Effect of condensate formation on long-distance radical cation migration in DNA

Effect of condensate formation on long-distance radical cation migration in DNA
August 5, 2005 (received for review June 4, 2005)
Published online before print September 21, 2005
Prolay Das, and Gary B. Schuster *
PNAS | October 4, 2005
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
Communicated by Mostafa A. El-Sayed, Georgia Institute of Technology, Atlanta, GA,
Long-distance radical cation transport was studied in DNA condensates. Linearized pUC19 plasmid was ligated to an oligomer containing a covalently linked anthraquinone group and six regularly spaced GG steps, which serve as traps for the migrating radical cation. Treatment of the linear, ligated plasmid with spermidine results in formation of condensates that were detected by light scattering and observed by transmission electron microscopy. Irradiation of the anthraquinone group in the condensate causes long-distance charge migration, which is detected by reaction at the remote guanines. The efficiency of charge migration in the condensate is significantly less than it is for the corresponding oligomer in solution. This result is attributed to a lower mobility for the migrating radical cation in the condensate, which is caused by inhibited formation of charge-transfer-effective states.
charge transfer | oxidative damage
It is well known that DNA is damaged by reactive chemical species. Extensive studies have shown that the one-electron oxidation of an oligonucleotide in solution creates a nucleobase radical cation (electron "hole") that may migrate hundreds of angstroms through duplex DNA before it is irreversibly trapped by reaction with H2O or O2 (1-3). Trapping occurs most commonly at a guanine, because it is the base with the lowest ionization potential (4), and this reaction leads to mutagenic products such as 8-oxoguanine (5-8). DNA within cells is tightly packed and does not closely resemble oligonucleotides in solution. An examination of radical-cation hopping through DNA in loosely organized nucleosome core particles showed that histone binding does not affect the pattern and extent of oxidation (9). However, it is not known how the long-distance radical-cation migration that is observed in oligonucleotides is affected by conversion of the DNA to a well ordered structure. We began the systematic investigation of this question by examining the reactions of radical cations that were specifically introduced into DNA condensates.
Multivalent cations like spermine or spermidine and proteins such as polylysine initiate DNA condensation (10-14). DNA condensates are nanometer-scale particles formed by the collapse of extended DNA chains into compact, ordered structures containing a small number of molecules (15, 16). These structures are recognized as models that are useful for studying gene packing in viruses, bacteria, and eukaryotic cells (17).
We prepared condensates formed from the linearized pUC19 plasmid (which contains 2,686 bp) that had been ligated to an oligonucleotide containing a covalently linked anthraquinone (AQ) group (for photoinitiated introduction of a radical cation) and a series of regularly spaced GG steps (as traps for the radical cation) (Fig. 1) (18). Dynamic light-scattering results and examination by transmission electron microscopy (TEM) shows that the ligated DNA sample is converted into condensates by the addition of spermidine. The condensates were irradiated with UV light (to introduce radical cations) and assayed by high-resolution PAGE. These studies show that long-distance radicalcation migration is less efficient in condensates than it is for DNA oligonucleotides in solution.
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