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Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
2007 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, 2351-2361 p.Article in journal (Refereed) Published
Abstract [en]

The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C−N and C−C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

Place, publisher, year, edition, pages
2007. Vol. 111, no 12, 2351-2361 p.
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-92096DOI: 10.1021/jp0676383ISI: 000245083600013PubMedID: 17388321OAI: oai:DiVA.org:uu-92096DiVA: diva2:165052
Available from: 2004-09-03 Created: 2004-09-03 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Quantum Chemical Studies of Protein-Bound Chromophores, UV-Light Induced DNA Damages, and Lignin Formation
Open this publication in new window or tab >>Quantum Chemical Studies of Protein-Bound Chromophores, UV-Light Induced DNA Damages, and Lignin Formation
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin.

The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.

The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed.

DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.

Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2004. 81 p.
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 1010
Keyword
Quantum chemistry, quantum chemistry, calculations, density functional theory, excited states, photochemistry, chromophores, absorption spectra, bathochromic shift, isomerization, UV radiation, DNA damages, cycloaddition reactions, photoenzymic repair, electron transfer, lignin, polymerization, phenoxy radicals, dilignols, Kvantkemi
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-4531 (URN)91-554-6030-5 (ISBN)
Public defence
2004-09-30, Siegbahnsalen, Ångströmlaboratoriet, Uppsala, 13:15
Opponent
Supervisors
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
2. Theoretical Photochemistry: Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts
Open this publication in new window or tab >>Theoretical Photochemistry: Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2008. 61 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 394
Keyword
Quantum chemistry, Quantum Chemistry, Halogenated Arenes, Phytochromobilin, Phytochrome, Ruthenium, 6-4 photoadducts, Photochemistry, Kvantkemi
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-8469 (URN)978-91-554-7096-8 (ISBN)
Public defence
2008-03-19, Häggsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2011-03-14Bibliographically approved

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