Modification of ribonucleic acid by chemical carcinogens. IV. Circular dichroism and proton magnetic resonance studies of oligonucleotides modified with N-2-acetylaminofluorene

Synthesis of oxygen-linked 8-phenoxyl-deoxyguanosine nucleoside analogues

Nucleobase adducts, which form in vivo by the nucleophilic attack of nucleobases on exogenous electrophilic species, can impact conformation and biological influences of the adducted nucleoside. Contemporary studies aim to address the occurrence and relevance of O-linked 8-phenoxy-purine adducts; however, preparative techniques for synthesizing these nucleosides were not previously described. Reported herein is a relatively facile synthesis of O-linked 8-dG phenol adducts with a wide variety of electron-donating, electron-withdrawing, and sterically demanding phenols.

Time-resolved resonance Raman investigation of the 2-fluorenylnitrenium ion reactions with C8 guanosine derivatives

A nanosecond time-resolved resonance Raman (ns-TR3) spectroscopic study of the reactions of the 2-fluorenylnitrenium ion with several C8-substituted guanosine derivatives is reported. The TR3 spectra show that the 2-fluorenylnitrenium ion reacts with the C8-substituted guanosine derivatives (C8-methylguanosine and C8-bromoguanosine) to produce C8 intermediates with the methyl and bromine moieties still attached to the intermediate species at the C8 position. The C8-bromoguanosine species was observed to be less reactive toward the 2-fluorenylnitrenium ion compared to the guanosine and C8-methylguanosine species. Comparison of the TR3 spectra to the results obtained from density functional theory calculations was used to characterize the C8 intermediates observed to learn more about their structure and properties. The implications of these results for the chemical reactivity of arylnitrenium ions toward substituted guanosine derivatives are briefly discussed.

Kinetics of hydrolysis of 8-(arylamino)-2'-deoxyguanosines

The 8-(arylamino)-2'-deoxyguanosines, or C-8 adducts, are the major adducts formed by reaction of N-arylnitrenium ions derived from carcinogenic and mutagenic amines with 2'-deoxyguanosine (d-G) and guanosine residues of DNA. The hydrolysis kinetics of three C-8 adducts 1a-c were determined by UV and HPLC methods at 20 degrees C under acidic, neutral, and mildly alkaline conditions. At pH < 2 the dominant hydrolysis process is spontaneous cleavage of the C-N bond of the doubly protonated substrate, 1H(2)(+2) (Scheme 2). The C-8 adducts are 2- to 5-fold more reactive than d-G under these conditions. At 3 < pH < 6 the hydrolysis kinetics are dominated by cleavage of the C-N bond of the monoprotonated nucleoside 1H(+). Under these conditions the hydrolysis kinetics are accelerated by 40- to 1300-fold over that of d-G. The rate increase appears to be caused by a combination of steric acceleration of C-N bond cleavage and a decrease in the ionization constant of 1H(+), K(a1), due to the electron-donating properties of the arylamino C-8 substituent. Under neutral pH conditions a slow (k(obs) approximately 10(-8) s(-1) to 5 x 10(-7) s(-1)) spontaneous cleavage of the C-N bond of the neutral nucleoside, 1, occurs that has not been previously reported for simple purine nucleosides. Finally, under mildly alkaline conditions a process consistent with spontaneous decomposition of the anion 1(-) or OH(-)-induced decomposition of 1 is observed. The latter process has been observed for other purine nucleosides, including the closely related 1d, and involves nucleophilic attack of OH(-) on C-8 to cleave the imidazole ring of the purine.

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.

Acetylaminofluorene and aminofluorene adducts inhibit in vitro transcription of a Xenopus 5S RNA gene only when located on the coding strand

Unique N-acetyl-2-aminofluorene (AAF) or 2-aminofluorene (AF) adducts were introduced into the Xenopus borealis somatic 5S RNA gene between the intragenic control region and the transcription termination site. The effects of these bulky adducts on transcription were studied in a cell-free extract derived from Xenopus laevis oocytes. AAF and AF adducts inhibit transcription only when they are on the template strand, whereas transcription passes through these adducts when they are placed on the nontemplate strand. In the presence of the AAF or AF adduct on the template strand, transcription usually terminates one nucleotide before the altered guanine residue. Premature termination at these bulky adducts does not block reinitiation of transcription, since several transcripts are produced per gene per hour on these damaged templates.

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)).

Furazolidone-induced interstrand cross-links in Vibrio cholerae DNA. Study of conformational change by circular dichroism

Vibrio cholerae DNA bearing furazolidone-induced interstand cross-links show a change in the characteristic circular dichroism spectra of the DNA itself in dilute buffer. The change in c.d. spectra was characterized by a shift of the positive band around 272 nm to lower wavelength and a loss of ellipticity of the negative band around 242 nm, and is similar to that exhibited by mitomycin linked Vibrio cholerae DNA under identical conditions and is suggestive of a conformational change of DNA bearing such cross-links. Both furazolidone-induced and mitomycin-induced cross-linking of Vibrio cholerae DNA inhibited the salt-induced conformation change, i.e. increase in winding angle of DNA, the percentage inhibition being greater for mitomycin-linked DNA.

The DNA bending by acetylaminofluorene residues and by apurinic sites

We have studied the distortions induced in double-stranded oligonucleotides by covalently bound acetylaminofluorene residues and by apurinic sites. Within the acetylaminofluorene-modified oligonucleotide three base-pairs are unpaired as detected by the chemical probes chloroacetaldehyde and osmium tetroxide. These two probes reveal that the bases adjacent to the apurinic site are paired. In both the modified double-stranded oligonucleotides, the backbone on the 5' side of the modification is more reactive with 1,10-phenanthroline copper than the backbone on the 3' side. On polyacrylamide gels, the ligated multimers of acetylaminofluorene or apurinic site-modified oligonucleotides migrate slower than the multimers of the unmodified oligonucleotides. It is suggested that the acetylaminofluorene-modified guanine residues and the apurinic sites behave more as hinge joints than as the centres of directed bends.

Circular dichroism of sanguinarine-DNA complexes: effect of base composition, pH and ionic strength

The interaction of sanguinarine with various naturally occurring and synthetic deoxyribonucleic acids of different base composition and sequence has been studied from the measurement of circular dichroism spectroscopy in buffer of various ionic strengths and pH values where physico-chemical properties of DNA remain unchanged. Binding of sanguinarine to DNA causes a change in the circular dichroism spectrum of DNA itself by showing the increase of both positive and negative bands and appearance of a broad positive band with peak at 340 nm. All systems studied exhibit extrinsic positive band that is independent of DNA base composition and sequence. Calf thymus DNA-sanguinarine complexes in different salt concentrations show that, at saturation, the magnitude of molar ellipticity at 340 nm increases with decreasing sodium ions concentration. Sanguinarine-DNA complexes in buffer of various pH values also show that the molar ellipticity at 340 nm is greater in acidic pH and lower in alkaline pH. It is concluded that the alterations of secondary structure of DNA upon binding of sanguinarine is maximum in buffer of low ionic strength and acidic pH and the number of bound alkaloid molecules per base pair, at saturation, is more in G-C rich DNA than in A-T rich DNA.

Conformation and configuration at the central amine nitrogen of a nucleotide adduct of the carcinogen 2-(acetylamino)fluorene as studied by 13C and 15N NMR spectroscopy

The conformation and configuration at the central nitrogen of the adduct 8-(N-fluoren-2-ylamino)-2'-deoxyguanosine 5'-monophosphate has been investigated by high-field 13C and 15N NMR spectroscopy. One-bond nitrogen-hydrogen coupling constants and 13C chemical shifts for the adduct as well as for the model compounds diphenylamine, 4-nitrodiphenylamine and 2-aminofluorene have been measured in nonaqueous solutions. The data indicate a near planar configuration at the amine nitrogen that links the guanine and fluorene rings of the adduct. The orientations about the guanyl-nitrogen and fluorenyl-nitrogen bonds place the two ring systems in either perpendicular (Type A) or helical (Type B) conformations. It is suggested, based on structural similarities to diarylamines, that the G-N-C bond angle of the adduct is greater than 120 degrees in order to reduce unfavorable steric interactions between the two ring systems. Space-filling molecular models of the adduct in duplex DNA show that the aminofluorene moiety can be oriented into both Type A and Type B conformations within the major groove. The configuration at nitrogen of diphenylamine, 4-nitrodiphenylamine and 2-aminofluorene has also been examined.

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

The deoxyhexanucleotide d(TACGTA) was synthesized by a modified phosphotriester method. The modified procedure made rapid synthesis of deoxyoligonucleotide possible in gram quantity. N-Acetoxy-2-acetylaminofluorene (AAAF) modified d(TACGTA). Thin layer chromatography and UV analysis of the acid treated AAF modified hexanucleotide showed that the covalent modification with AAF took place exclusively at C(8) of guanine in d(TACGTA). d(TACGTA) and AAF modified d(TACGTA) were purified by preparative high performance liquid chromatography (HPLC). The pure products were characterized by 1H and 31P-NMR. The circular dichroism (CD) spectrum of d(TACGTA) was consistent with DNA in the B form even in the presence of 4 M NaCl whereas the modified hexamer had nearly inverted spectrum in the absence of any added salt. Both NMR and CD analyses indicated profound alteration of conformation of d(TACGTA) upon covalent modification with AAF. The stabilization of the Z-like conformation in the modified hexamer under physiological conditions of salt and temperature suggests biological relevance.

N-acetoxy-2-acetylaminofluorene modification of a deoxyoligonucleotide duplex

The carcinogen N-acetoxy-2-acetylaminofluorene was reacted with d (CCACGCACC) to form a covalent adduct with attachment at the single guanine. The sample was purified, mixed 1:1 with d (GGTGCGTGG) and studied by thermal denaturation experiments. The Tm for the mixture was 35 +/- 3 degrees C, consistent with duplex formation. The method of continuous variation shows that the modified oligomer, d (CCACGAAFCACC), forms a 1:1 duplex with d (GGTGCGTGG). Circular dichroism spectra also indicate the formation of a duplex and suggest that the modified duplex has a left-handed conformation. Addition of the intercalating drug ethidium alters the CD spectrum of the modified duplex, resulting in a CD spectrum similar to that of ethidium bound to right-handed DNA.

Conformational changes induced in DNA by the in vitro reaction with the mutagenic amine: 3-N,N-acetoxyacetylamino-4,6-dimethyldipyrido (1,2-a: 3', 2'-d) imidazole

The conformation of synthetic or natural DNAs modified in vitro by covalent binding of N-AcO-A-Glu-P-3 was investigated by fluorescence and circular dichroism. In all cases, substitution occurs mainly on the C8 of guanine residues. In modified poly(dG-dC).poly(dG-dC) or poly(dA-dC).poly(dG-dT) in B conformation, A-Glu-P-3 residues interact strongly with the bases whereas in Z conformation these residues are largely exposed to the solvent and interact weakly with the bases. A-Glu-P-3 and N-acetyl-2-aminofluorene (AAF) residues are equally efficient to induce the B-Z transition of poly(dG-dC).poly(dG-dC) and of poly(dA-dC).poly(dG-dT). Modifications of poly(dG).poly(dC) and calf thymus DNA indicate strong interactions between A-Glu-P-3 and the bases.

13C- and 31P-NMR studies of the conformation of carcinogen-modified nucleic acid dimers

The effect of the carcinogen acetylaminofluorene (AAF) on nucleic acid structure was examined using 13C- and 31P-NMR spectroscopies. Conformational effects were compared in two AAF-modified dinucleoside monophosphates (ApG and GpA) and two AAF-modified deoxydinucleotides (dpApG and dpGpA). Changes in adenine 13C chemical shifts on formation of the AAF-adduct and as a function of temperature provided evidence of base stacking. Differences in fluorene 13C chemical shifts between the AAF-modified dimer and AAF-modified monomer provided evidence of fluorene stacking. The effect of forming the adduct on the phosphate backbone was examined using 31P-NMR. A correlation was demonstrated between the degree of adenine-fluorene stacking on one hand and the change in conformation of the backbone conformation on the other.

13C-NMR studies of the effects of the carcinogen acetylaminofluorene on the conformation of dinucleoside monophosphate

13C-NMR spectra are obtained in aqueous solution of dinucleoside monophosphates (ApG and GpA) and of their adducts formed by the addition of the carcinogen acetylaminofluorene (AAF) to the C8 position of the guanine. The base and sugar carbons of all dimers and adducts are assigned. The task of assigning base and carbohydrate resonances was accomplished using a series of reference compounds. Significant changes in many of the carbon resonances of the adducts are observed suggesting three general conformational changes, namely: (1) chemical shift changes are noted in base carbon atom resonances as a function of temperature and adduct formation which are indicative of stacking effects; (2) large upfield shifts of the furanose C2' resonance of the guanosine-adduct indicate a shift to higher populations of the syn conformation. Other shifts of carbohydrate resonances are indicative of a change in conformation of the carbohydrate itself. (3) Large temperature effects on linewidth of several fluorine and furanose resonances indicate interconversion of various conformers in the dimer adduct.

An internal fluorene model for iodo-N-2-acetylaminofluorene modified DNA

Minimized conformational potential energy calculations have been performed for the 7-iodo (AAIF) and 7-fluoro (AAFF) derivatives of N-2-acetylaminofluorene (AAF), linked covalently to guanine C-8 in dCpdG. Both the iodo and the fluoro derivatives are carcinogenic and mutagenic. The lowest energy forms on the dinucleoside monophosphate level have syn guanine and fluorene-cytidine stacking. However, the iodo adduct cannot adopt this conformation in larger polymers, according to earlier experimental studies (Fuchs et al., Biochemistry, 15 (1976) 3347) and model building, because of iodine's large Van der Waal's radius. Therefore, a model consistent with all the experimental evidence, incorporating the second lowest energy conformation in B form duplex (dCdG)3 was constructed. In this model the modified guanine is syn, yet still stacked with the adjacent cytidine in one direction, the fluorene is located primarily at the helix interior between the base pairing sites, rupturing two base pairs, and the iodine atom and its adjoining ring protrude to the helix exterior.

Lack of Z-DNA conformation in mitomycin-modified polynucleotides having inverted circular dichroism

Poly(dG-dC) . poly(dG-dC) and Micrococcus lysodeikticus DNA were modified by exposure to reductively activated mitomycin C, an antitumor antibiotic. The resulting covalent drug-polynucleotide complexes displayed varying degrees of CD inversions, which are strikingly similar to the inverted spectrum observed with Z-DNA. The following criteria have been used to establish, however, that the inverted CD pattern seen in mitomycin C-polynucleotide complexes does not reflect a Z-DNA conformation. (i) The ethanol-induced transition of poly(dG-dC) . poly(dG-dC) from B to Z conformation is not facilitated but rather is inhibited by mitomycin C modification. This may be due to the presence of crosslinks, (ii) Radioimmunoassay indicated no competition for Z-DNA-specific antibody by any of the mitomycin C-modified polynucleotides, (iii) 31P NMR of the complexes yielded a single relatively narrow resonance, which is inconsistent with the dinucleotide repeat characteristic of Z-DNA. Alternative explanations for the inverted CD pattern include a drug-induced left-handed but non-Z conformational change or the superposition of an induced CD onto the CD of B-DNA due to drug-base electronic interactions. These results illustrate the need for caution in interpreting CD changes alone as an indication of Z-DNA conformation.

Force field conformational analysis of aminofluorene and acetylaminofluorene substituted deoxyguanosine

The hepatocarcinogen N-hydroxy-2-acetylaminofluorene forms two C8-substituted deoxyguanosine adducts in vivo. The conformation of these adducts, as well as 2'-deoxyguanosine and 8-amino-2'-deoxyguanosine has been studied with Allinger's force field. Using the glycoside rotation as a reaction coordinate, multidimensional potential energy surface were determined by relaxing all internal degrees of freedom. The calculations indicate the 2'-deoxyguanosine should exist as a mixture of syn and anti forms, that the syn form is slightly favored for 8-amino-2'-deoxyguanosine, that N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) will only be found in the syn conformation and that, although the syn form is also more stable for N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), it will have a substantially greater proportion of the anti-conformer than is found with dG-C8-AAF. The results of the force field calculations are discussed in relation to the effects these adducts may have on DNA structure.

The B goes to Z transition of poly(dG-dC) . poly(dG-dC) modified by some platinum derivatives

Poly(dG-dC) . poly(dG-dC) was modified by chlorodiethylenetriamino platinum (II) chloride, cis-dichlorodiammine platinum (II) and trans-dichlorodiammine platinum (II), respectively. The conformation of these modified poly(dG-dC) . poly(dG-dC) was studied by circular dichroism. In 4 M Na+, the circular dichroism spectra of poly(dG-dC)dien-Pt (0 less than or equal to rb less than or equal to 0.2) are similar (rb is the amount of bound platinum per base). It is concluded that the conformation of these polymers belongs to the Z-family. Dien-Pt complexes stabilize the Z-form. The midpoint of the Z goes to B transition of poly(dG-dC)dien-Pt(0.12) is at 0.2 M NaCl. Moreover another B goes to Z transition is observed at lower salt concentration (midpoint at 6 mM NaCl). In 1 mM phosphate buffer, the stability of Z-poly(dG-dC)dien-Pt(0.12) is greatly affected by the presence of small amounts of EDTA. Poly(dG-dC) . poly(dG-dC) modified by cis-Pt and trans-Pt complexes do not adopt the Z-form even in high salt concentration.

Three-state models of furanose pseudorotation

A general procedure is described to treat the pseudorotation of the furanose ring in terms of a three-state conformational equilibrium. In addition to the principal n (C3'-endo) and s (C2'-endo) puckering domains, the unusual e (01'-endo) intermediate is included in the analysis. Each of these three conformational categories is represented by a blend of five closely related puckered forms rather than by a single rotational isomeric state. Using this model together with experimentally measured nmr coupling constants, the puckering populations of various nucleic acid analogs are estimated. The conventional two-state n/s equilibria is confirmed in ordinary ribose and deoxyribose systems. The e domain, however, is found to be of major importance in several chemically modified furanoses including certain pyrimidine deoxynucleosides damaged by radiation and various nucleosides and nucleotides forced by bulky substituents on the base into unusual syn glycosyl arrangements. The "free" pseudorotation of these modified systems is not detected by conventional two-state puckering analyses.

Conformational changes of poly(dG-dC) . poly(dG-dC) modified by the carcinogen N-acetoxy-N-acetyl-2-aminofluorene

Poly (dG-dC) . poly(dG-dC) was modified by the reaction with N-acetoxy-N-acetyl-2-aminofluorene. The conformations of poly(dG-dC) . poly(dG-dC) and of poly d(G-C)AAF were studied by circular dichroism under various experimental conditions. In 95% ethanol, the two polynucleotides adopt the A-form. In 3.9 M LiCl, the transition B-form-C-form is observed with poly(dG-dC) . poly (dG-dC) but not with poly d(G-C)AAF. In 1 mM phosphate buffer, poly d(G-C)AAF behaves as a mixture of B- and Z-form, the relative percentages depending upon the amounts of modified bases. The percentage of Z-form is decreased by addition of EDTA and is increased by addition of Mg++. Spermine favors the Z-form in modified and unmodified polynucleotides. No defect in the double helix of poly d(G-C)AAF is detected by SI endonuclease.

Alternative conformations of DNA modified by N-2-acetylaminofluorene

Modification of DNA by the carcinogen N-acetoxy-N-2-acetylaminofluorene gives two adducts, a major one at the C-8 position of guanine and a minor one at the N-2 position with differing conformations. Binding at the C-8 position results in a large distortion of the DNA helix referred to as the "base displacement model" with the carcinogen inserted into the DNA helix and the guanosine displaced to the outside. The result is increased susceptibility to nuclease S1 digestion due to the presence of large, single-stranded regions in the modified DNA. In contrast, the N-2 adduct results in much less distortion of the helix and is less susceptible to nuclease S1 digestion. A third and predominant adduct is formed in vivo, the deacetylated C-8 guanine adduct. The conformation of this adduct has been investigated using the dimer dApdG as a model for DNA. The attachment of aminofluorene (AF) residues introduced smaller changes in the circular dichroism (CD) spectra of dApdG than binding of acetylaminofluorene (AAF) residues. Similarly, binding of AF residues caused lower upfield shifts for the H-2 and H-8 protons of adenine than the AAF residues. These results suggest that AF residues are less stacked with neighboring bases than AAF and induce less distortion in conformation of the modified regions than AAF. An alternative conformation of AAF-modified deoxyguanosine has been suggested based on studies of poly(dG-dC).(dG-dC). Modification of his copolymer with AAF to an extent of 28% showed a CD spectrum that had the characteristics of the left-handed Z conformation seen in unmodified poly(dG-dC).poly(dG-dC) at high ethanol or salt concentrations. Poly(dG-dC).poly(dG-dC) which does not undergo the B to Z transition at high ethanol concentrations, did not show this type of conformational change with high AAF modifications. Differences in conformation were suggested by single-strand specific nuclease S1 digestion and reactivity with anticytidine antibodies. Highly modified poly(GS-dC).poly(DG-dC) was almost completely resistant to nuclease S1 hydrolysis, while, modified DNa and poly(dG).poly(dC) are highly susceptible to digestion. Two possible conformations for deoxyguanosine modified at the C-8 position by AAF are compared depending on whether its position is in alternating purine-pyrimidine sequences or random sequence DNA.

Cooperative structural transition of PM2 DNA at high ionic strength and its dependence on DNA damages

Pohl and Jovin have shown that poly(dG--dC) . poly (dG--dC) in solution undergoes a cooperative transition at 2.5 M NaCl at neutral pH. The two forms of the polymer are structurally different as indicated by a change in ethidium bromide intercalation and in circular dichroism (CD). Wang et al. and Davies and Zimmerman have suggested that the low salt form of the polymer might correspond to the B form of DNA (right-handed helix) and the high salt form to the Z form of DNA (left-handed helix). We describe here a salt-induced transition of supercoiled PM2 DNA from a form which passes through nitrocellulose filters to a form which is retained by these filters. The transition occurs between 2.5 and 3.5 M NaCl. The dependence of the apparent equilibrium constant on the salt concentration indicates a cooperative transition. Irradiation of DNA with UV light or alkylation with N-acetoxyacetylaminofluorene (AAAF) shifts the transition to lower salt concentrations. The transition can also be observed with linear DNA but requires a much higher salt concentration.

Conformation of poly(dG-dC) . poly(dG-dC) modified by the carcinogens N-acetoxy-N-acetyl-2-aminofluorene and N-hydroxy-N-2-aminofluorene

Poly(dG-dC) . poly(dG-dC) was modified by reaction with N-acetoxy-N-acetyl-2-aminofluorene (N-AcO-AAF). Two samples with 6.6% and 8.5% modified bases were prepared. The modified bases are randomly distributed along the polymer chain, as deduced from competition experiments between antibodies against N-2-(guanosin-8-yl)-acetylaminofluorene, modified poly(dG-dC) . poly(dG-dC), and modified DNAs. Circular dichroism studies show that poly(dG-dC) . poly(dG-dC) modified by N-AcO-AAF is much more sensitive to the addition of alcohol than poly(dG-dC) . poly(dG-dC). In about 50% (vol/vol) alcohol, both polynucleotides have the same conformation, which is the Z form or a Z-like form. Moreover, in low salt and in the absence of alcohol, poly(dG-dC) . poly(dG-dC) modified by N-AcO-AAF is partially in the Z form. Poly(dG-dC) . poly(dG-dC) modified by N-hydroxy-N-2-aminofluorene can also adopt the Z form, but the transition is induced at a higher percentage than that of poly(dG-dC) . poly(dG-dC) modified by N-AcO-AAF. In low salt and in the absence of alcohol, no Z form was detected in poly(dG-dC) . poly(dG-dC) modified by N-hydroxy-N-2-aminofluorene.

Molecular models of induced DNA premutational damage and mutational pathways for the carcinogen 4-nitroquinoline 1-oxide and its metabolites

The carcinogen 4-nitroquinoline 1-oxide (4NQO) and its metabolites undergo intercalative or covalent binding with DNA. Recent evidence indicates that the latter binding pattern is probably facilitated by an initial weaker intercalative interaction that can align potentially reactive sites on a 4NQO-metabolite and adjacent stacked bases. In the present study, we have proposed numerous possible covalent reaction products between 4NQO and its metabolites with DNA mini-helices based on chemical properties and key 'short-contacts' after energy-minimization in 21 different intercalative-like complexes. It is known from numerous experimental studies that 90% of the quinoline-bound DNAs in vivo involve guanine with the remaining 10% apparently involving adenine residues. The results of the present study suggest that this trend is not due to the greater affinity of the quinolines for guanine, but instead results from secondary processes involving the preferential formation of apurinic sites at aralkyl-adenine residues over that of aralkyl-guanine residues. In addition, observed mutational patterns can be rationalized in terms of the proposed reaction-products. The role of DNA repair mechanisms in the removal and correction of the different proposed reaction products are discussed. The binding pattern of several other aromatic carcinogens are similar to those depicted in the present work for the 4NQO-metabolites; hence the present study may be of some general significance.

Modification of deoxyribonucleic acid by a diol epoxide of benzo[a]pyrene. Relation to deoxyribonucleic acid structure and conformation and effects on transfectional activity

The effects of secondary structure on DNA modification by (+/-)-7 beta, 9 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenzol[a]pyrene [(+/-)BPDE I] were investigated. No differences in the total extent of (+/-) BPDE I binding to double- and single-stranded calf thymus DNA were found. High-performance liquid chromatography (LC) of the nucleoside adducts obtained from hydrolysates of native and denatured calf thymus, as well as from superhelical and linear plasmid DNA, indicated that in all cases the major adduct (60--80% of total adducts) was formed by reaction of the (+) enantiomer of BPDE I with the N-2 position of dG residues in the DNA. A minor adduct formed from the reaction of the (-) enantiomer with dG residues was also detected and was present in greater amounts in denautred DNA than in native DNA. Small amounts of BPDE I--dA and BPDE I--dC adducts were also detected in both the single- and double-stranded DNAs. Restriction enzyme analysis of BPDE I modified SV40 and phage lambda DNA provided evidence that the modification of DNA by this carcinogen is fairly random with respect to nucleotide sequence. Partial hydrolysis of modified plasmid DNA by the single-strand-specific S1 nuclease and LC analysis of the nucleoside adducts in the digested and undigested fractions of the DNA revealed no preferential excision by the S1 nuclease of the different BPDE I--deoxynucleoside adducts. Functional changes in BPDE I modified DNA were demonstrated. With increasing extents of modification, there was a decrease in the ability of plasmid DNA to transfect a receptive Escherichia coli strain to antibiotic resistance.

Reactivity of the antibodies to DNA modified by the carcinogen N-acetoxy-N-acetyl-2-aminofluorene

Rabbits were immunized with native DNA modified by the carcinogen N-acetoxy-N-acetyl-2-aminofluorene. The interactions between the purified antibodies to nDNA-AAF (or the Fab fragments) and several ligands have been studied. By radioimmunoassay, nDNA-AAF, dDNA-AAF, and GMP-AAF were found to bind to the antibodies with about the same affinity. GMP-AF interacts slightly less, and GMP and N-OH-AAF do not interact. The values of the association constants deduced from fluorescence measurements for the binding of the Fab fragments to nDNA-AAF, dDNA-AAF, and GMP-AAF, in 50 mM NaCl, pH 7.5, are of the same order of magnitude. The values of the association constants with nDNA-AAF and dDNA-AAF depend upon salt concentration. From this variation; it is deduced that 1-1.5 phosphate groups interact by charge--charge interactions with the Fab fragments. The absorption and circular dischroism spectra of GMP-AAF, nDNA-AAF, and dDNA-AAF bound to the Fab fragments show that the Fab fragments induce similar perturbation to the three ligands. These results lead to the conclusion that the immunodeterminant group is the dGMP-AAF residue.

Reactivity of antibodies to guanosine modified by the carcinogen N-acetoxy-N-2-acetylaminofluorene

N-(guanosin-8-yl) acetylaminofluorene (Guo-AAF) was prepared by the reaction of N-acetoxy-N-2-acetylaminofluorene (AAAF) and guanosine. Antibodies to Guo-AAF were elicited in rabbits by immunization with bovine serum albumin-Guo-AAF conjugate. The antibodies were purified by affinity chromatography on a Sepharose-Guo-AAF column. The reactivity of these antibodies towards several ligands was studied by radioimmunoassay. The antibodies have the same affinity for double stranded DNA-AAF and single stranded DNA-AAF. Thus the geometry of the regions of DNA substituted by AAF residues is the same in native and denatured DNA. The affinity of the antibodies is smaller for DNA-AAF than for Guo-AAF. This can be due in part to the stacking of AAF residues with the adjacent bases as shown by the study of the interactions between the antibodies and AAF-oligonucleotides. The circular dichroism spectra of AAF-oligonucleotides bound to the antibodies are reported.

Benzo(a)pyrene 7,8-dihydrodiol-9,10-oxide modification of DNA: relation to chromatin structure and reconstitution

Purified duck reticulocyte DNA was incubated in vitro with a 7,8-dihydrodiol-9,10-oxide derivative of benzo(a)pyrene (BPDE). The carcinogen-modified DNA was somewhat more susceptible to partial digestion by the single strand specific endonuclease S1 than unmodified DNA, suggesting slight denaturation of the helix at sites of modification. Chromatin was reconstituted in vitro utilizing this carcinogen-modified DNA and unmodified-chromatin associated proteins. This reconstituted chromatin showed the same kinetics and extent of digestion by Staphylococcal nuclease, and similar nucleosome profiles on sucrose density gradient centrifugation, as those obtained with native chromatin or chromatin reconstituted with unmodified DNA. Moreover, polyacrylamide gel electrophoresis of DNA fragments obtained from nuclease digests gel electrophoresis of DNA fragments obtained from nuclease digests of the reconstituted chromatins suggested that the chromatin containing carcinogen-modified DNA had the same subnucleosome structure as that reconstituted with unmodified DNA. In a separate set of studies intact duck reticulocyte chromatin was reacted directly with BPDE. Nuclease digestion studies indicated that 65% of the carcinogen was bound to the 'open' regions of chromatin, and 35% to 'closed' regions. These results indicate that although convalent binding of a benzo(a)pyrene (BP) derivative to DNA produces local distortions in conformation of the helix, this modification does not appear to interfere with the ability of the DNA to associate with histones to form nucleosome structures. In addition, although DNA in the open regions of chromatin is more susceptible to reaction with the BP derivative, there is appreciable reaction with the DNA associated with histones.

Computer-generated graphic models of the N2-substituted deoxyguanosine adducts of 2-acetylaminofluorene and benzo[a]pyrene and the O6-substituted deoxyguanosine adduct of 1-naphthylamine in the DNA double helix

Computer models of three deoxyguanosine-carcinogen adducts in double-helical DNA are presented. The carcinogen moiety is rotated and the best fit within the double helix is evaluated. The 2-acetylaminofluorene (AAF) derivative, 3-(deoxyguanosin-N2-yl)-AAF, is found to be situated within the minor groove, has very little freedom of rotation and causes little helical distortion. The (+)-anti-benzo[a]-pyrene (BP)-diol epoxide-N2 adduct, 10beta-(deoxyguanosin-N2-yl)-7beta, 8alpha,9alpha-trihydroxy-7,8,9,10-tetrahydro-BP, has a similar fit with a greater degree of steric interaction, suggesting that this adduct could cause some local destabilization. The 1-naphthylamine (NA) derivative, N1-(deoxyguanosine-O6-yl)-1-NA, resides within the major groove, does not perturb the helix and has considerable freedom of movement.

Conformation of dinucleoside monophosphates modified with benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide as measured by circular dichroism

The conformational properties of GpU modified with the reactive derivative of benzo[a]pyrene, (+/-)-7beta,8alpha-dihydroxy-9alpha,10alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, has been investigated utilizing circular dichroism spectroscopy. Binding of this carcinogen to the N2 of G residues in GpU resulted in the formation of four compounds (I to IV) representing two pairs of diastereoisomers. The molar ellipticity values of the modified dimers were approximately twofold higher than those of the modified guanosine monomers. These values were decreased appreciably when the spectra of the dimers were obtained at 80 degrees C or in methanol rather than at 25 degrees C in water, suggesting that under the latter conditions there is a stacking interaction between the carcinogen and the neighboring uridine residue. Based on these results, a conformation is proposed for modified GpU. It includes insertion of the benzo[a]pyrene moiety, by rotation of the modified guanine residue about its glycoside bond, coplanar to the neighboring uridine and perpendicular to the phosphodiester backbone.

Conformation of DNA modified with a dihydrodiol epoxide derivative of benzo[a]pyrene

The conformation of calf thymus DNA modified by reaction with (+/-)-7beta,8alpha-dihydroxy-9alpha,10alpha-epoxy7,8,9,10-tetrahydrobenzo[a]pyrene, which binds covalently mainly to the 2-amino group of guanosine residues, was studied. With samples in which 1.5 or 2.2% of the bases were modified, there was a slight decrease in Tm during heat denaturation and a slight increase in susceptibility to the single strand specific nuclease S1. In a DNA sample in which 4.5% of the bases were modified, there was an appreciable decrease in Tm and a marked increase in susceptibility to S1 nuclease. The kinetics of the reaction of the modified DNAs with formaldehyde provided evidence for locally destabilized regions ranging from 1 to 7 base plates, depending on the extent of modification. Alkaline and neutral sucrose gradient analyses revealed no evidence for strand breakage in the 1.5 and 2.2% modified samples, although single-strand breaks were found in the 4.5% modified samples. Taken together, these results suggest that DNA molecules containing a covalently bound benzo[a]pyrene derivative have an altered conformation characterized by small localized regions which are destabilized and easily denatured. The conformational changes associated with the covalent binding of the benzo[a]pyrene derivative to native DNA appear to be different from, and less marked, than those associated with the covalent binding of N-2-acetylaminofluorene to native DNA.

Adduct formation between the carcinogen N-acetoxy-2-acetylaminofluorene and synthetic polydeoxyribonucleotides

The chemical carcinogen N-acetoxy-2-acetylaminofluorene (NA-AAF) was reacted with poly(dG-dC) - poly(dG-dC); poly dG - poly dC; poly(dA-dT) - poly (dA-dT); and poly dA - poly dT under a variety of conditions. Poly (dG-homo GC polymer and 10--20 more reactive the A + T polymers. Lowering the ionic strength increased the extent of reaction, while pH change (8.9 vs. 5.5) had only a small effect. If ionic strength was adjusted so that the two guanine-containing polymers showed equal thermal stability (as judged by Tm) then the alternating copolymer was 7 times as reactive as the homopolymer. In aggreement with previous investigators, the major product was found to be 8-(N-2-fluorenylacetamido) deoxyguanosine.

Comparative orientation of the fluorene residue in native DNA modified by N-acetoxy-N-2-acetylaminofluorene and two 7-halogeno derivatives

Native calf thymus DNA was reacted with N-acetoxy-N-2-acetylaminofluorene (N-AcO-AAF) and its 7-fluoro and 7-iodo derivatives. Different ways of purification of the fluorene modified DNA samples were checked in order ot obtain a nucleic acid free from all noncovalently bound fluorene residues. The decrease in melting temperature in DNA samples modified by N-AcO-AAF(DNA-AAF) was carefully reinvestigated. From these experiments, we conclude that the melting temperature decrease is equal to 1.15 degree C per percent of modified bases, in DNA-AAF samples. Electric dichroism measurements on sonicated DNA samples modified by the different fluorene derivatives show the fluorene ring perpendicular to the helix axis in the case of the N-AcO-AAF and its fluoro derivative, and lying alone the phosphate-sugar backbone in the case of the iodo derivative. The results presented in this paper, along with those obtained earlier, led us to propose an "insertion-denaturation model" for the mode of binding of N-Aco-AAF and its fluoro derivative, and an "outside binding model" for the iodo derivative. Discrepancies with the data obtained by Chang et al.((1974) Biochemistry 13,2142-2148) concerning the melting temperature decrease and the electric dichroism results are observed and discussed.