7-Azido-actinomycin D: a photoaffinity probe of the sequence specificity of DNA binding by actinomycin D.

Actinomycin D (ActD) is a DNA-binding antitumor antibiotic that appears to act in vivo by inhibiting RNA polymerase. The mechanism of DNA binding of ActD has attracted much attention because of its strong preference for 5'-dGpdC-3' sequences. Binding is thought to involve intercalation of the tricyclic aromatic phenoxazone ring into a GC step, with the two equivalent cyclic pentapeptide lactone substituents lying in the minor groove and making hydrogen bond contacts with the 2-amino groups of the nearest neighbor guanines. Recent studies have indicated, however, that binding is also influenced by next-nearest neighboring bases. We have examined this higher order specificity using 7-azido-actinomycin-D as a photoaffinity probe, and DNA sequencing techniques to quantitatively monitor sites of covalent photoaddition. We found that GC doublets were strongly preferred only if the 5'-flanking base was a pyrimidine and the 3'-flanking base was not cytosine. In addition we observed a previously unreported preference for binding at a GG doublet in the sequence 5'-TGGG-3'.

Sequence preferences of covalent DNA binding by anti-(+)- and anti-(-)-benzo[a]pyrene diol epoxides.

The sequence preferences of formation of piperidine-labile adducts of guanine by individual (+)- and (-)-isomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene [anti-(+)- and anti-(-)-BPDE] were examined by techniques analogous to chemical DNA sequencing. Data were obtained on over 1200 bases with anti-(-)-BPDE and 1000 bases with anti-(+)-BPDE. Guanines on average yielded more labile adducts than other bases, and the reactivities of guanines with both anti-(+)- and anti-(-)-BPDE isomers were found to be distinctly nonrandom with respect to DNA sequence. The most and least reactive guanines, defined in terms of the upper and lower 10 percentiles of reactivity, differed on average by a factor of 17. This range of guanine reactivities was correlated with distinct sequence preferences, which differed in part for the two isomers. The strongest determinant for preferred reaction of anti-(-)-BPDE to form a labile adduct at a guanine was the presence of a 3'-flanking guanine, but a thymine 5'-flanking a guanine also generally enhanced reactivity. The triplets containing central guanines most preferred by anti-(-)-BPDE were AGG, CGG, and TG(G greater than T greater than C,A). anti-(+)-BPDE also formed labile adducts preferentially at AGG and CGG triplets, but not at TGN triplets. Significant effects of next-nearest-neighbor bases on guanine reactivities were also noted.

Photoaffinity approaches to determining the sequence selectivities of DNA-small molecule interactions: actinomycin D and ethidium.

The DNA photoaffinity ligands, 7-azidoactinomycin D and 8-azidoethidium, form DNA adducts that cause chain cleavage upon treatment with piperidine. Chemical DNA sequencing techniques were used to detect covalent binding. The relative preferences for modifications of all possible sites defined by a base pair step (e.g. GC) were determined within all quartet contexts such as (IGCJ). These preferences are described in terms of 'effective site occupations', which express the ability of a ligand to covalently modify some base in the binding site. Ideally, the effective site occupations measured for photoaffinity agents can also be related to site-specific, non-covalent association constants of the ligand. The sites most reactive with 7-azidoactinomycin D were those preferred for non-covalent binding of unsubstituted actinomycin D. GC sites were most reactive, but next-nearest neighbors exerted significant influences on reactivity. GC sites in 5'-(pyrimidine)GC(purine)-3' contexts, particularly TGCA, were most reactive, while reactivity was strongly suppressed for GC sites with a 5'-flanking G, or a 3'-flanking C. High reactivities were also observed for bases in the first (5') GG steps in TGGT, TGGG and TGGGT sequences recently shown to bind actinomycin D with high affinity. Pyrimidine-3',5'-purine steps and GG steps flanked by a T were most preferred by 8-azidoethidium, in agreement with the behavior of unsubstituted ethidium. The good correspondence between expected and observed covalent binding preferences of these two azide analogs demonstrates that photoaffinity labeling can identify highly preferred sites of non-covalent DNA binding by small molecules.

Improved high-performance liquid chromatography analysis of 32P-postlabeled 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-DNA adducts using in-line precolumn purification.

An improved HPLC-based 32P-postlabeling assay has been developed for the analysis of DNA modified with the food carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Postlabeled samples are loaded onto a C18 precolumn and adducted bases are retained while excess radioactivity and unmodified DNA bases are eluted directly to waste through a switching valve. The use of this HPLC in-line precolumn purification (HIPP) technique allows entire postlabeled samples to be analyzed without prior removal of inorganic phosphate and unmodified DNA bases. The method has a sample to sample precision of 15% and accuracy of 20%, at adduct levels of 2 adducts/10(7) bases and shows a linear relationship between signal and adduction levels from 1 adduct per 10(4) to approximately 2 +/- 1 adducts per 10(9) bases. Individual postlabeled DNA samples can be analyzed by HPLC in less than 1 h, allowing high throughput. The use of calf-thymus DNA (CT-DNA), highly modified with PhIP, or DNA isolated from mice chronically fed a PhIP-modified diet shows two major PhIP-DNA adduct peaks and three additional minor adduct peaks when labeled under ATP-limiting conditions. Isolation of the HPLC purified peaks and analysis by thin layer chromatography (TLC) matches the five HPLC peaks to the spots typically seen by TLC, including N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5- b]pyridine (dG-C8-PhIP). Variations in digestion techniques indicate a potential resistance of the PhIP-DNA adducts to the standard enzymatic digestion methods. Attempts at adduct intensification by solid phase extraction, nuclease P1 enrichment or 1-butanol extraction decreased PhIP-DNA adduct peaks and introduced a large early eluting peak. Removal of the 3'-phosphate with nuclease P1 following the kinase labeling reaction simplifies the HPLC profile to one major peak (dG-C8-PhIP monophosphate) with several minor peaks. In addition to the high resolution provided by HPLC separation of the PhIP-DNA adducts, this method can be adjusted for analysis of other DNA adducts and is readily automated for high throughput.

Non-covalent DNA groove-binding by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine.

The cooked meat mutagen 2-amino-1-methyl-6-phenyl-imidazo[4,5-b]pyridine (PhIP) is metabolized in vivo to electrophilic intermediates that covalently bind to DNA guanines. Here we address the mechanism of PhIP's non-covalent interaction with DNA by using spectroscopic and computational methodologies. NMR methodologies indicated that upon addition of DNA, PhIP aromatic protons underwent a small, 0.11-0.12 p.p.m. upfield shift. DNA phosphorus resonances of non-covalent PhIP-DNA complexes broadened and slightly shifted upfield, while DNA base imino proton resonances shifted slightly downfield relative to DNA alone. UV and fluorescence spectra of PhIP titrated with DNA showed no detectable shifting and hypochromism of absorbance or fluorescence bands. In the presence of DNA, PhIP fluorescence was efficiently quenched by acrylamide, but not by silver ion. Further, the NMR spectra suggest that PhIP is in fast exchange with the DNA, and is slightly specific for adenine-thymine (A-T) sequences. Finally, structural arguments based on quantum chemistry calculations suggested that PhIP and its metabolites are unlikely to intercalate into DNA. These data collectively indicate that PhIP non-covalently binds in a groove of DNA.

Evidence of involvement of multiple sites of metabolism in the in vivo covalent binding of dibenzo[a,h]pyrene to DNA.

The in vivo formation of dibenzo[a,h]pyrene-DNA adducts in mouse skin was assessed by laser-excited fluorescence spectroscopy at 77 and 4.2 K. Two adducts were identified with fluorescence origin bands at approximately 383.5 and 407.2 nm, and these were shown to possess pyrene and benzo[a]pyrene (B[a]P) chromophores, respectively. Both DNA-bound chromophores displayed considerable electron-phonon coupling and likely assume a highly base-stacked or quasi-intercalated configuration within DNA duplexes. The presence of B[a]P and pyrene aromatic systems indicates that two-electron or monooxygenation metabolism occurred on either the a or h benzo moieties (which are equivalent) in the former case, and on both these rings in the latter case. The presence of two adduct species agrees with 32P-postlabeling analysis of the DNA, which showed the presence of two major adducts in both thin-layer and high-performance liquid chromatographic separations.

Separation and identification of DNA-carcinogen adduct conformers by polyacrylamide gel electrophoresis with laser-induced fluorescence detection.

We have developed a separation protocol utilizing high-resolution polyacrylamide gel electrophoresis (PAGE) to isolate stable anti-benzo[a]pyrene diol epoxide adducts of oligodeoxynucleotides. Both enantiomers produced multiple adduct species. The distribution of adduct types could be quantitated by densitometry of autoradiograms or Cerenkov counting of eluted oligomers modified by anti-BPDE isomers. Laser-induced fluorescence (LIF) spectra of eluted adducts at 4.2 K (fluorescence line-narrowing spectroscopy) and 77 K revealed that bands corresponded to pure conformers of pyrene chromophore. Carcinogen-modified oligodeoxynucleotides were single-stranded, but there were often considerable stacking interactions between the pyrenyl residues and the oligonucleotide bases, indicating that electrophoresed oligomers were single-stranded but in a native, versus random coil, conformation. The ability to identify and quantitate adducts by PAGE-LIF, coupled with the high resolution and sensitivity of both techniques, makes PAGE and LIF in tandem a potentially powerful tool in the study of chemical carcinogenesis or other ligand-DNA interactions.

Heterogeneous DNA adduct formation in vitro by the acetylated food mutagen 2-(acetoxyamino)-1-methyl-6-phenylimidazo[4,5-b]pyridine: a fluorescence spectroscopic study.

The food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) forms adducts to DNA guanine bases at the C-8 position. No other DNA adduction site has been verified for PhIP, nor has any experimental data been collected on the conformation of the PhIP-DNA covalent complex. To determine if multiple PhIP-DNA adduct species exist, or if PhIP-DNA adducts assume multiple conformations, 2-(acetoxyamino)-1-methyl-6-phenylimidazo[4,5-b]-pyridine (N-acetoxy-PhIP) was reacted with calf thymus DNA, followed by an evaluation of the resulting adduct complexes by fluorescence spectroscopy. Approximately 20% of the N-acetoxy-PhIP formed covalent complexes with DNA. Two major and several minor spots were observed by 32P-postlabeling, suggesting a minimum of two major adduct species. UV/vis spectra of the PhIP-modified DNA also showed heterogeneous formation of PhIP-DNA adducts. Fluorescence excitation and emission spectroscopy with or without fluorescence quenching (silver ion and acrylamide) was used to evaluate the number of adducts formed, and the low-resolution conformation of each adduct. Four adduct fluorophores were observed and assigned the nomenclature PAi, where "PA" denotes PhIP Adduct and i = 1-4 in order of fluorescence emission band energies, with 1 the highest and 4 the lowest energy, respectively. Excitation maxima for the adduct fluorophores ranged from 340 to 370 nm, and emission maxima ranged from 390 to 420 nm. The fluorescence from adduct PA1 was quenched by silver but not acrylamide, suggesting a helix-internal configuration. Adduct PA2 fluorescence was strongly enhanced upon silver binding but was not affected by acrylamide, also indicating that this adduct was internal. The fluorescence from adducts PA3 and PA4 was quenched by acrylamide but not silver; thus PA2 and PA3 were tentatively assigned as solvent-accessible. These data are the first suggesting heterogeneous formation of PhIP adducts to intact DNA, but we cannot as yet determine how many chemical species of adduct are formed or if a given species exists in multiple conformations.

Sequence dependence of benzo[a]pyrene diol epoxide-DNA adduct conformer distribution: a study by laser-induced fluorescence/polyacrylamide gel electrophoresis.

Low-temperature laser-induced fluorescence techniques in combination with polyacrylamide gel electrophoresis (LIF/PAGE) were used to study the binding of (-)-anti- and (+)-anti-benzo[a]pyrene 7,8-dihydrodiol 9,10-epoxide (anti-BPDE) to several sequence-defined duplex oligomers. Two of the oligomers contain central 5'-RAGGAR-3' sequences (R = purine) which appear to be frequently mutated by racemic (+/-)-anti-BPDE in endogenous genes of cells cultured in vitro. Two contain a central 5'-CCGG-3' or 5'-TGGT-3' sequence which are strongly preferred for covalent binding but appear to be not so frequently mutated. Binding of the two enantiomers to the latter two sequences yielded a distribution of BPDE-N2-dG adduct conformations similar to those from binding to highly polymerized, random sequence DNA in vitro which, for (+/-)-anti-BPDE, means that the helix-external conformation of the N2-dG adduct is dominant. Binding of (-)-anti-BPDE to the 5'-RAGGAR-3' sequences yielded more partially base-stacked and less base-stacked (quasi-intercalated) conformer than observed for random sequence DNA. Importantly, the (+)-anti-BPDE in binding to the more mutagenically inclined 5'-RAGGAR-3' sequences yielded little external-type adduct in comparison to the other two sequences and random sequence DNA. Moreover, an unusually high proportion of the (+)-anti-BPDE adducts formed with the 5'-RAGGAR-3' sequences result from cis stereoaddition, which yields a partially base-stacked configuration. Since the (+)-anti-BPDE appears to be the more mutagenic, this result suggests a possible role of internal adduct conformations in mutagenesis.

Characterization of nucleoside and DNA adducts formed by S-(1-acetoxymethyl)glutathione and implications for dihalomethane-glutathione conjugates.

S-(1-Acetoxymethyl)glutathione (GSCH(2)OAc) was synthesized and used as a model for the reaction of glutathione (GSH)-dihaloalkane conjugates with nucleosides and DNA. Previously, S-[1-(N(2)-deoxyguanosinyl)methyl]GSH had been identified as the major adduct formed in the reaction of GSCH(2)OAc with deoxyguanosine. GSCH(2)OAc was incubated with the three remaining deoxyribonucleosides to identify other possible adducts. Adducts to all three nucleosides were found using electrospray ionization mass spectrometry (ESI MS). The adduct of GSCH(2)OAc and deoxyadenosine was formed in yield of up to 0.05% and was identified as S-[1-(N(7)-deoxyadenosinyl)methyl]GSH. The pyrimidine deoxyribonucleoside adducts were formed more efficiently, resulting in yields of 1 and 2% for the GSCH(2)OAc adducts derived from thymidine and deoxycytidine, respectively, but their lability prevented their structural identification by (1)H NMR. On the basis of the available UV spectra, we propose the structures S-[1-(N(3)-thymidinyl)methyl]GSH and S-[1-(N(4)-deoxycytidinyl)methyl]GSH. Because adduct degradation occurred most rapidly at alkaline and neutral pH values, an enzymatic DNA digestion procedure was developed for the rapid hydrolysis of DNA to deoxyribonucleosides at acidic pH. DNA digests were completed in less than 2 h with a two-step method, which consisted of a 15 min incubation of DNA with high concentrations of deoxyribonuclease II and phosphodiesterase II at pH 4.5, followed by incubation of resulting nucleotides with acid phosphatase. Analysis of the hydrolysis products by HPLC-ESI-MS indicated the presence of the thymidine adduct.

Identification and quantitation of 7,12-dimethylbenz[a]anthracene-DNA adducts formed in mouse skin.

Identification and quantitation of the depurination and stable DNA adducts of 7,12-dimethylbenz[a]anthracene (DMBA) formed by cytochrome P450 in rat liver microsomes previously established one-electron oxidation as the predominant mechanism of activation of DMBA to bind to DNA. In this paper we report the identification and quantitation of the depurination and stable DMBA-DNA adducts formed in mouse skin. The depurination adducts, which constitute 99% of all the adducts detected, are DMBA bound at the 12-methyl group to the N-7 of adenine or guanine, namely, 7-methylbenz[a]anthracene (MBA)-12-CH2-N7Ade and 7-MBA-12-CH2-N7Gua. The depurination adducts were identified by HPLC and fluorescence line narrowing spectroscopy. The stable DNA adducts were analyzed by the 32P-postlabeling method. Almost 4 times as much of the depurination adduct 7-MBA-12-CH2-N7Ade (79%) was formed compared to 7-MBA-12-CH2-N7Gua (20%). The stable adducts accounted for only 1% of all the adducts detected and 80% of these were formed from DMBA diolepoxide. The binding of DMBA to DNA specifically at the 12-CH3 group is consistent with the results of carcinogenicity experiments in which this group plays a key role. When DMBA was bound to RNA or denatured DNA in reactions catalyzed by microsomes or by horseradish peroxidase (HRP), no depurination DNA adducts of DMBA were detected. The amount of stable DNA adducts observed with denatured DNA was 70% lower in the HRP system and 30% lower in the microsomal system compared to native DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of crystal structure and theory for 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine.

The crystal structure of the food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b] pyridine (PhIP) has been determined by single-crystal X-ray crystallography. Crystals grown by evaporation of an aqueous solution form in the monoclinic space group P2(1)/n with two molecules of PhIP per asymmetric unit, along with six water molecules. The phenyl groups of these two PhIP molecules have torsion angles of different magnitude with respect to the plane of the imidazopyridine moiety. To maintain centrosymmetry, the crystal also contains an oppositely torsioned symmetry equivalent of each. The amino groups of both PhIP molecules take part in an extensive hydrogen bond network with the water of crystallization, forming long channels through the crystals parallel to the crystallographic b axis. The diffraction results are compared to theoretical calculations of the optimized geometry for a single PhIP molecule in vacuo as well as with water hydrogen-bonded to the exocyclic amine. In general, the agreement between the X-ray crystal structure of PhIP and its theory-derived counterpart in vacuo is within the combined experimental-theoretical uncertainty. The C-N bond to the exocyclic amine and the neighboring C=N imidazole bond are exceptions. This is attributed to the combined neglect of the crystal environment, waters of hydration, and the lack of coplanarity between the imidazole ring and the amine group in the calculations. To address the effect of waters of hydration, additional calculations were performed to optimize the geometry of a PhIP molecule with two water molecules hydrogen-bonded to the exocyclic amine. The resulting C-N exocyclic amine and C=N imidazole bond lengths were closer to those obtained by X-ray diffraction. The accord between theory and experiment demonstrates the utility of applying theory to (1) accurately predict structures of PhIP metabolites and intermediates that are too labile for study by conventional structural techniques such as X-ray crystallography and (2) assist in studying the mechanisms by which PhIP and its metabolites interact with proteins and DNA.