Carcinogen-induced alteration of DNA structure

Reactions of deoxyribonucleotide bases with sulfooxymethyl or halomethyl polycyclic aromatic hydrocarbons induce unwinding of DNA supercoils

Torsional stress in double-stranded DNA enables and regulates facets of chromosomal metabolism, replication, and transcription and requires regulatory enzymatic systems including topoisomerases and histone methyltransferases. As such, this machinery may be subject to deleterious effects from reactive mutagens, including ones from carcinogenic polycyclic aromatic hydrocarbon (PAH) adduct formation with DNA. Supercoiled plasmid DNA was investigated for its torsional responses to adducts formed in vitro from PAH benzylic carbocation reactive intermediates created spontaneously by release of leaving groups. PAH sulfate esters were found to (1) unwind DNA in a concentration dependent manner, and (2) provide maximum unwinding in a pattern consistent with known carcinogenicities of the parent PAHs, that is, 6-methylbenzo[a]pyrene > 7,12-methylbenz[a]anthracene > 3-methylcholanthrene > 9-methylanthracene > 7-methylbenz[a]anthracene > 1-methylpyrene. Supercoil unwinding was demonstrated to be dependent on the presence of sulfate or chloride leaving groups such that reactive carbocations were generated in situ by hydrolysis. In silico modeling of intercalative complex topology showed PAH benzylic carbocation reactive functional groups in alignment with target nucleophiles on guanine bases in a 5'-dCdG-3' pocket in agreement with known formation of nucleotide adducts. Inhibitory or modulatory effects on PAH-induced supercoil unwinding were seen with ascorbic acid and an experimental antineoplastic agent Antineoplaston A10 in agreement with their known anticarcinogenic properties. In summary, the reactive PAH intermediates studied here undoubtedly participate in well-known mutational mechanisms such as frameshifts and apurinic site generation. However, they are also capable of random disruption of chromosomal supercoiling in a manner consistent with the known carcinogenicities of the parent compounds, and this mechanism may represent an additional detrimental motif worthy of further study for a more complete understanding of chemical carcinogenicity.

Biotransformation of benzo[a]pyrene in Ahr knockout mice is dependent on time and route of exposure

Benzo[a]pyrene (BP) is an ubiquitous environmental pollutant with potent mutagenic and carcinogenic properties. The Ah receptor (Ahr) is important in the metabolic activation of BP and is therefore central to BP-induced carcinogenesis. Although Ahr(-/-) mice are refractory to BP-induced carcinogenesis, higher levels of BP-DNA and -protein adducts were formed in them than in wild-type mice. These results indicated the presence of an Ahr-independent and/or a slower biotransformation of BP in Ahr knockout mice. To address this issue further, we have now performed a time-course experiment, with mice receiving a single oral dose of BP (100 mg/kg). Wild-type mice have an effective clearance of BP metabolites, mainly through 3-hydroxybenzo[a]pyrene and 9-hydroxybenzo[a]pyrene in the feces with reduced levels of DNA and protein adducts in the examined tissues. On the other hand, the Ahr(-/-) mice appear to have a lower metabolic clearance of BP resulting in increased levels of DNA and protein adducts and of unmetabolized BP. In addition, we have performed an administration route experiment and found that skin-exposed Ahr(-/-) mice showed lower levels of protein adducts along with markedly reduced P450 1B1 expression, but only in the exposed area, as compared with the wild-type mice. In addition, the systemic uptake of BP is increased in the Ahr(-/-) mice as compared with the wild-type mice. Hence, the lack of a functional Ah receptor results in an Ahr-independent biotransformation of BP with a slower clearance of BP and higher levels of DNA and protein adducts, but the distribution and levels of BP and BP-protein adducts are clearly dependent on the route of exposure.

DNA–carcinogen interaction: covalent DNA-adducts of benzo(a)pyrene 7, 8-dihydrodiol 9, 10-epoxides studied by biochemical and biophysical techniques

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll and Peto, 1981). An important and prevalent class of potent carcinogenic compounds present in he environment is polycyclic aromatic hydrocarbons (PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive.

DNA–carcinogen interaction: covalent DNA-adducts of benzo(a)pyrene 7, 8-dihydrodiol 9, 10-epoxides studied by biochemical and biophysical techniques

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll & Peto, 1981). An important and prevalent class of potent carcinogenic compounds present in the environment is polycyclic aromatic hydrocarbons (PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive

DNA–carcinogen interaction: covalent DNA-adducts of benzo(a)pyrene 7, 8-dihydrodiol 9, 10-epoxides studied by biochemical and biophysical techniques

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll & Peto, 1981). An important and prevalent class of potent carcinogenic compounds present in the environment is polycyclic aromatic hydrocarbons (PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive.

DNA–carcinogen interaction: covalent DNA-adducts of benzo(a)pyrene 7, 8-dihydrodiol 9, 10-epoxides studied by biochemical and biophysical techniques

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll and Peto, 1981). An important and prevalent class of potent carcinogeniccompounds present in the environment is polycyclic aromatic hydrocarbons(PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive.

Quantitative analysis of benzo[a]pyrene biotransformation and adduct formation in Ahr knockout mice

Benzo[a]pyrene (BP) is an ubiquitous environmental pollutant with potent mutagenic and carcinogenic properties. The Ah receptor (Ahr) is involved in the metabolic activation of BP and is therefore important in the induction of chemical carcinogenesis. In this study, the relationship between Ahr genotype and biotransformation of BP in internal organs was investigated in Ahr (+/+), Ahr (+/-) and Ahr (-/-) mice. The mice were treated with BP (100mg/kg) by gavage. Gene expression was measured after 24h by real-time RT-PCR and showed induction of Cyp1a1 in liver and lung, and Cyp1b1 in lung in both Ahr (+/+) and Ahr (+/-). No induction of the Cyp genes was observed in the Ahr (-/-). There was a significant basal expression of Cyp1b1 in the liver of all genotypes, and this expression was independent of the BP exposure. Analyzed by HPLC-fluorescence, there were increased levels of protein and DNA adducts, metabolites, conjugates and unmetabolized BP in the internal organs of Ahr (-/-) as compared to Ahr (+/+) and Ahr (+/-) mice. This may be partly explained by a delayed bioactivation of BP in the Ahr deficient mice. The BP metabolism observed in the Ahr (-/-) mice is also evidence of an Ahr independent biotransformation of BP.

Free-energy perturbation methods to study structure and energetics of DNA adducts: results for the major N2-dG adduct of benzo[a]pyrene in two conformations and different sequence contexts

The potent mutagen/carcinogen benzo[a]pyrene (B[a]P) is activated to (+)-anti-B[a]PDE, which induces a variety of mutations (e.g., G --> T, G --> A, etc.) via its major adduct [+ta]-B[a]P-N2-dG. One hypothesis is that adducts (such as [+ta]-B[a]P-N2-dG) induce different mutations via different conformations, probably when replicated by different lesion-bypass DNA polymerases (DNAPs). We showed that Escherichia coli DNAP V was responsible for G --> T mutations with [+ta]-B[a]P-N2-dG in a 5'-TGT sequence (Yin et al., (2004) DNA Repair 3, 323), so we wish to study conformations of this adduct/sequence context by molecular modeling. The development of a CHARMM-based molecular dynamics (MD) simulations protocol with free-energy calculations in the presence of solvent and counterions is described. A representative base-pairing and base-displaced conformation of [+ta]-B[a]P-N2-dG in the 5'-TGT sequence are used: (1) BPmi5, which has the B[a]P moiety in the minor groove pointing toward the base on the 5'-side of the adduct, and (2) Gma5, which has the B[a]P moiety stacked with the surrounding base pairs and the dG moiety displaced into the major groove. The MD output structures are reasonable when compared to known NMR structures. Changes in DNA sequence context dramatically affect the biological consequences (e.g., mutagenesis) of [+ta]-B[a]P-N2-dG. Consequently, we also developed a MD-based free-energy perturbation (FEP) protocol to study DNA sequence changes. FEP involves the gradual "fading-out" of atoms in a starting structure (A) and "fading-in" of atoms in a final structure (B), which allows a realistic assessment of the energetic and structural changes when two structures A and B are closely related. Two DNA sequence changes are described: (1) 5'-TGT --> 5'-TGG, which involves two steps [T:A --> T:C --> G:C], and (2) 5'-TGT --> 5'-TGC, which involves three steps [T:A --> T:2AP --> C:2AP --> C:G], where 2AP (2-aminopurine) is included, because T:2AP and C:2AP retain more-or-less normal pairing orientations between complementary bases. FEP is also used to evaluate the impact that a 5'-TGT to 5'-UGT sequence change might have on mutagenesis with [+ta]-B[a]P-N2-dG. In summary, we developed (1) a CHARMM-based molecular dynamics (MD) simulations protocol with free-energy calculations in the presence of solvent and counterions to study B[a]P-N2-dG adducts in DNA duplexes, and (2) a MD-based free-energy perturbation (FEP) protocol to study DNA sequence context changes around B[a]P-N2-dG adducts.

Epimerization and stability of two new cis-benzo[a]pyrene tetrols by the use of liquid chromatography-fluorescence and mass spectrometry

Quantitative determination of the hydrolysis products from proteins and DNA gives valuable information regarding the reactive metabolite that forms the protein and DNA adduct. Quantification of protein-benzo[a]pyrene (BP) adducts represents a more sensitive method than quantification of BP-DNA adducts. The aim of the present study was to identify two hydrolysis products from BP-derived protein adducts found in vitro and in vivo in a previous study. Male Wistar rats were injected i.p. with BP, and serum albumin was isolated and subjected to acid hydrolysis at 70 degrees C for 3 h. The hydrolysate was subjected to LC separation, and fractions of the two unknown compounds were collected. The molecular masses of the two unknown compounds were in accordance with being tetrols as judged by LC electrospray mass spectrometry. The fragmentation patterns were characteristic of tetrols with formation of the molecular ion and the loss of water molecules. In addition, the compounds were subjected to acid hydrolysis at 70 degrees C with 0.1 M HCl for 3 h. We observed that two of the known tetrols epimerized to the two unknown tetrols and vice versa. This is probably a characteristic epimerization involving not only position C(10)-OH but also another site like position C(7)-OH. The in vivo findings of the two unknown adducts are probably the result of the formation of BPDE III in the metabolism of BP. These two tetrols must then have the C(7)-OH and C(8)-OH groups in a cis position.

Molecular modeling of the major benzo[a]pyrene N2-dG adduct in cases where mutagenesis results are known in double stranded DNA

The potent mutagen/carcinogen benzo[a]pyrene (B[a]P) is metabolically activated to (+)-anti-B[a]PDE, which induces a full spectrum of mutations (e.g. GC-->TA, GC-->AT, etc.). One hypothesis for this complexity is that different mutations are induced by different conformations of its major adduct [+ta]-B[a]P-N2-dG when bypassed during DNA replication (probably by different DNA polymerases). Previous molecular modeling studies suggested that B[a]P-N2-dG adducts can in principle adopt at least 16 potential conformational classes in ds-DNA. Herein we report on molecular modeling studies with the eight conformations most likely to be relevant to base substitution mutagenesis in 10 cases where mutagenesis has been studied in ds-DNA plasmids in E. coli with B[a]P-N2-dG adducts of differing stereoisomers and DNA sequence contexts, as well as in five cases where the conformation is known by NMR. Of the approximately 11,000 structures generated in this study, the computed lowest energy structures are reported for 120 cases (i.e. eight conformations and 15 examples), and their conformations compared. Of the eight conformations, four are virtually always computed to be high in energy. The remaining four lower energy conformations include two with the BP moiety in the minor groove (designated: BPmi5 and BPmi3), and two base-displaced conformations, one with the dG moiety in the major groove (designated: Gma5) and one with the dG in the minor groove (designated: Gmi3). Interestingly, these four are the only conformations that have been observed for B[a]P-N2-dG adducts in NMR studies. Independent of sequence contexts and adduct stereochemistry, BPmi5 structures tend to look reasonably similar, as do BPmi3 structures, while the base-displaced structures Gma5 and BPmi3 tend to show greater variability in structure. A correlation was sought between modeling and mutagenesis results in the case of the low energy conformations BPmi5, BPmi3, Gma5 and Gma3. Plots of log[(G-->T)/(G-->A)] versus energy[(conformation X)-(conformation Y)] were constructed for all six pairwise combinations of these four conformations, and the only plot giving a straight line involved Gma5 and Gmi3. While this finding is striking, its significance is unclear (as discussed).

Molecular modeling of four stereoisomers of the major B[a]PDE adduct (at N(2)-dG) in five cases where the structure is known from NMR studies: molecular modeling is consistent with NMR results

The potent mutagen/carcinogen benzo[a]pyrene (B[a]P) is metabolically activated to (+)-anti-B[a]PDE, which is known to induce a variety of mutations (e.g., GC --> TA, GC --> AT, etc.). One hypothesis for this complexity is that different mutations are induced by different conformations of its major adduct [+ta]-B[a]P-N(2)-dG when bypassed during DNA replication (perhaps by different DNA polymerases). Our previous molecular modeling studies have suggested that conformational complexity might be extensive in that B[a]P-N(2)-dG adducts appeared capable of adopting at least sixteen potential conformational classes in ds-DNA [e.g., Kozack and Loechler (1999) Carcinogenesis 21, 1953], although only eight seemed likely to be relevant to base substitution mutagenesis. Such molecular modeling studies are only likely to be valuable for the interpretation of mutagenesis results if global minimum energy conformations for adducts are found and if the differences in the energies of these different conformations can be computed reasonably accurately. One approach to assessing the reliability of our molecular modeling techniques is considered herein. Using a five-step molecular modeling protocol, which importantly included a molecular dynamics version of simulated annealing, eight conformations are studied in each of five cases. (The five cases are listed below, and were chosen because in each case the preferred solution conformation is known from a NMR study.) Of the eight conformations studied, the one computed to be lowest in energy is the same conformation as the one observed by NMR in four of the five cases: 5'-CGC sequence with [+ta]-, [-ta]-, and [+ca]-B[a]P-N(2)-dG, and 5'-TGC sequence with [+ta]-B[a]P-N(2)-dG. In the fifth case (5'-CGC sequence with [-ca]-B[a]P-N(2)-dG), the known NMR conformation is computed to be second lowest in energy, but it is within approximately 1.7 kcal of the computed lowest energy conformation. These results suggest that molecular modeling is surprisingly accurate in computing lowest energy conformations and that it should be useful in assessing the relative energies of different conformations. This is especially important given that currently molecular modeling is the only means available to study the energetics of minor conformations of DNA adducts.

Fluorescence measurements of DNA-bound metabolites of benzo(a)pyrene derivatives with different carcinogenic effects

(+/-)-trans-dihydroxy-7,8-dihydrobenzo(a)pyrene (BP-7,8-diol) and 9-hydroxybenzo(a)pyrene (9-OH-BP) were metabolized by rat liver microsomes in the presence of calf thymus DNA, resulting in preferential DNA binding of fluorescent (+)-anti-BP-7,8-diol-9,10-epoxide (BPDE) and 9-OH-BP-4,5-epoxide, respectively. When the DNA is denatured the fluorescence intensities of the bound metabolites change in a characteristic manner. Fluorescence decay measurements show that the intensity changes are due to changes in lifetimes of the excited states. Model substances for the bound metabolites were studied in solvents of different polarity. We found that the fluorescence changes observed after denaturation of the DNA may be explained as solvent polarity effects, so that denaturation forces the bound metabolites from a more hydrophobic environment to a hydrophilic one. Fluorescence depolarization studies as a function of temperature in combination with previous linear dichroism studies show that both BPDE and 9-OH-BP-4,5-epoxide form rigidly associated complexes with native DNA.

Toward an understanding of the role of DNA adduct conformation in defining mutagenic mechanism based on studies of the major adduct (formed at N(2)-dG) of the potent environmental carcinogen, benzo[a]pyrene

The process of carcinogenesis is initiated by mutagenesis, which often involves replication past damaged DNA. One question - what exactly is a DNA polymerase seeing when it incorrectly copies a damaged DNA base (e.g., inserting dATP opposite a dG adduct)? - has not been answered in any case. Herein, we reflect on this question, principally by considering the mutagenicity of one activated form of benzo[a]pyrene, (+)-anti-B[a]PDE, and its major adduct [+ta]-B[a]P-N(2)-dG. In previous work, [+ta]-B[a]P-N(2)-dG was shown to be capable of inducing>95% G-->T mutations in one sequence context (5'-TGC), and approximately 95% G-->A mutations in another (5'-AGA). This raises the question - how can a single chemical entity induce different mutations depending upon DNA sequence context? Our current working hypothesis is that adduct conformational complexity causes adduct mutational complexity, where DNA sequence context can affect the former, thereby influencing the latter. Evidence supporting this hypothesis was discussed recently (Seo et al., Mutation Res. [in press]). Assuming this hypothesis is correct (at least in some cases), one goal is to consider what these mutagenic conformations might be. Based on molecular modeling studies, 16 possible conformations for [+ta]-B[a]P-N(2)-dG are proposed. A correlation between molecular modeling and mutagenesis work suggests a hypothesis (Hypothesis 3): a base displaced conformation with the dG moiety of the adduct in the major vs. minor groove gives G-->T vs. G-->A mutations, respectively. (Hypothesis 4, which is a generalized version of Hypothesis 3, is also proposed, and can potentially rationalize aspects of both [+ta]-B[a]P-N(2)-dG and AP-site mutagenesis, as well as the so-called "A-rule".) Finally, there is a discussion of how conformational complexity might explain some unusual mutagenesis results that suggest [+ta]-B[a]P-N(2)-dG can become trapped in different conformations, and why we think it makes sense to interpret adduct mutagenesis results by modeling ds-DNA (at least in some cases), even though the mutagenic event must occur at a ss/ds-DNA junction in the presence of a DNA polymerase.

A novel approach for analyzing the structure of DNA modified by Benzo[a]pyrene diol epoxide at single-molecule resolution

Benzo[a]pyrene diol epoxide (BPDE) has been shown to bind specifically to the exocyclic amino group of deoxyguanosine in duplex DNA. Interestingly, this metabolite exhibits stereoselectivity in its tumorigenic and mutagenic effects. It is thought that local DNA conformation is altered at the site of the adduct, resulting in aberrant biological processes, and that in certain sequence contexts BPDE-DNA adducts induce bends in the DNA. In the work presented here, we compared DNA structural alterations of BPDE-modified DNA and unmodified DNA via tapping mode atomic force microscopy (AFM). DNA fragments 366 base pairs (bp) in length were generated by PCR from the duplicated multiple-cloning site of pBEND2 inserted into pGEM-3Zf(-), and either mock-modified or treated with BPDE to give modification levels between 1 and 5% of the nucleotides. Control or BPDE-modified DNA was adsorbed to mica and visualized in air by AFM. The contour lengths and end-to-end lengths of individual molecules were measured. The ratio of end-to-end distance to contour length was significantly smaller for modified DNA molecules than for the unmodified DNA preparation, although the frequency distributions of the contour lengths were similar for the two preparations. This suggests BPDE-DNA adducts cause significant bending of DNA molecules, confirming previous conclusions based on more indirect measurements. The average induced bend angle for BPDE-DNA adducts is estimated to be at least 30 degrees.

Hydrophobic forces dominate the thermodynamic characteristics of UvrA-DNA damage interactions

The Escherichia coli DNA repair proteins UvrA, UvrB and UvrC work together to recognize and incise DNA damage during the process of nucleotide excision repair (NER). To gain an understanding of the damage recognition properties of UvrA, we have used fluorescence spectroscopy to study the thermodynamics of its interaction with a defined DNA substrate containing a benzo[a]pyrene diol epoxide (BPDE) adduct. Oligonucleotides containing a single site-specifically modified N2-guanine (+)-trans-, (-)-trans-, (+)-cis-, or (-)-cis-BPDE adducts were ligated into 50-base-pair DNA fragments. All four stereoisomers of DNA-BPDE adducts show an excitation maximum at 350 nm and an emission maximum around 380 to 385 nm. Binding of UvrA to the BPDE-DNA adducts results in a five to sevenfold fluorescence enhancement. Titration of the BPDE-adducted DNA with UvrA was used to generate binding isotherms. The equilibrium dissociation constants for UvrA binding to (+)-trans-, (-)-trans-, (+)-cis-, and (-)-cis- BPDE adduct were: 7.4+/-1.9, 15. 8+/-5.4, 11.3+/-2.7 and 22.4+/-2.0 nM, respectively. There was a large negative change in heat capacity DeltaCpo,obs, (-3.3 kcal mol-1 K-1) accompanied by a relatively unchanged DeltaGoobs with temperature. Furthermore, varying the concentration of KCl showed that the number of ions released upon formation of UvrA-DNA complex is about 3.4, a relatively small value compared to the contact size of UvrA with the substrate. These data suggest that hydrophobic interactions are an important driving force for UvrA binding to BPDE-damaged DNA.

Sequence dependence and characteristics of bends induced by site-specific polynuclear aromatic carcinogen-deoxyguanosine lesions in oligonucleotides

The tumorigenic metabolite of benzo[a]pyrene, the (+)-7R,8S,9S,10R enantiomer, and the nontumorigenic mirror-image isomer, (-)-7S,8R,9R, 10S, of r7,t8-dihydroxy-t9,10-epoxy-7,8,9, 10-tetrahydrobenzo[a]pyrene (anti-BPDE) bind covalently to the exocyclic amino group of deoxyguanosine (N2-dG) in native DNA. These adducts can cause structural perturbations such as DNA bends, which in turn may influence the cellular processing of these lesions. The characteristics of bends in site-specifically modified oligodeoxyribonucleotide duplexes induced by single (+)- and (-)-anti-[BP]-N2-dG lesions were examined by self-ligation and gel electrophoresis techniques. The modified residues (dG*) were centrally positioned in the 11-mer oligonucleotide d(CACAXG*XACAC) complexed with the natural complementary strands, with X = T or C, or in oligonucleotides 16 or 22 base pairs long with the same centrally positioned 11-mer. Among the four stereochemically distinct lesions, the 10S(+)-trans-anti-[BP]-N2-dG adducts were significantly more bent than any of the other three stereoisomeric adducts and were selected for detailed studies. In the TG*T sequence context (X = T), the retardation factor RL (apparent length of multimer/sequence length) is approximately independent of the phasing (distance, in base pairs, between the lesions) of the adducts with respect to the helical repeat (10.5 base pairs/helix turn). In contrast, in the CG*C sequence context (X = C), RL is markedly lower in the case of ligated 16-mers than in the case of ligated 11-mer duplexes. The dependence of RL on the phasing of the bends as a function of the helical repeat, indicate that the bends associated with (+)-trans-anti-[BP]-N2-dG lesions are relatively rigid in the d(...CG*C...).d(...GCG...) sequences, and flexible in the d(...TG*T...).d(...ACA...) sequence context. These differences are attributed to the orientations of the pyrenyl residues on the 5'-side of the modified deoxyguanosine residues in the minor groove and to the intrinsic roll and tilt characteristics of DNA dinucleotide steps CG, GC, TG, and GT. The influence of flanking bases on the extent and character of DNA bending suggest that base sequence effects may be important in the cellular processing of (+)-trans-anti-[BP]-N2-dG lesions.

Bending and circularization of site-specific and stereoisomeric carcinogen-DNA adducts

The potent tumorigen and mutagen (+)-7(R),8(S)-dihydroxy-9(S), 10(R)-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene ((+)-anti-BPDE) is a metabolite of benzo[a]pyrene that binds predominantly to the exocyclic amino group of guanine residues in DNA in vivo and in vitro. While the (-)-7S,8R,9R,10Senantiomer, (-)-anti-BPDE, also reacts with DNA to form similar covalent N2-deoxyguanosyl adducts, this diol epoxide is nontumorigenic and its mutagenic activities are different from those of (+)-anti-BPDE. In this work, T4 ligase-induced cyclization methods have been employed to demonstrate that the (+)-anti-[BP]-N2-dG lesions (G*) cause significantly greater amounts of bending and circularization of the one-base overhang undecamer duplex 5'-d(CACAT[G*]TACAC).d(TGTACATGTGG) than the stereoisomeric oligonucleotide duplex with G* = (-)-anti-[BP]-N2-dG. In the case of the (+)-anti-BPDE-modified oligonucleotides, the ratio of circular to linear DNA multimers reaches values of 8-9 for circle contour sizes of 99-121 base pairs, while for the (-)-anti-[BP]-N2-dG-modified DNA this ratio reaches a maximum value of only approximately 1 at 154-176 base pairs. Assuming a planar circle DNA model, the inferred bending angles for 90-92% of the observed circular ligation products range from 30 to 51 degrees per (+)-trans-anti-[BP]-N2-dG lesion and from 20 to 40 degrees per (-)-trans-anti-[BP]-N2-dG lesion. In the case of unmodified DNA, the probability of circular product formation is at least 1 order of magnitude less efficient than in the BPDE-modified sequences and about 90% of the circular products exhibit bending angles in the range of 14 -19 degrees . In the most abundant circular products observed experimentally, the bending angles are 40 degrees and 26 +/- 2 degrees per (+)-anti-[BP]- or (-)-anti-[BP]-modified 11-mer; these values correspond to a net contribution of 21-26 degrees and 5-19 degrees , respectively, to the observed overall bending per lesion. The coexistence of circular DNA molecules of different sizes and, therefore, different average bending angles per lesion, suggest that the lesions induce both torsional flexibility and flexible bends, which permit efficient cyclization, especially in the case of (+)-trans-[BP]-N2-dG adducts. The NMR characteristics of (+)-trans-[BP]-N2-dG lesion in the 11-mer duplex 5'-d(CACAT[G*]TACAC).d(GTGTACATGTG) indicate that all base pairs are intact, except at the underlined base pairs. This suggests a distortion in the normal conformation of the duplex on the 5'-side of the modified guanosine residue, which may be due to bending enhanced base pair opening and bending induced by the bulky carcinogen residue. The implications of base sequence-dependent flexibilities and conformational mobilities of anti-[BP]-N2-dG lesions on DNA replication and mutation are discussed.

DNA damage can alter the stability of nucleosomes: effects are dependent on damage type

We have investigated the effects of DNA damage by (+/-)-anti-benzo[a]pyrene diol epoxide (BPDE) and UV light on the formation of a positioned nucleosome in the Xenopus borealis 5S rRNA gene. Gel-shift analysis of the reconstituted products indicates that BPDE damage facilitates the formation of a nucleosome onto this sequence. Competitive reconstitution experiments show that average levels of 0.5, 0.9, and 2.1 BPDE adducts/146 bp of 5S DNA (i.e., the size of DNA associated with a nucleosome core particle) yield changes of -220, -290, and -540 cal/mol, respectively, in the free energy (delta G) of nucleosome formation. These values yield increases of core histone binding to 5S DNA (K(a)) of 1.4-, 1.6-, and 2.5-fold, compared with undamaged DNA. Conversely, irradiation with UV light decreases nucleosome formation. Irradiation at either 500 or 2500 J/m2 of UV light [0.6 and 0.8 cyclobutane pyrimidine dimer/146 bp (on average), respectively] results in respective changes of +130 and +250 cal/mol. This translates to decreases in core histone binding to irradiated 5S DNA (K(a)) of 1.2- and 1.5-fold compared with undamaged DNA. These results indicate that nucleosome stability can be markedly affected by the formation of certain DNA lesions. Such changes could have major effects on the kinetics of DNA processing events.

Conformational studies of the (+)-trans, (-)-trans, (+)-cis, and (-)-cis adducts of anti-benzo[a]pyrene diolepoxide to N2-dG in duplex oligonucleotides using polyacrylamide gel electrophoresis and low-temperature fluorescence spectroscopy

Using polyacrylamide gel electrophoresis (PAGE) and low-temperature, laser-induced fluorescence line narrowing (FLN) and non-line narrowing (NLN) spectroscopic methods, the conformational characteristics of stereochemically defined and site-specific adducts derived from the binding of 7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene (anti-BPDE, a metabolite of the environmental carcinogen benzo[a]pyrene), to DNA were studied. The focus of these studies was on the four stereochemically distinct anti-BPDE modified duplexes 5'-d(CCATCGCTACC).(GGTAGCGATGG), where G denotes the lesion site derived from trans or cis addition of the exocyclic amino group of guanine to the C10 position of either (+) or (-)-anti-BPDE. PAGE experiments under non-denaturing conditions showed that the (+)-trans adduct causes a significantly greater retardation in the electrophoretic mobility than the other three adducts, probably the result of important adduct-induced distortions of the duplex structure. Low-temperature fluorescence studies in frozen aqueous buffer matrices showed that the (+)-trans adduct adopts primarily an external conformation with only minor interactions with the helix, but a smaller fraction (approximately 25%) appears to exists in a partially base-stacked conformation. The (-)-trans adduct exists almost exclusively (approximately 97%) in an external conformation. Both cis adducts were found to be intercalated; strong electron-phonon coupling observed in their FLN spectra provided additional evidence for significant pi-pi stacking interactions between the pyrenyl residues and the bases. FLN spectroscopy is shown to be suitable for distinguishing between trans and cis adducts, but lesions with either (+)- or (-)-trans, or (+)- or (-)-cis stereochemical characteristics showed very similar vibrational patterns.(ABSTRACT TRUNCATED AT 250 WORDS)

Mechanisms of quenching of the fluorescence of a benzo[a]pyrene tetraol metabolite model compound by 2'-deoxynucleosides

The hydrophobic interactions of bulky polycyclic aromatic hydrocarbons with nucleic acid bases and the formation of noncovalent complexes with DNA are important in the expressions of the mutagenic and carcinogenic potentials of this class of compounds. The fluorescence of the polycyclic aromatic residues can be employed as a probe of these interactions. In this work, the interactions of the (+)-trans stereoisomer of the tetraol 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), a hydrolysis product of a highly mutagenic and carcinogenic diol epoxide derivative of benzo[a]pyrene, were studied with 2'-deoxynucleosides in aqueous solution by fluorescence and UV spectroscopic techniques. Ground-state complexes between BPT and the purine derivatives 2'-deoxyguanosine (dG), 2'-deoxyadenosine (dA), and 2'-deoxyinosine (dI) are formed with association constants in the range of approximately 40-130 M(-1). Complex formation with the pyrimidine derivatives 2'-deoxythymidine (dT), 2'-deoxycytidine (dC), and 2'-deoxyuridine (dU) is significantly weaker. Whereas dG is a strong quencher of the fluorescence of BPT by both static and dynamic mechanisms (dynamic quenching rate constant k(DYN) = [2.5 +/- 0.4] x 10(9) M(-1)s(-1), which is close to the estimated diffusion-controlled value of approximately 5 x 10(9) M(-1)s(-1), both dA and dI are weak quenchers and form fluorescence-emitting complexes with BPT. The pyrimidine derivatives dC, dU, and dT are efficient dynamic fluorescence quenchers (k(DYN) approximately [1.5-3.0] x 10(9) M (-1)s(-1), with a small static quenching component due to complex formation evident only in the case of dT. None of the four nucleosides dG, dA, dC and dT are dynamic quenchers of BPT in the triplet excited state; the observed lower yields of triplets are attributed to the quenching of single excited states of BPT by 2'-deoxynucleosides without passing through the triplet manifold of BPT. Possible fluorescence quenching mechanisms involving photoinduced electron transfer are discussed. The strong quenching of the fluorescence of BPT by dG, dC and dT accounts for the low fluorescence yields of BPT-native DNA and of pyrene-DNA complexes.

Linear dichroism spectroscopy of nucleic acids

This review will consider solution studies of structure and interactions of DNA and DNA complexes using linear dichroism spectroscopy, with emphasis on the technique of orientation by flow. The theoretical and experimental background to be given may serve, in addition, as a general introduction into the state of the art of linear dichroism spectroscopy, particularly as it is applied to biophysical problems.

cis-Diamminedichloroplatinum (II) modified chromatin and nucleosomal core particle probed with DNase I

Chromatin and nucleosomal core particles were modified with cis-diamminedichloroplatinum (II) and the nucleoprotein complexes then digested with DNase I. Limited digestion of the modified chromatin containing cis-Pt(NH3)2Cl2 mediated cross-links involving the non-histone chromosomal proteins (Scovell et al. (1987) Biochem. Biophys. Res. Commun. 142, 826-835) does not release the low mobility proteins and excises only about 20% of the high mobility proteins 1, 2, and E. This supports previous findings that the low mobility proteins are involved primarily in protein-protein cross-links. In addition, the covalent cross-links between DNA and the high mobility proteins 1, 2, and E are relatively inaccessible to DNase I, in marked contrast to their accessibility to micrococcal nuclease. Furthermore, gels of the denatured DNA fragments obtained from digestion of both modified chromatin and nucleosomal core particle reveal virtually no difference in the 10n base repeat pattern, indicating no detectable change in the DNA-protein interactions upon DNA modification. This suggests that the predominant modification produced on core particle DNA, whether contained within higher order chromatin structure or in the core particle itself, is one which does not significantly alter the helical twist of the DNA within these nucleoprotein assemblies.

Covalent bonding of bay-region diol epoxides to nucleic acids

Although the solution chemistry of diol epoxides is now fairly well understood, a great deal remains to be elucidated regarding their reaction in the presence of DNA. Not only DNA but also small molecules are capable of sequestering diol epoxides in aqueous solutions with equilibrium constants on the order of 10(2)-10(4) M-1. In the case of DNA, at least two major families of complexes are presently recognized, possibly the result of groove binding vs. intercalation. As is the case for diol epoxides free in solution, the complexed diol epoxides undergo solvolysis to tetraols and in some cases possibly to keto diols as well. Fractionation between covalent bonding and solvolysis from within the complex(s) is determined more by the nature of the parent hydrocarbon from which the diol epoxide is derived than any other factor. Studies of a wide variety of alkylating and arylating agents have show that practically every potentially nucleophilic site on DNA can serve as a target for modification. In the case of the diol epoxides, practically all of the modification occurs at the exocyclic amino groups of the purine bases. In contrast to the diol epoxides, other epoxides such as those derived from aflatoxin B1, vinyl chloride, propylene, 9-vinylanthracene, and styrene preferentially bind to the aromatic ring nitrogens N-7 in guanine and N-3 in adenine (cf. Chadha et al., 1989). Molecular modeling as well as the spectroscopic evidence suggests that the hydrocarbon portion of the diol epoxides lies in the minor groove of DNA when bound to the exocyclic 2-amino group of guanine and in the major groove when bound to the exocyclic 6-amino group of adenine. Detailed conformational analysis of adducted DNA should prove to be extremely valuable in developing mechanistic models for the enzymatic processing of chemically altered DNA. At present, the critical lesion or lesions responsible for induction of neoplasia remains obscured by the large number of apparently noncritical adducts which form when polycyclic hydrocarbon diol epoxides bond to DNA.

Excimer fluorescence of (+)-anti-benzo (a)pyrene diol epoxide covalently bound to poly(dG-dC): structural implications

Fluorescence of (+)-anti-benzo(a)pyrene diol epoxide [(+)-anti-BPDE] covalently bound to poly(dG-dC) has been studied with steady-state and time-resolved techniques. Extensive formation of excimers is found, even at small (0.008) BPDE/nucleotide ratios. This indicates favored covalent binding to bases close to already modified guanines. Both fluorescence excitation spectra and lifetime measurements reveal two populations of (+)-anti-BPDE adducts: one that can form excimers and one that cannot. Three excimer lifetimes (4.5, 29, and 83 ns) are observed. Differently shifted monomer and excimer excitation spectra are discussed in terms of pyrene-pyrene exciton interactions, consistent with a distance shorter than 7 A between the excimer-forming BPDE chromophores.

Fluorescence spectroscopy of benzo[a]pyrene diol epoxide-DNA adducts. Conformation-specific emission spectra

The fluorescence characteristics of adducts derived from the covalent binding of the highly tumorigenic (+) and the non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) to native calf thymus DNA are significantly different from one another both at room temperature and at 77 K. The ratio R of fluorescence intensities of the (0,0) band I (situated near 380 nm) and vibronic band V (near 400 nm) of the pyrene ring system in the BPDE-DNA adducts and of the tetraol (BPT) hydrolysis product of BPDE is very sensitive to the polarity of the solvent, thus mimicking the well known behavior of pyrene itself (A. Nakajima, 1971, Bull. Chem. Soc. Jpn. 44, 3272). The fluorescence excitation and emission spectra of the (+)-BPDE-DNA adducts are relatively sharp and only slightly red-shifted (2-3 nm) with respect to those of BPT in aqueous buffer solution, and R = 1.07 when the fluorescence is excited at the maximum of the absorption spectrum; this compares with R = 1.17 for BPT in water, R = 0.75 in ether, and R = 0.84 for noncovalently intercalated BPT. These results suggest that the pyrene ring system in the covalent (+)-BPDE-DNA adducts is located in an environment which is relatively exposed to the aqueous environment, while physically intercalated BPT molecules are located at hydrophobic binding sites. The fluorescence characteristics of the (-)-BPDE-DNA adducts are more heterogeneous and thus more complex than those of the (+)-adducts. The R ratio depends rather strongly on the wavelength of excitation; a minor, more highly fluorescent and relatively solvent-accessible form of adducts exhibits an R ratio of 1.01. The major, less solvent accessible form is characterized by a larger red shift in the absorption spectrum (approximately 10 nm) and emission spectrum (approximately 6 nm for the (0,0) band) relative to BPT, and an R ratio of 1.07. These characteristics suggest that the local environments of the pyrenyl residues in the (-)-BPDE-DNA adducts are significantly different from those of BPT bound noncovalently to DNA by the intercalation mechanism. Fluorescence methods, particularly at low temperatures where the bands are better resolved and the fluorescence yields are significantly greater than at room temperature, can also be used to distinguish covalent DNA adducts derived from the binding of (+)-BPDE and (-)-BPDE to native double-stranded DNA.

Linear dichroism properties and orientations of different ultraviolet transition moments of benzo[a]pyrene derivatives bound noncovalently and covalently to DNA

Linear dichroism and absorption methods are used to study the orientations of transition moments of absorption bands of polycyclic aromatic epoxide derivatives which overlap with those of the DNA band in the 240-300 nm region. Both the short and long axes of the pyrene residues of 1-oxiranylpyrene (1-OP) and the (+) and (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) noncovalently bound to double-stranded native DNA are oriented approximately perpendicular to the axis of the DNA helix, consistent with intercalative modes of binding. The covalent binding of these three epoxide derivatives to DNA is accompanied by reorientations of both the short and long axes of the pyrene residues. Covalent adducts derived from the highly mutagenic (+)-anti-BPDE are characterized by tilts of the short axis within 35 degrees or less, and of the long axis by more than 60-80 degrees, with respect to the planes of the DNA bases. In the adducts derived from the binding of the less mutagenic (-)-anti-BPDE and 1-OP epoxide derivatives to DNA, the long axes of the pyrenyl rings are predominantly oriented within 25 degrees of the planes of the DNA bases; however, in the case of the (-) enantiomer of BPDE, there is significant heterogeneity of conformations. In the case of the 1-OP covalent DNA adducts, the short axis of the pyrene ring system is tilted away from the planes of the DNA bases, and the pyrene ring system is not intercalated between DNA base-pairs as in the noncovalent complexes. The stereochemical properties of the saturated 7,8,9,10-ring in BPDE, or the lack of the 7 and 8 carbon atoms in 1-OP, do not seem to affect noncovalent intercalative complex formation which, most likely, is influenced mainly by the flat pyrenyl residues. These structural features, however, strongly influence the conformations of the covalent adducts, which in turn may be responsible for the differences in the mutagenic activities of these molecules.

Adduct-induced base-shifts: a mechanism by which the adducts of bulky carcinogens might induce mutations

Most carcinogens have been shown to be mutagens, and DNA adducts are formed when mutagenic/carcinogenic substances react with DNA. It is generally believed these adducts (or their derivatives) induce misreplication events that result in mutations. Many of the more potently mutagenic substances are bulky and three-dimensionally complex, such as the polycyclic aromatic hydrocarbons, aromatic amines, and aflatoxins; little is known about the mechanisms by which they induce mutations. Several theories exist and herein an additional mechanism is proposed by which bulky adducts might induce mutations at GC base pairs. Molecular modeling in conjunction with molecular mechanical calculation is used to assess if the mutagen/carcinogen moiety of the adduct might be able to shift the position of the base moiety of the adduct in such a way that misreplication events might be facilitated. This mechanism is referred to as adduct-induced base-shift, and two classes appeared possible; adduct-induced base-wobble and adduct-induced base-rotation. The latter has been proposed previously. By adduct-induced, base-wobble, the mutagen/carcinogen moiety of the adduct induces a shift in the position of the base moiety of the adduct with respect to the helix axis, which might facilitate mispairing events that are reminisent of non-Watson/Crick pairing that occurs at the wobble base of tRNA during translation. For example, in some guanine adducts, the guanine appears more thymine-like, which might facilitate G.A mispairing and thereby ultimately GC to TA transversion mutations. Adduct-induced base-rotation involves the rotation of the adducted base from the anti to the syn conformation and a variety of mispairing events might result.

Mapping the binding site of aflatoxin B1 in DNA: molecular modeling of the binding sites for the N(7)-guanine adduct of aflatoxin B1 in different DNA sequences

Aflatoxin B1 (AFB1), a potent mutagen and carcinogen, forms an adduct exclusively at the N(7) position of guanine, but the structure of this adduct in double stranded DNA is not known. Molecular modeling (using the program, PSFRODO) in conjunction with molecular mechanical calculation (using the program, AMBER) are used to assess the binding modes available to this AFB1 adduct. Two modes appear reasonable; in one the AFB1 moiety is intercalated between the base pair containing the adducted guanine and the adjacent base pair on the 5'-side in reference to the adducted guanine, while in the second it is bound externally in the major groove of DNA. Rotational flexibility appears feasible in the latter providing four, potential binding sites. Molecular modeling reveals that the binding sites around the reactive guanine in different sequences are not uniformly compatible for interaction with AFB1. As the sequence is changed, one particular external binding site would be expected to give a pattern of reactivities that is reasonably consistent with the observed sequence specificity of binding that AFB1 shows in its reaction with DNA (Benasutti, M., Ejadi, S., Whitlow, M. D. and Loechler, E. L. (1988) Biochemistry 27, 472-481). The AFB1 moiety is face-stacked in the major groove with its long axis approximately perpendicular to the helix axis. Favorable interactions are formed between exocyclic amino groups that project into the major groove on cytosines and adenines surrounding the reactive guanine, and oxygens in AFB1; unfavorable interactions involve van der Waals contacts between the methyl group on thymine and the AFB1 moiety. "Some of the sequence specificity of binding data can be rationalized more readily if it is assumed that 5'-GG-3' sequences adopt an A-DNA structure." Based upon molecular modeling/potential energy minimization calculation, it is difficult to predict how reactivity would change in different DNA sequences in the case of the intercalative binding mode; however, several arguments suggest that intercalation might not be favored. From these considerations a model of the structure for the transition state in reaction of AFB1 with DNA is proposed involving one particular external binding site.

Reactions of stereoisomeric and structurally related bay region diol epoxide derivatives of benz[a]anthracene with DNA. Conformations of noncovalent complexes and covalent carcinogen-DNA adducts

The modes of reaction of the tumorigenic bay region diol epoxide anti-BADE [+/-)-trans-3,4-diol-anti-1,2-epoxy-1,2,3,4-tetrahydrobenz[a]anthr acene) and the less potent tumor initiating diastereomer syn-BADE [+/-)-trans-3,4-diol-syn-1,2-epoxy-1,2,3,4-tetrahydrobenz[a]anthra cene) with native, double-stranded DNA were compared. The bay-region diol epoxide derived from 3-methylcholanthrene (3-MCDE, racemic trans-9,10-diol-anti-7,8-epoxy-7,8,9,10-tetrahydromethylcholanthrene+ ++) was included in this study in order to assess the effects of the methyl and methylene substituents on the reactivity with DNA. Utilizing linear dichroism and other spectroscopic methods, it is shown that all three diol epoxides forn non-covalent complexes with DNA. The diastereomers anti-BADE and syn-BADE form intercalative physical complexes, but the association constant K of the syn-diastereomer is about 6-7 times smaller than for anti-BADE; this effect is ascribed to the bulky quasi-diaxial conformation of the diol epoxide ring in the syn diastereomer. The value of K (4000 M-1) is similar for anti-BADE and 3-MCDE, although the latter is not intercalated in the classical sense since the short axis of the molecule is tilted closer to the axis of the DNA double helix. The conformations of the covalent DNA adducts are interpreted in terms of a quasi-intercalative conformation (site I), and a conformation in which the long axes of the polycyclic molecules are tilted closer to the axis of the helix (site II). Both tumorigens, anti-BADE and 3-MCDE, undergo a marked re-orientation from a non-covalent site I to a covalent site II conformation upon binding chemically with the DNA bases, although a small fraction of the covalent anti-BADE adducts remains quasi-intercalated; in contrast, the alkyl substituents in 3-MCDE not only prevent the formation of intercalative physical complexes, but also the formation of site I covalent adducts. In the case of the less tumorigenic syn-BADE, both the non-covalent complexes and the covalent adducts are of the site I-type. The bay-region diol epoxide of benz[a]anthracene and of 3-methylcholanthrene display a similar pattern of reactivities and covalent adduct conformations as the bay region diol epoxide derivatives of benz[a]pyrene, suggesting that adduct conformation might be an important factor in determining the levels of mutagenic and tumorigenic activities of this class of compounds.

Preparation and characterization in solution of oligonucleotides alkylated by activated carcinogenic polycyclic aromatic hydrocarbons

The effects of aralkylation of selected oligonucleotides by a bulky chemical carcinogen, 7,12-dimethylbenz(a)anthracene (after activation) have been studied. The aralkylation involves the base adenine, designated A* at the modification site, in the center of synthetic heptameric, nonameric and pentadecameric oligonucleotides; complementary strands lacking any modification were also synthesized. The products were studied by UV melting curves and CD spectral techniques. Duplex formation was modified by such aralkylation of a central base in the oligomers. The extent of duplex formation was found to depend on chain length as follows: no evidence was found for duplex formation of the heptamer d(GTCA*GAC) + d(GTCTGAC); the nonamer, d(GTGCA*ATCC) + d(GGATTGCAC), appears to form a duplex at high salt concentrations and reduced temperature; the pentadecamer, d(CCGCT-GCGA*TCCGGC) + d(GCCGGATCGCAGCGG), forms a duplex at low salt concentration and room temperature, but its melting temperature is lower than that of the nonalkylated parent system. CD-spectra for the duplexes formed by the nonamer or pentadecamer are indicative of a right-handed helical conformations. On phosphordiesterase digestion it appears that the aralkylated adenine and the base on its 5'-side act as "stops" for enzymatic digestion from either direction. We suggest, from model building, that this inhibition of phosphodiesterase activity is the result of the steric bulk and disposition of the polycyclic aromatic hydrocarbon. We further suggest that unusual base pairing (mismatching), such as A...A, which would lead to an AT transversion, may be favored by the bulkiness of the aromatic group.

A-DNA accommodates adducts derived from diol epoxides of polycyclic aromatic hydrocarbons bound in a "side-stacking" mode

The minor groove of undistorted A-DNA provides a good binding site for planar, hydrophobic moieties such as unmetabolized polycyclic aromatic hydrocarbons (PAHs), and the base pairs at the ends of short oligodeoxynucleotide helices. It also accommodates the chief adduct derived from the metabolically activated form of the carcinogen benzo[a]pyrene. B-DNA lacks such a site. Computerized models have been generated for the major (N2-guanine-linked) adducts formed at this site by both + and - enantiomers of anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (anti-BPDE) with poly(dG).poly(dC) in the A-DNA conformation. The BPDE adducts lie in the shallow, relatively hydrophobic minor groove of the A-DNA after empirical potential energy minimization using the program AMBER. We term this binding mode "side-stacking." The side-stacked + anti-BPDE may constitute the chief carcinogenic lesion derived from benzo[a]pyrene.

Conformations and selective photodissociation of heterogeneous benzo(a)pyrene diol epoxide enantiomer-DNA adducts

The covalent binding of the tumorigenic (+) enantiomer and the nontumorigenic (-) enantiomer of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,19-tetrahydrobenzo(a)pyrene (BPDE) to double-stranded native DNA gives rise to heterogeneous adducts, especially in the case of (-)-BPDE. The covalent (+)-BPDE-DNA adducts are predominantly of the external site II type, while the (-)-BPDE-DNA adducts are predominantly of the quasi-intercalative, site I type (65%), with 35% of site II adducts. The site I adducts can be selectively photodissociated with near-ultraviolet light (quantum yields in the range 0.0003-0.005); the external site II adducts (photodissociation quantum yield 3 X 10(-5) are 10-100-times more stable. The photolability of covalent (-)-BPDE-DNA adducts accounts for the discrepancies in the linear dichroism properties of these complexes reported previously. Fluorescence quenching data, previously utilized to assess the degree of solvent exposure of the pyrenyl residues in covalent adducts, were in some cases significantly influenced by the presence of highly fluorescent tetraol dissociation products. After correcting for this effect, it is shown that the fluorescence of the external site II (+)-BPDE-DNA adducts is sensitive to acrylamide, while the fluorescence of the dominant site I (-)-BPDE-DNA adducts is not affected by this fluorescence quencher, as expected for adducts with considerable carcinogen-base stacking interactions.

Sequence selectivity, a test of the nature of the covalent adduct formed between benzo[a]pyrene and DNA

A theoretical study is presented of the energetic and structural properties of covalent adducts of benzo[a]pyrene and a DNA fragment. Energy optimisation is performed with the use of minimiser with constraints and an advanced semiempirical energy formula. Three types of adducts are studied: an external complex with the benzopyrene located in the DNA minor groove and two types of intercalative complexes with the carcinogen situated on the 3' side and 5' side of the covalently bound guanine. For each of the adducts the effects of DNA base sequence are examined. It is shown that the results for the intercalative complex with the carcinogen situated on the 5' side of the modified guanine correlate with the experimentally determined sequence preference.

Kinetic flow dichroism study of conformational changes in supercoiled DNA induced by ethidium bromide and noncovalent and covalent binding of benz[a]pyrene diol epoxide

The dynamic conformational changes due to the noncovalent intercalative binding of ethidium bromide and racemic trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE), and the covalent binding of BPDE to supercoiled phi X174 DNA, have been studied by gel electrophoresis and a novel application of a kinetic flow linear dichroism technique. The magnitude of the linear dichroism (delta A) of the DNA oriented in the flow gradient is sensitive to the hydrodynamic shape of the DNA molecule which is affected by the binding of the drug or the carcinogen BPDE. While the linear dichroism of ethidium bromide supercoiled DNA is time independent, the delta A spectra of BPDE-DNA reaction mixtures vary on time scales of minutes, which correspond to the reaction rate constant of BPDE to form 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene hydrolysis products and covalent DNA adducts. The rapid noncovalent intercalation of BPDE causes an initial large increase in delta A (up to 250%, corresponding to the dichroism observed with relaxed circular DNA), followed by a slower decrease in the linear dichroism signal. This decrease in delta A is attributed to the removal of intercalated diol epoxide molecules and the resulting reversible increase in the number of superhelical turns. The kinetic flow dichroism spectra indicate that the noncovalent BPDE-DNA complexes are intercalative in nature, while the covalent adducts are characterized by a very different conformation in which the long axes of the pyrenyl residues are oriented at a large angle with respect to the average orientation of the planes of the DNA bases.(ABSTRACT TRUNCATED AT 250 WORDS)

Electron microscopic visualization of DNA single strand breaks

DNA single strand breaks (ssb) have been induced in FLC/C cells in culture. They have been visualized in the electron microscope after decoration with biotin-avidin-ferritin complexes and spreading as monomolecular mixed films. This allowed one to determine the average number of decorated ssbs per unit of DNA length applying straight-forward and simple evaluation methods. This method has been used to investigate the DNA alterations by benzo[a]pyrene (B[a]P) on FLC/C culture cells. Thus a B[a]P-DNA damage curve can be constructed as a regression with a correlation coefficient of r = 0.97, while its isomer benzo[e]pyrene (B[e]P) known to have only low mutagenicity under the same experimental conditions is virtually without effect. The method has further informational potential regarding damage distribution and repair of DNA.

Binding of enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-benzo[a]pyrene to polynucleotides

DNA covalent binding studies with enantiomers of trans-7,8-dihydroxy- anti-9,10-epoxy-7,8,9,10-tetrahydro-benzo[a]pyrene (anti-BPDE) have been carried out by means of spectroscopic techniques (UV, CD, and fluorescence). Synthetic polynucleotides are employed to investigate binding differences between the G.C and A.T base pairs and to elucidate the bases for the stereoselective covalent binding of DNA toward anti-BPDE. The results indicate that of all the polynucleotides studied, only poly(dA-dT).poly(dA-dT) exhibits predominant intercalative covalent binding towards (+)-anti-BPDE and suffers the least covalent modification. Only minor intercalative covalent contributions are found in alternating polymer poly(dA-dC).poly(dG-dT). These observations parallel the DNA physical binding results of anti-BPDE and its hydrolysis products. They support the hypothesis that intercalative covalent adducts derive from intercalative physical binding while the external covalent adducts derive from external bimolecular associations. In contrast to the A.T polymers, the guanine containing polymers exhibit pronounced reduction in covalent modification by (-)-anti-BPDE. The intercalative covalent binding mode becomes relatively more important in the adducts formed by the (-) enantiomer as a consequence of decreased external guanine binding. These findings are consistent with the guanine specificity, stereoselective covalent binding at dG, the absence of stereoselectivity at dA for anti-BPDE, and the enhanced binding heterogeneity for the (-) enantiomer as found in the native DNA studies. The possible sequence and/or conformational dependence of such stereoselective covalent binding is indicated by the opposite pyrenyl CD sign exhibited by (+)-anti-BPDE bound to polynucleotides with pyrimidine on one strand and purine on another vs. that bound to polymers containing alternating purine-pyrimidine sequences.

High-resolution mapping of carcinogen binding sites on DNA

We have used a photochemical method to map covalent binding sites of the carcinogen benzo[a]pyrenediol epoxide (BPDE) within DNA from the transcriptional control region of the chicken adult beta-globin gene. Our preliminary low-resolution mapping has demonstrated that this region contains highly preferred BPDE binding sites [Boles, T.C., & Hogan, M.E. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 5623-5627]. Here, we find that BPDE binding at individual G residues in this region is influenced by nearest-neighbor interactions and also by longer range interactions that may be attributable to sequence-specific variation of DNA secondary structure. Our findings suggest that long poly(dG) sequences should be preferred sites for BPDE action in other genes.

Covalent binding of (+)- and (-)-trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyr ene to B and Z DNAs

Circular dichroism (CD) as well as absorption spectral measurements reveals that poly(dG-m5dC).poly(dG-m5dC) suffers more extensive covalent modification by (+)-dihydroxy-anti-epoxybenzo[a]pyrene [(+)-anti-BPDE] than its unmethylated counterpart and that the covalently attached pyrenyl moiety exhibits stronger stacking interactions with the bases in the methylated polymer as suggested by the much larger pyrenyl spectral red shifts, most likely the consequence of intercalation. Stereoselective binding properties of these polymers are evidenced by the much reduced preference for the (-) enantiomer. Modifications due to (+)-anti-BPDE on the 50 microM hexaamminecobalt induced Z DNAs are much less pronounced and much less stereoselective, with the pyrenyl spectral characteristics being distinct from those of the B form. Salt titrations on the (+)-anti-BPDE modified poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC) indicate much reduced cooperativity on the B to Z transition when compared to the unmodified counterparts. Evidence also suggests that covalent modification by anti-BPDE inhibits the B to Z conversion of base pairs in its immediate vicinity, presumably through intercalative stabilization of the B conformer at high salt. In contrast to stabilizing the B conformation for the proximal base pairs, covalent lesion by (+)-anti-BPDE appears to destabilize distal base pairs with the consequence of kinetic facilitation of B to Z transformation for these regions. Interesting differential effects on the reverse Z to B transforming abilities of these two enantiomers are observed with the covalent binding of the (-) isomer showing higher potency for inducing such conversion.

A comparison of the intercalative binding of non-reactive benzo[a]pyrene metabolites and metabolite model compounds to DNA

The reversible DNA physical binding of a series of non-reactive metabolites and metabolite model compounds derived from benzo[a]pyrene (BP) has been examined in UV absorption and in fluorescence emission and fluorescence lifetime studies. Members of this series have steric and pi electronic properties similar to the highly carcinogenic metabolite trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) and the less potent metabolite 4,5-epoxy-4,5-dihydrobenzo(a)pyrene (4,5-BPE). The molecules examined are trans-7,8-dihydroxy-7,8-dihydrobenzo[a]-pyrene (7,8-di(OH)H2BP), 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (tetrol) 7,8,9,10-tetrahydrobenzo[a]pyrene (7,8,9,10-H4BP), pyrene, trans-4,5-dihydroxy-4,5-dihydrobenzo[a]pyrene (4,5-di(OH)H2BP) and 4,5-dihydrobenzo[a]pyrene (4,5-H2BP). In 15% methanol at 23 degrees C the intercalation binding constants of the molecules studied lie in the range 0.79-6.1 X 10(3) M-1. Of all the molecules examined the proximate carcinogen 7,8-di(OH)-H2BP is the best intercalating agent. The proximate carcinogen has a binding constant which in UV absorption studies is found to be 2.8-6.0 times greater than that of the other hydroxylated metabolites. Intercalation is the major mode of binding for 7,8-di(OH)H2BP and accounts for more than 95% of the total binding. Details concerning the specific role of physical bonding in BP carcinogenesis remain to be elucidated. However, the present studies demonstrate that the reversible binding constants for BP metabolites are of the same magnitude as reversible binding constants which arise from naturally occurring base-base hydrogen bonding and pi stacking interactions in DNA. Furthermore, previous autoradiographic studies indicate that in human skin fibroblasts incubated in BP, pooling of the unmetabolized hydrocarbons occurs at the nucleus. The high affinity of 7,8-di(OH)H2BP for DNA may play a role in similarly elevating in vivo nuclear concentrations of the non-reactive proximate carcinogen.