Lack of interference of DNA single-strand breaks with the measurement of double-strand breaks in mammalian cells using the neutral filter elution assay

An electrical probe of protein-DNA interactions on DNA-modified surfaces

DNA charge transport chemistry is found to provide a sensitive method for probing protein-dependent changes in DNA structure and enzymatic reactions. Here we describe the development of an electrochemical assay of protein binding to DNA-modified electrodes based upon the detection of associated perturbations in DNA base stacking. Gold electrode surfaces that were modified with loosely packed DNA duplexes, covalently crosslinked to a redox-active intercalator and containing the binding site of the test protein, were constructed. Charge transport through DNA as a function of protein binding was then assayed. Substantial attenuation in current is seen in the presence of the base-flipping enzymes HhaI methylase and uracil DNA glycosylase, as well as with TATA-binding protein. When restriction endonuclease PvuII (R.PvuII) binds to its methylated target, little base-stacking perturbation occurs and little diminution in current flow is observed. Importantly, the kinetics of restriction by R.PvuII of its nonmethylated target is also easily monitored electrochemically. This approach should be generally applicable to assaying protein--DNA interactions and reactions on surfaces.

Characterization and mapping of DNA damage induced by reactive metabolites of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) at nucleotide resolution in human genomic DNA

The nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is an important tobacco-specific carcinogen associated with lung cancer. Its complex enzymatic activation, leading to methyl and pyridyloxobutyl (POB)-modified DNA, makes DNA damage difficult to characterize and quantify. Therefore, we use the NNK analogue 4-[(acetoxymethyl)nitrosamino]-1-(3-pyridyl)-1-butanone (NNKOAc) to induce damage in genomic DNA, and to map the sites and frequency of adducts at nucleotide resolution using ligation-mediated polymerase chain reaction and terminal transferase-dependent polymerase chain reactions (LMPCR and TDPCR). NNKOAc induced single-strand breaks in a concentration-dependent manner. Post-alkylation treatments, including hot piperidine or digestion with the enzymes Escherichia coli 3-methyladenine-DNA glycosylase II, formamidopyrimidine-DNA glycosylase, Escherichia coli endonuclease III, or phage T4 UV endonuclease V did not increase the level of DNA breaks in NNKOAc-treated DNA. Detection of DNA damage using LMPCR was possible only when POB-DNA was 5'-phosphorylated prior to the LMPCR procedure. NNKOAc generated damage at all four bases with the decreasing order guanine>adenine>cytosine>thymine. In contrast to NNKOAc damage distribution patterns, those induced by N-nitroso(acetoxymethyl)methylamine, a methylating NNK analog, induced damage principally at G positions detectable by enzymatic means that did not require phosphorylation. Analysis of damage distribution patterns, reveals a high frequency of damage in the p53 gene in codons 241 and 245 and a lower frequency of damage in codon 248. We analyzed the 3' termini of the NNKOAc induced single-strand breaks using a (32)P-post-labeling assay or a nucleotide exchange reaction at the 3'-termini catalyzed by T4 DNA polymerase combined with endonuclease IV treatment. Both methods indicate that the 3' termini of the single-strand breaks are not hydroxyl groups and are blocked by an unknown chemical structure that is not recognized by endonuclease IV. These data are consistent with POB-phosphotriester hydrolysis leading to strand breaks in DNA. The POB-damage could be mutagenic because NNKOAc produces single-strand breaks with the products being a 5'-hydroxyl group and a 3'-blocking group and strand breaks. These results represent the first step in determining if NNK pyridyloxobutylates DNA with sequence specificity similar to those observed with other model compounds.

Sensitivity of neutral filter elution but not PFGE can be modified by non-dsb chromatin damage

Hamster V79 fibroblast cells and human squamous carcinoma cells (Caski) were exposed to 60Co radiation and DNA double-strand break (dsb) induction was analysed by DNA elution at neutral pH from polycarbonate filter or out of an agarose matrix in pulsed-field electrophoresis (PFGE). While dsb yields were equal for the two cell lines (using 125-iodine calibration) a reduced responsiveness of filter elution was found for V79 versus Caski cells. This difference could be abolished when additional single-strand breaks (ssb) were introduced by an incubation at 10(-4) M H2O2 for up to 40 min that itself did not give a response in neutral elution. No such lack of specificity for the detection of dsb was seen in electrophoretic elution where also the influence of peroxide incubation was absent. The presumed potential of ssb to modify dsb detection was paralleled by the kinetics of dsb rejoining: a pronounced transient increase of DNA elution from filters was observed for V79 cells (less prominent with Caski cells) at 15-40 which is thought to reflect the occurrence of secondary ssb from incisions during base damage repair. Rejoining measured by PFGE did not show this behaviour. The results suggest that ssb may aid decondensation of the chromatin during lysis of cells required for an efficient release of dsb fragments when supported on filters, but which depends on cell type and is less critical in electrophoretic elution out of an agarose matrix. This involvement of ssb in the neutral filter elution assay appears to be contrary to published data obtained with different experimental systems. The finding of an increase of DNA elution from filters due to hyperthermia at 45 degrees C is also taken to indicate an involvement of non-dsb chromatin damage in the response of filter elution at neutral pH with V79 but not with Caski cells.