Synthesis, modification with N-acetoxy-2-acetylaminofluorene and physicochemical studies of DNA model compound d(TACGTA)

Synthesis and characterization of oligonucleotides containing site-specific bulky N2-aralkylated guanines and N6-aralkylated adenines

7-Bromomethylbenz[a]anthracene is a known mutagen and carcinogen. The two major DNA adducts produced by this carcinogen, i.e., N2-(benz[a]anthracen-7-ylmethyl)-2'-deoxyguanosine (2, b[a]a2G) and N6-(benz[a]anthracen-7-ylmethyl)-2'-deoxyadenosine (4, b[a]a6A), as well as the simpler benzylated analogs, N2-benzyl-2'-deoxyguanosine (1, bn2G) and N6-benzyl-2'-deoxyadenosine (3, bn6A), were prepared by direct aralkylation of 2'-deoxyguanosine and 2'-deoxyadenosine. To determine the site-specific mutagenicity of these bulky exocyclic amino-substituted adducts, the suitably protected nucleosides were incorporated into 16-base oligodeoxyribonucleotides in place of a normal guanine or adenine residues which respectively are part of the ATG initiation codon for the lac Z' alpha-complementation gene by using an in situ activation approach and automated phosphite triester synthetic methods. The base composition and the incorporation of the bulky adducts into synthetic oligonucleotides were characterized after purification of the modified oligonucleotides by enzymatic digestion and HPLC analysis.

Genetic toxicity of 2-acetylaminofluorene, 2-aminofluorene and some of their metabolites and model metabolites

2-Acetylaminofluorene and 2-aminofluorene are among the most intensively studied of all chemical mutagens and carcinogens. Fundamental research findings concerning the metabolism of 2-acetylaminofluorene to electrophilic derivatives, the interaction of these derivatives with DNA, and the carcinogenic and mutagenic responses that are associated with the resulting DNA damage have formed the foundation upon which much of genetic toxicity testing is based. The parent compounds and their proximate and ultimate mutagenic and carcinogenic derivatives have been evaluated in a variety of prokaryotic and eukaryotic assays for mutagenesis and DNA damage. The reactive derivatives are active in virtually all systems, while 2-acetylaminofluorene and 2-aminofluorene are active in most systems that provide adequate metabolic activation. Knowledge of the structures of the DNA adducts formed by 2-acetylaminofluorene and 2-aminofluorene, the effects of the adducts on DNA conformation and synthesis, adduct distribution in tissues, cells and DNA, and adduct repair have been used to develop hypotheses to understand the genotoxic and carcinogenic effects of these compounds. Molecular analysis of mutations produced in cell-free, bacterial, in vitro mammalian, and intact animal systems have recently been used to extend these hypotheses.

A circular dichroism study on the conformation of d(CGT) modified with N-acetyl-2-aminofluorene or 2-aminofluorene

The trinucleotide d(CGT) was modified by covalent binding of the carcinogen N-acetyl-2-aminofluorene (AAF) or 2-aminofluorene (AF) at the C8 position of the guanine base. The conformations of d(CGT)-AAF and -AF were studied by comparing the absorption and circular dichroism properties with those of dCMP + dGMP-AAF or -AF + dTMP in a molar ratio of 1:1:1 and AAF- and AF-containing dGMP. For both AAF- and AF-d(CGT) complexes the results show significant stacking interactions between the fluorene residue and the base(s) and are discussed in terms of the conformation of d(CGT)-AAF and -AF. In d(CGT)-AF we observe a clear interaction between AF and thymine, whereas the C-G stack is still intact. In the case of d(CGT)-AAF the C-G stack is weakened and the glycosidic rotation angle of dGuo-C8-AAF is most probably syn. The specific fluorene-base interactions persist at elevated temperatures. The carcinogen-base interactions are stronger in the AAF-carrying d(CGT) than in the case of the deacetylated complex. This is consistent with the higher mobility of the AF-adduct and its conformationally heterogeneous appearance in DNA.

Nuclease P1-mediated fluorescence postlabeling assay of AAF modified DNA model d(TACGTA) and calf-thymus DNA

Fluorescence postlabeling assay for DNA damage combines enzymatic digestion of modified DNA to nucleoside monophosphates and fluorescence postlabeling. However, to facilitate the quantitative release of bulky adducts that are not readily obtained as mononucleotides, a different mechanism is essential. In order to test the application potential of nuclease P1-mediated fluorescence postlabeling to assay bulky adduct, d(TACGTA) was reacted with N-acetoxy-2-acetylamino-fluorene. The major product, characterized by nmr as AAF adduct of the guanine moiety at the C-8 position, was used as a DNA model. Nuclease P1 digestion of the modified oligomer excised the adduct in two forms (3:1) which were identified as AAF modified d(pGpT) and dpG respectively by cochromotography with authentic markers. Fluorescence postlabeling assay of AAF modified d(TACGTA) detected both forms of the excised adduct. The application of the overall procedure to assay AAF modified calf-thymus DNA demonstrated that the extension of fluorescence postlabeling technique from the mononucleotide to the dinucleotide version expands the scope of the assay.

Micellar electrokinetic capillary chromatographic separation and laser-induced fluorescence detection of 2'-deoxynucleoside 5'-monophosphates of normal and modified bases

Micellar electrokinetic chromatography is used to separate dansylated nucleotides, both normal and modified species. The high separation power allows detection of minor components present in less than 1 part per thousand of the major components. Laser-excited fluorescence is used to detect the separated components at the 6 x 10(-18) mol level or 10(-9) M injected material. Combined with high-performance liquid chromatographic enrichment prior to labeling, this technique can be used to assess DNA damage in carcinogenesis studies.

Fluorescence postlabeling assay of cis-thymidine glycol monophosphate in X-irradiated calf-thymus DNA

DNA damage was induced by irradiating calf-thymus DNA with a GE Maxitron-250 as an X-ray source. The use of nitrous oxide as a scavenger of solvated electrons in the irradiation process, resulted in essentially a monoreactant system of the biologically important hydroxyl radical. A novel approach combining the enzymatic digestion of the irradiated DNA to nucleoside 5' monophosphates and fluorescence postlabeling was applied to detect a specific modified nucleotide induced by ionizing radiation, namely the 5,6-dihydroxy-5,6-dihydrothymine lesion. This modification, often referred to as the glycol lesion, is polar and is generated mainly as the cis stereoisomers. In order to demonstrate the detection of this lesion in DNA by fluorescence labeling, the lesion was first produced chemically in a DNA model compound d(CGTA). The modified oligomers were isolated intact by HPLC and characterized by NMR as cis stereoisomers of glycol derivatives of d(CGTA). The major isomer of the modified d(CGTA) was enzymatically digested to yield 5' monophosphates. The digest was chromatographed by HPLC to enrich the modified nucleotide. The fraction containing the modified nucleotide was labeled with dansyl chloride. The fluorescent labeled nucleotide was chromatographed by HPLC. The same overall procedure was applied to DNA X-irradiated in aqueous solution. With a conventional fluorescence detector, HPLC analysis of the fluorescence labeled nucleotides detected 1 modified nucleotide/10(6) normal nucleotides from 100 micrograms DNA. The two cis glycol lesions were detected in the irradiated DNA by co-chromatography with fluorescent labeled markers. The initial assay of the modified oligomer demonstrated that the same stereoisomer of cis glycol was induced as a major modified nucleotide by both chemical oxidation and ionizing radiation.

Minor-groove binding models for acetylaminofluorene modified DNA

Minimized potential energy calculations have been employed to locate and evaluate energetically a number of different models for DNA modified at carbon-8 of guanine by acetylaminofluorene (AAF). Three different duplex nonamer sequences were investigated. In addition to syn guanine models which have some denaturation and a Z-DNA model, we have found two new types of structures in which guanine remains syn and the AAF is placed in the minor groove of a B-DNA helix. One type features Hoogsteen base pairing between the modified guanine and protonated cytosine, with a sharply bent helix. The other (here termed the "wedge" model because the aromatic amine is wedged into the minor groove) maintains a single hydrogen bond between O6 of the modified guanine and N3 of protonated cytosine, with much less deformation of the helix, and close Van der Waals contacts between the AAF and the walls of the minor groove. Both types of structures (as well as the related forms produced by deprotonation of cytosine) are energetically important in all three sequences examined. The wedge-type model, which is most favored except in alternating G-C sequences, has been previously observed in a combined NMR and computational characterization of an aminofluorene (AF) modified guanine opposite adenine in a DNA duplex undecamer (D. Norman, P. Abuaf, B.E. Hingerty, D. Live, D. Grunberger, S. Broyde and D.J. Patel, Biochemistry 28, 7462 (1989)).

Synthesis and application of fluorescent labeled nucleotides to assay DNA damage

A facile method was developed to covalently attach a fluorophore to the 5'-phosphate of a nucleic acid. The procedure, illustrated by coupling 5'-dNmp (N = A,C,G,T) with 5-dimethylaminonaphthalene 1-sulfonyl chloride, commonly known as Dansyl chloride, involves 5'-phosphoramidation with ethylenediamine (EDA) followed by conjugation of the free aliphatic amino group of the phosphoramidate with Dansyl chloride. This method is also applicable to multi-incorporation of fluorescent labels in the nucleic acids. The reaction of 5'-Amp with a polyamine such as poly L-lysine (PLL, mol. wt., 4000) resulted in a phosphoramidate with multiple amino groups, which after isolation and conjugation with fluorescamine gave dAmp with multilabeled fluorophores. A condition was devised to separate the four dansylated mononucleotides of DNA, conjugated via ethylenediamine linker, by reverse phase HPLC. The elution profile could be monitored with a variable wavelength detector at 254 nm and 340 nm corresponding to the absorption of the nucleotides and the dansyl moiety, respectively. The detection limit was 2 nmol at 254 nm. The use of a fluorescence detector enhanced the detection sensitivity to a sub-picomole level (200 fmol). Samples of a DNA model, d(pCpGpTpA) and calf-thymus DNA were digested enzymatically to 5'-mononucleotides and labeled with Dansyl chloride. HPLC analysis of the dansylated digests from these samples, both before and after irradiation, suggests that the combination of enzymatic digestion and fluorescence postlabeling could be a novel approach to assay DNA damage.

Radiation damage to dinucleoside monophosphates: mediated versus direct damage

The mediation of radiation-induced damage to dinucleoside monophosphate by oxygen and by glutathione was studied. The sequence isomers d(TpA) and d(ApT) were X-irradiated in aqueous solutions and the products isolated by reverse-phase high-performance liquid chromatography. The main products were characterized by proton NMR spectroscopy. In the presence of oxygen the principal products are the formamido derivative formed by breakdown of thymine and the aldehyde derivative formed at the 5' end of the dinucleoside monophosphate, both nucleoside monophosphates and free bases. In the presence of glutathione, the two stereoisomers of the 5,6-dihydrothymine derivatives are prominent. Radiation-induced damage to d(TpA) and d(ApT) in the solid state was also studied.