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Jian Y, Maximowitsch E, Liu D, Adhikari S, Li L, Domratcheva T. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. Chemistry 2017; 23:7526-7537. [PMID: 28370554 DOI: 10.1002/chem.201700045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,School of Chemistry & Chemical Engineering, Shaanxi Normal University (SNNU), No. 620, West Chang'an Avenue, Xi'an, Shaanxi, 710119, P. R. China
| | - Egle Maximowitsch
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
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Winnacker M, Kool ET. Artificial genetic sets composed of size-expanded base pairs. Angew Chem Int Ed Engl 2013; 52:12498-508. [PMID: 24249550 PMCID: PMC5497059 DOI: 10.1002/anie.201305267] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Indexed: 12/23/2022]
Abstract
We describe in this Minireview the synthesis, properties, and applications of artificial genetic sets built from base pairs that are larger than the natural Watson-Crick architecture. Such designed systems are being explored by several research groups to investigate basic chemical questions regarding the functions of the genetic information storage systems and thus of the origin and evolution of life. For example, is the terrestrial DNA structure the only viable one, or can other architectures function as well? Working outside the constraints of purine-pyrimidine geometry provides more chemical flexibility in design, and the added size confers useful properties such as high binding affinity and helix stability as well as fluorescence. These features are useful for the investigation of fundamental biochemical questions as well as in the development of new biotechnological, biomedical, and nanostructural tools and methods.
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Affiliation(s)
- Malte Winnacker
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
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Winnacker M, Kool ET. Künstliche genetische Systeme bestehend aus vergrößerten Basenpaaren. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305267] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Jissy AK, Konar S, Datta A. Molecular Switching Behavior in Isosteric DNA Base Pairs. Chemphyschem 2013; 14:1219-26. [DOI: 10.1002/cphc.201201083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 12/22/2022]
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Liu D, Zhou Y, Pu J, Li L. Expanding the horizon of the thymine isostere biochemistry: unique cyclobutane dimers formed by photoreaction between a thymine and a toluene residue in the dinucleotide framework. Chemistry 2012; 18:7823-33. [PMID: 22588824 PMCID: PMC3374913 DOI: 10.1002/chem.201200816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Indexed: 11/07/2022]
Abstract
Substituted toluenyl groups are considered as close isosteres of the thymine residue. They can be recognized by DNA polymerases as if they were thymine. These toluene derivatives are generally inert toward radical additions, including the [2+2] photo-cycloadditions, due to the stable structure of the aromatic ring and are usually used as solvents for radical reactions. Surprisingly, after incorporating toluene into the dinucleotide framework, we found that the UV excited thymine residue readily dimerizes with the toluenyl moiety through a [2+2] photo-addition reaction. Furthermore, the reaction site on the toluenyl moiety is not the C5=C6 bond, as commonly observed in cyclobutane pyrimidine dimers, but the C4=C5 or C3=C4 instead. Such a reaction pattern suggests that in the stacked structure, it is one of these bonds, not the C5=C6, that is close to the thymine C5=C6 bond. A similar structural feature is found in DNA duplex with a thymine replaced by a 2,4-difluorotoluene. Our results argue that although the substituted toluenyl moieties closely mimic the size and shape of the thymine residue, their more hydrophobic nature determines that they stack on DNA bases differently from the natural thymine residue and likely cause local conformational changes in duplex DNA.
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Affiliation(s)
- Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
| | - Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202 (USA)
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Urata H, Yamaguchi E, Funai T, Matsumura Y, Wada SI. Incorporation of thymine nucleotides by DNA polymerases through T-Hg(II)-T base pairing. Angew Chem Int Ed Engl 2011; 49:6516-9. [PMID: 20602391 DOI: 10.1002/anie.201002142] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hidehito Urata
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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Urata H, Yamaguchi E, Funai T, Matsumura Y, Wada SI. Incorporation of Thymine Nucleotides by DNA Polymerases through T-HgII-T Base Pairing. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002142] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zhang D, Domke KF, Pettinger B. Tip-Enhanced Raman Spectroscopic Studies of the Hydrogen Bonding between Adenine and Thymine Adsorbed on Au (111). Chemphyschem 2010; 11:1662-5. [DOI: 10.1002/cphc.200900883] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Pfaff DA, Clarke KM, Parr TA, Cole JM, Geierstanger BH, Tahmassebi DC, Dwyer TJ. Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding? J Am Chem Soc 2008; 130:4869-78. [PMID: 18341343 DOI: 10.1021/ja7103608] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.
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Affiliation(s)
- Danielle A Pfaff
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, USA
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Somoza A, Chelliserrykattil J, Kool ET. The roles of hydrogen bonding and sterics in RNA interference. Angew Chem Int Ed Engl 2007; 45:4994-7. [PMID: 16802393 DOI: 10.1002/anie.200601311] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alvaro Somoza
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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Somoza A, Chelliserrykattil J, Kool ET. The Roles of Hydrogen Bonding and Sterics in RNA Interference. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200601311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Matray TJ, Kool ET. Selective and Stable DNA Base Pairing without Hydrogen Bonds. J Am Chem Soc 1998; 120:6191-6192. [PMID: 20852721 PMCID: PMC2939750 DOI: 10.1021/ja9803310] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tracy J Matray
- Department of Chemistry, University of Rochester Rochester, New York 14627
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