo-ku, Kyoto, Japan
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3
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Nowak-Karnowska J, Chebib Z, Milecki J, Franzen S, Skalski B. Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine. Chembiochem 2014; 15:2045-9. [PMID: 25111776 DOI: 10.1002/cbic.201402182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 02/03/2023]
Abstract
The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine ((FS) U), in the sequence context 5'-A(FS) UA-3' and incorporated into a synthetic oligonucleotide either at its 3'- or 5'-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.
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Affiliation(s)
- Joanna Nowak-Karnowska
- Centre of Advanced Technology, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland)
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4
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Bibal B, Mongin C, Bassani DM. Template effects and supramolecular control of photoreactions in solution. Chem Soc Rev 2014; 43:4179-98. [DOI: 10.1039/c3cs60366k] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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5
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Feng L, Sha R, Seeman NC, Chaikin PM. Topological interaction by entangled DNA loops. PHYSICAL REVIEW LETTERS 2012; 109:188301. [PMID: 23215338 PMCID: PMC3758925 DOI: 10.1103/physrevlett.109.188301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 06/01/2023]
Abstract
We have discovered a new type of interaction between micro- or nanoscale particles that results from the entanglement of strands attached to their surfaces. Self-complementary DNA single strands on a particle can hybridize to form loops. A similar proximal particle can have its loops catenate with those of the first. Unlike conventional thermodynamic interparticle interactions, the catenation interaction is strongly history and protocol dependent, allowing for nonequilibrium particle assembly. The interactions can be controlled by an interesting combination of forces, temperature, light sensitive cross-linking and enzymatic unwinding of the topological links. This novel topological interaction may lead to new materials and phenomena such as particles strung on necklaces, confined motions on designed contours and surfaces, and colloidal Olympic gels.
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Affiliation(s)
- Lang Feng
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
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6
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Kobori A, Yamauchi T, Nagae Y, Yamayoshi A, Murakami A. Novel photoresponsive cross-linking oligodeoxyribonucleotides having a caged α-chloroaldehyde. Bioorg Med Chem 2012; 20:5071-6. [PMID: 22871262 DOI: 10.1016/j.bmc.2012.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/13/2012] [Accepted: 07/13/2012] [Indexed: 01/06/2023]
Abstract
We have developed photoresponsive cross-linking oligodeoxyribonucleotides (ODNs) for sequence-selective interstrand covalent bond formation toward target nucleotides. A phosphoramidite derivative of α-chloroaldehyde whose carbonyl group was converted to a bis(2-nitrobenzyl)acetal group was prepared for the synthesis of photoresponsive α-chloroaldehyde (PCA)-conjugated ODN. The bis(2-nitrobenzyl)acetal group of a PCA-thymidine conjugate was completely removed by UV irradiation at 365 nm (400 mW/cm(2)) for 1 min. Photo-cross-linking studies revealed that PCA-ODN selectively reacted with the target nucleotides having an adenine or a cytosine moiety at the frontal position of the α-chloroaldehyde group.
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Affiliation(s)
- 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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7
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Pasternak K, Pasternak A, Gupta P, Veedu RN, Wengel J. Photoligation of self-assembled DNA constructs containing anthracene-functionalized 2'-amino-LNA monomers. Bioorg Med Chem 2011; 19:7407-15. [PMID: 22079866 DOI: 10.1016/j.bmc.2011.10.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/13/2011] [Accepted: 10/17/2011] [Indexed: 11/20/2022]
Abstract
Efficient synthesis of a novel anthracene-functionalized 2'-amino-LNA phosphoramidite derivative is described together with its incorporation into oligodeoxynucleotides. Two DNA strands with the novel 2'-N-anthracenylmethyl-2'-amino-LNA monomers can be effectively cross-linked by photoligation at 366 nm in various types of DNA constructs. Successful application of three differently functionalized 2'-amino-LNA monomers in self-assembled higher ordered structures for simultaneous cross-linking and monitoring of assembly formation is furthermore demonstrated.
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Affiliation(s)
- Karol Pasternak
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Tanabe K, Matsumoto E, Ito T, Nishimoto SI. Radiolytic cyclization of stem-and-loop structured oligodeoxynucleotide with neighboring arrangement of α,ω-bis-disulfides. Org Biomol Chem 2010; 8:4837-42. [PMID: 20820660 DOI: 10.1039/c0ob00275e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Upon X-ray irradiation of hypoxic aqueous solution, modified oligodeoxynucleotides (ODNs) bearing a pair of disulfides at both ends of the strand that forms a stem-and-loop structure with a neighboring arrangement of α,ω-bis-disulfides underwent efficient cyclization via an intramolecular exchange reaction at the disulfide moieties with a multiple turnover process. Mechanistic studies revealed that hydrogen atoms generated in the radiolysis of water are key active species initiating a chain reaction to produce cyclic ODN disulfides, in which addition of hydrogen atom results in dissociation of the original disulfide bond to generate a thiyl radical intermediate as the chain carrier for the succeeding disulfide exchange into cyclization. The properties were also assessed for the resultant cyclic ODN disulfide that has several favorable features for use in the transcriptional decoy strategy. The cyclic ODN disulfides produced by the present radiolytic method showed high thermal stability, resistance to nuclease, and high binding activity to a representative transcriptional factor of nuclear factor κB.
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Affiliation(s)
- Kazuhito Tanabe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan.
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9
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Yoshimura Y, Okada H, Fujimoto K. Photoreversible DNA end capping for the formation of hairpin structures. Org Biomol Chem 2010; 8:1523-6. [PMID: 20237661 DOI: 10.1039/b924989c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a photoreversible DNA end capping via 3-cyanovinylcarbazole nucleoside. Doubly end-capped oligodeoxynucleotide (ODN) exhibits increased stability against snake venom phosphodiesterase and shows high thermal stability.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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10
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Mukae M, Ihara T, Tabara M, Jyo A. Anthracene–DNA conjugates as building blocks of designed DNA structures constructed by photochemical reactions. Org Biomol Chem 2009; 7:1349-54. [DOI: 10.1039/b821869b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Ogino M, Taya Y, Fujimoto K. Highly selective detection of 5-methylcytosine using photochemical ligation. Chem Commun (Camb) 2008:5996-8. [PMID: 19030564 DOI: 10.1039/b813677g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-cyanovinyl-2'-deoxyuridine ((C)U) with high selectivity and present a new methylation detection method using a photoligation-based DNA chip assay.
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Affiliation(s)
- Masayuki Ogino
- Japan Science and Technology Agency, Ishikawa, 923-1211, Japan
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12
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Ogasawara S, Yoshimura Y, Hayashi M, Saito I, Fujimoto K. Highly Efficient Method for Constructing a Single-Stranded Comb-Like Oligonucleotide via Reversible Photocrosslinking. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Balaz M, Li BC, Jockusch S, Ellestad GA, Berova N. Tetraarylporphyrin as a selective molecular cap for non-Watson-Crick guanine-adenine base-pair sequences. Angew Chem Int Ed Engl 2007; 45:3530-3. [PMID: 16625664 DOI: 10.1002/anie.200504431] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Milan Balaz
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA.
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Ogino M, Fujimoto K. Photochemical synthesis of R-shaped DNA toward DNA recombination and processing in vitro. Angew Chem Int Ed Engl 2007; 45:7223-6. [PMID: 17009378 DOI: 10.1002/anie.200603161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Masayuki Ogino
- School of Materials Science, Japan Advanced Institute of Science and Technology, Asahidai, Nomi, Ishikawa 923-1292, Japan
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15
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Yoshimura Y, Noguchi Y, Fujimoto K. Highly sequence specific RNA terminal labeling by DNA photoligation. Org Biomol Chem 2006; 5:139-42. [PMID: 17164918 DOI: 10.1039/b615715g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report the nonenzymatic terminal labeling of oligoribonucleotide (ORN) by using template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine ((CV)U) with high selectivity.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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16
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Ogino M, Fujimoto K. Photochemical Synthesis of R-Shaped DNA toward DNA Recombination and Processing In Vitro. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200603161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Yoshimura Y, Noguchi Y, Sato H, Fujimoto K. Template-directed DNA photoligation in rapid and selective detection of RNA point mutations. Chembiochem 2006; 7:598-601. [PMID: 16502477 DOI: 10.1002/cbic.200500534] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Balaz M, Li BC, Jockusch S, Ellestad GA, Berova N. Tetraarylporphyrin as a Selective Molecular Cap for Non-Watson–Crick Guanine–Adenine Base-Pair Sequences. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Yoshimura Y, Fujimoto K. Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside. CHEM LETT 2006. [DOI: 10.1246/cl.2006.386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Fujimoto K, Matsuda S, Yoshimura Y, Matsumura T, Hayashi M, Saito I. Site-specific transition of cytosine to uracil via reversible DNA photoligation. Chem Commun (Camb) 2006:3223-5. [PMID: 17028750 DOI: 10.1039/b605289d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report that deamination coupled with 5-carboxyvinyldeoxyuridine-mediated photobranching causes the heat-induced transition of cytosine to uracil with high efficiency without any side reaction.
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Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan.
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