Steric effects on water accessability control sequence-selectivity of radical cation reactions in DNA

Journal of the American Chemical Society

Volumn 129, Issue 27, 2007, Pages 8408-8409

  Cleveland, Charles L ^a   Barnett, Robert N ^a   Bongiorno, Angelo ^a   Joseph, Joshy ^a   Liu, Chusheng ^a   Schuster, Gary B ^a   Landman, Uzi ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATION; DOUBLE STRANDED DNA; GUANINE; OLIGOMER; RADICAL; WATER;

ARTICLE; CALCULATION; COMPLEX FORMATION; DNA SEQUENCE; ELECTRIC POTENTIAL; MOLECULAR DYNAMICS; OXIDATION; REACTION ANALYSIS; SEQUENCE ANALYSIS; SIMULATION; STEREOCHEMISTRY; THERMODYNAMICS; X RAY ANALYSIS;

BASE SEQUENCE; CATIONS; DNA; WATER;

EID: 34447555697     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja071893z     Document Type: Article

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14. See Supporting Information for details.
15. + counter ions (three on each strand) located near the phosphate groups. The calculations used density functional theory (spin-density functional for the radical cations) with the generalized gradient approximation (GGA) [Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868.] and norm conserving soft pseudopotentials.
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19. The partial charges of uracil where taken as those fitted for simulations of RNA. TIP3P potentials [Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 183, 79, 926.] were used for water. No cutoffs were used for either the electrostatic or Lennard-Jones interactions.
20. The samples were irradiated for 10 min (single hit conditions) at 350 nm, where only AQ absorbs, in air-saturated sodium phosphate buffer solution (pH 7) at ambient temperature. In the quantitative analyses of relative reactivity, interference caused by end effects was eliminated by considering only the four central "identical" GG steps, but including the others does not change the conclusion.
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