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Itaya R, Idei W, Nakamura T, Nishihara T, Kurihara R, Okamoto A, Tanabe K. Changes of C≡C Triple Bond Vibration that Disclosed Non-Canonical Cytosine Protonation in i-Motif-Forming Oligodeoxynucleotides. ACS OMEGA 2021; 6:31595-31604. [PMID: 34869984 PMCID: PMC8637604 DOI: 10.1021/acsomega.1c04074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/05/2021] [Indexed: 05/09/2023]
Abstract
Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative (PC) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in PC in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.
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Affiliation(s)
- Ryota Itaya
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Wakana Idei
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Takashi Nakamura
- Faculty
of Bioscience, Nagahama Institute of Bio-Science
and Technology, 1266
Tamura-cho, Nagahama 526-0829, Japan
| | - Tatsuya Nishihara
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Ryohsuke Kurihara
- School
of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Akimitsu Okamoto
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Kazuhito Tanabe
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
- . Phone: +81-42-759-6229. Fax: +81-42-759-6493
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Crystal Structure, Raman Spectroscopy and Dielectric Properties of New Semiorganic Crystals Based on 2-Methylbenzimidazole. CRYSTALS 2019. [DOI: 10.3390/cryst9110573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
New single crystals, based on 2-methylbenzimidazole (MBI), of MBI-phosphite (C16H24N4O7P2), MBI-phosphate-1 (C16H24N4O9P2), and MBI-phosphate-2 (C8H16N2O9P2) were obtained by slow evaporation method from a mixture of alcohol solution of MBI crystals and water solution of phosphorous or phosphoric acids. Crystal structures and chemical compositions were determined by single crystal X-ray diffraction (XRD) analysis and confirmed by XRD of powders and elemental analysis. Raman spectroscopy of new crystals evidences the presence in crystals of MBI-, H3PO3-, or H3PO4- and water molecules. Dielectric properties of crystals reveal strong increase and low frequency dispersion of dielectric constant and losses at heating, indicating the appearance of proton conductivity. At low temperatures in MBI-phosphate-2, an increase of dielectric constant analogous to quantum paraelectric state is observed.
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Zhang R, Hong DL, He XT, Chen FH, Jiao J, Zhao XQ, Li X, Luo YH, Sun BW. Protonation-induced ligand distortion of spin-crossover complexes. INORG CHEM COMMUN 2019. [DOI: 10.1016/j.inoche.2018.09.005] [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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Effects of protonation on the optical and photophysical properties of ReCl(CO)3(dppz–TAA) and [Ru(bpy)2(dppz–TAA)]2+. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Monczak K, Peuntinger K, Sorsche D, Heinemann FW, Guldi DM, Rau S. Synthesis and Characterization of a Trisheteroleptic RuII-Based Molecular Switch. Chemistry 2014; 20:15426-33. [DOI: 10.1002/chem.201403418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Indexed: 11/07/2022]
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Meyer-Ilse J, Bauroth S, Bräutigam M, Schmitt M, Popp J, Beckert R, Rockstroh N, Pilz TD, Monczak K, Heinemann FW, Rau S, Dietzek B. Modified bibenzimidazole ligands as spectator ligands in photoactive molecular functional Ru-polypyridine units? Implications from spectroscopy. Dalton Trans 2014; 43:17659-65. [DOI: 10.1039/c4dt01399a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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