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

Abstract

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 I t 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 H 2 O or O 2 (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 (t...

Attenuation of DNA charge transport by compaction into a nucleosome core particle

“…We are currently investigating this hypothesis by performing DNA CT studies on rNCPs formed from DNA sequences of varying thermodynamic stability and sequence. We also note that our observation of decreased DNA damage in both the AQ-157TG-NCP aggregates and the AQ-157TG rNCPs is similar to the results in a recent report by Das and Schuster ( 52 ) on DNA CT reactions in DNA–spermidine condensates. The similarities between these two studies indicates that one of the constant effects of in vivo DNA packaging, in all of its guises, may be to decrease DNA oxidative damage arising from long-range CT reactions.…”

One-electron oxidation of DNA: thymine versus guanine reactivity

“…The results reported here suggest that one electron oxidation of duplex DNA will result in reaction at thymine only in sequences that do not contain guanine, or perhaps in complex DNA constructs that contain conformations or structures that inhibit radical cation hopping such as was found to be the case for some DNA condensates. 28…”

Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

“…One of the hallmarks of the long-distance oxidation of normal, guanine-containing DNA is that the amount of strand cleavage at a particular guanine is sequence dependent and characteristically decreases exponentially with the distance between the site of initial oxidation (at the AQ group, for example) and a particular guanine. 6, 63 This behavior has been interpreted in terms of the phonon-assisted polaron-hopping model. 1,6,63, 64 We investigated three DNA oligomers, DNA(5,9,10), containing a uniform set of TT steps separated by AA, ATA, or ATATA sequences, respectively.…”