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- Bunta, Juraj, et al.
(författare)
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Solvating, manipulating, damaging, and repairing DNA in a computer
- 2007
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Ingår i: International Journal of Quantum Chemistry. - New York : Wiley. - 0020-7608 .- 1097-461X. ; 107:2, s. 279-291
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Tidskriftsartikel (refereegranskat)abstract
- This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically.
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| 5. |
- Naomé, Aymeric, et al.
(författare)
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Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:14, s. 4789-4801
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Tidskriftsartikel (refereegranskat)abstract
- We present results of molecular dynamics (MD) simulations of a double-stranded DNA fragment of sequence 5'-d(CGCGAGTTCGCG)-3' and 3'-d(GCGCTCAAGCGC)-5' in its native form and altered with guanine in the G6/C19 base pair replaced by 8-oxoguanine (8oxoG). DNA was simulated in solution with Na+ counterions and explicit water molecules. Trajectories were analyzed for radial distribution functions (RDFs), spatial distribution functions (SDFs), residence times, and occupancies, for both water and ions. Structural parameters of DNA fragments were also considered. Particularly, we report sensible differences in the statistical and dynamical behavior of water and ions between the healthy and lesion containing models. Structural features such as sugar phosphate backbone torsion angles also significantly differ. We conclude that 8oxoG noticeably modifies its close environment and that the observed changes in the vicinity of the lesion site might help the enzymes in charge of cleansing 8oxoG from human DNA to locate the aberration in its intrahelical context. This work supports the existence of a determinant early recognition mode of 8oxoG; for hOGG1.
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| 6. |
- Schyman, Patric, et al.
(författare)
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Hydrogen Abstraction from Deoxyribose by a Neighboring 3 '-Uracil Peroxyl Radical
- 2009
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:18, s. 6574-6578
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical examination of the reactivity of the uracil-5-peroxyl radical when abstracting a hydrogen atom from a neighboring 5'-deoxyribose in 5'-ApU-5-peroxyl-3' has been performed using density functional theory with the MPWB1K functional. Halogenated uracils are often used as radiosensitizers in DNA since the reactive uracil-5-yl radical is formed upon radiation and is known to create strand break and alkali-labile sites. Under aerobic conditions, such as in the cell, it has been proposed that the uracil-5-peroxyl radical is formed and would be the damaging agent. Our results show low reactivity for the uracil-5-peroxyl radical, determined by calculating the activation and reaction energies for the plausible hydrogen abstraction sites C1', C2' and C3' of the neighboring 5'-deoxyribose. These findings support the hypothesis that hydrogen abstraction primarily occurs by the uracil-5-yl radical, also under aerobic conditions, prior to formation of the peroxyl radical.
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| 7. |
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| 8. |
- Schyman, Patric, et al.
(författare)
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Hydrogen Abstraction from Deoxyribose by a Neighbouring Uracil-5-yl Radical
- 2007
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 9, s. 5975-5979
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen abstraction from the C1 and C2 positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5-AU-3 DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1 and C2. When adenine is neutral there is a preference for the C1 site and when the adenine is a radical cation the C2 site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1 is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1 the preferred site for abstraction.
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| 10. |
- Schyman, Patric, et al.
(författare)
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Hydroxyl radical - thymine adduct induced DNA damages
- 2008
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Ingår i: Chemical Physics Letters. - Amsterdam : Elsevier. - 0009-2614 .- 1873-4448. ; 458:1-3, s. 186-189
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Tidskriftsartikel (refereegranskat)abstract
- DNA damages caused by a 5-hydroxy-5,6-dihydrothymine-6-yl radical (5-OHT-6yl) abstracting a C20 hydrogen from a neighboring sugar (inter-H abstraction) have been theoretically investigated using hybrid DFT in gas phase and in water solution. The inter-H abstraction was here shown to be comparable in energy (24 kcal mol 1) with the intra-H abstraction in which the 5-OHT-6yl abstracts a C20 hydrogen from its own sugar. The effect of a neutrally or a negatively charged phosphate group was also studied and the results show no significant impact on the activation energy of the hydrogen abstraction whereas base release and strand break reactions are affected.
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