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Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Beijing Normal University.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Beijing Normal University.
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2011 (English)In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 10, 2366-2377 p.Article in journal (Refereed) Published
Abstract [en]

We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.

Place, publisher, year, edition, pages
2011. Vol. 111, no 10, 2366-2377 p.
Keyword [en]
DNA oligonucleotides, DFT, excited states
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-33578DOI: 10.1002/qua.22524ISI: 000289994300023Scopus ID: 2-s2.0-79955381712OAI: oai:DiVA.org:kth-33578DiVA: diva2:416166
Note
QC 20110520Available from: 2011-05-10 Created: 2011-05-10 Last updated: 2017-12-11Bibliographically 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.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2011:15
National Category
Theoretical Chemistry
Research subject
SRA - Molecular Bioscience
Identifiers
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)
Opponent
Supervisors
Note
QC 20110530Available from: 2011-05-30 Created: 2011-05-09 Last updated: 2011-05-30Bibliographically approved

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