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Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.ORCID-id: 0000-0003-0007-0394
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2010 (Engelska)Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 44, s. 14096-14102Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.

Ort, förlag, år, upplaga, sidor
2010. Vol. 114, nr 44, s. 14096-14102
Nyckelord [en]
DEFICIENT HUMAN-CELLS, MOLECULAR-DYNAMICS, CRYSTAL-STRUCTURE, MAMMALIAN-CELLS, REPAIR, PHOTOLYASE, THYMINE, PHOTOPRODUCTS, MECHANISM, PATHWAYS
Nationell ämneskategori
Kemi
Identifikatorer
URN: urn:nbn:se:kth:diva-27071DOI: 10.1021/jp107873wISI: 000283703400022Scopus ID: 2-s2.0-78149250709OAI: oai:DiVA.org:kth-27071DiVA, id: diva2:376381
Anmärkning
QC 20101210Tillgänglig från: 2010-12-10 Skapad: 2010-12-06 Senast uppdaterad: 2017-12-11Bibliografiskt granskad
Ingår i avhandling
1. Theoretical studies on photophysics and photochemistry of DNA
Öppna denna publikation i ny flik eller fönster >>Theoretical studies on photophysics and photochemistry of DNA
2010 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH Royal Institute of Technology, 2010. s. 76
Serie
Trita-BIO-Report, ISSN 1654-2312 ; 2011:15
Nationell ämneskategori
Teoretisk kemi
Forskningsämne
SRA - Molekylär biovetenskap
Identifikatorer
urn:nbn:se:kth:diva-33531 (URN)978-91-7415-977-6 (ISBN)
Disputation
2011-06-14, FA32, AlbaNova University Center, Roslagstullsbacken 21,, Stockholm, 10:00 (Engelska)
Opponent
Handledare
Anmärkning
QC 20110530Tillgänglig från: 2011-05-30 Skapad: 2011-05-09 Senast uppdaterad: 2011-05-30Bibliografiskt granskad

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