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Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Stockholm University.
Beijing Institute of Technology.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-6706-651X
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2011 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, 10976-10982 p.Article in journal (Refereed) Published
Abstract [en]

Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

Place, publisher, year, edition, pages
2011. Vol. 115, no 37, 10976-10982 p.
Keyword [en]
National Category
Chemical Sciences
URN: urn:nbn:se:kth:diva-33526DOI: 10.1021/jp204128kISI: 000294875100020ScopusID: 2-s2.0-80052856745OAI: diva2:415911
QC 20111010Available from: 2011-05-09 Created: 2011-05-09 Last updated: 2011-10-17Bibliographically approved
In thesis
1. Theoretical studies on photophysics and photochemistry of DNA
Open this publication in new window or tab >>Theoretical studies on photophysics and photochemistry of DNA
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels.

Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments.

We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2010. 76 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2011:15
National Category
Theoretical Chemistry
Research subject
SRA - Molecular Bioscience
urn:nbn:se:kth:diva-33531 (URN)978-91-7415-977-6 (ISBN)
Public defence
2011-06-14, FA32, AlbaNova University Center, Roslagstullsbacken 21,, Stockholm, 10:00 (English)
QC 20110530Available from: 2011-05-30 Created: 2011-05-09 Last updated: 2011-05-30Bibliographically approved

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Ai, Yue-JieHua, Wei-JieLuo, Yi
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