Conformation of the deoxydinucleoside monophosphate dCpdG modified at carbon 8 of guanine with 2-(acetylamino)fluorene

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

C8-Guanine modifications: effect on Z-DNA formation and its role in cancer

Participation of Z DNA in normal and disease related biological processes.

C8-linked bulky guanosine DNA adducts: experimental and computational insights into adduct conformational preferences and resulting mutagenicity

Bulky DNA adducts are formed through the covalent attachment of aryl groups to the DNA nucleobases. Many of these adducts are known to possess conformational heterogeneity, which is responsible for the variety of mutagenic outcomes associated with these lesions. The present contribution reviews several conformational and mutagenic themes that are prevalent among the DNA adducts formed at the C8-site of the guanine nucleobase. The most important conclusions obtained (to date) from experiments are summarized including the anti/syn conformational preference of the adducts, their potential to inflict DNA mutations and mismatch stabilization, and their interactions with DNA polymerases and repair enzymes. Additionally, the unique role that computer calculations can play in understanding the structural properties of these adducts are highlighted.

Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates

M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.

A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4)

Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607–4616]. Our goal is to elucidate on a structural level how AAF-dG can be harbored in the Dpo4 active site opposite an incoming dCTP, using molecular modeling and molecular dynamics simulations, since AAF-dG prefers the syn glycosidic torsion. Both anti and syn conformations of the templating AAF-dG in a Dpo4 ternary complex were investigated. All four dNTPs were studied. We found that an anti glycosidic torsion with C1′-exo deoxyribose conformation allows AAF-dG to be Watson–Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting. The AAF is situated in the Dpo4 major groove open pocket with fluorenyl rings 3′- and acetyl 5′-directed along the modified strand, irrespective of dNTP. With AAF-dG syn, the fluorenyl rings are in the small minor groove pocket and the active site region is highly distorted. The anti-AAF-dG conformation with C1′-exo sugar pucker can explain the preferential incorporation of dC by Dpo4. Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed.

Total energy of deoxyguanosine bonded to N-2-acetylaminofluorene by the semi-empirical modified-neglect of differential diatomic overlap method

We have computed the total energy surface as a function of two important torsion angles of the carcinogen N-2-acetylaminofluorene (AAF) bonded to the carbon C8 of deoxyguanosine using the semi-empirical quantum mechanical method, MNDO. One global minimum and one local minimum are found separated by an appreciable barrier. The equilibrium geometries show the rearrangement of AAF and the base consistent with experimental observations of previous investigators.

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

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

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

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

Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)-DNA

The structure of Z-DNA, currently accepted as a model for all left-handed DNAs, fails to provide convincing explanations for at least four well established properties of left-handed DNA polymers in solution. However, the major discrepancies between theory and experiment are resolved by the structure presently proposed for Z[WC]-DNA, a new left-handed, zig-zag double helix with Watson-Crick-type backbone directions. Structural features of Z[WC]-DNA include the presence of an additional H-bond between each guanine N2-amino group and an adjacent phosphate oxygen, the capacity to form four-stranded, base-matched complexes that should readily precipitate from solution, and backbone progressions that are the same as B-DNA (opposite to Z-DNA). However, since Z[WC]-DNA and Z-DNA have many parameters in common, they could be difficult to distinguish in a majority of existing experiments. In view of the close relationship of the new helix to B-DNA, which allows a relatively unhindered right-to-left transition in handedness, Z[WC]-DNA is theorized to be the left-handed structure preferentially generated in vivo by the torque available in naturally occurring DNA supercoils.

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)).

Prediction of DNA structure from sequence: a build-up technique

A build-up technique has been devised that permits prediction of DNA structure from sequence. No experimental information is employed other than the force field parameters. This strategy for dealing with the multiple minimum problem requires a supercomputer to make the necessary global searches. The number of energy minimization trials that were made for each of the 16 deoxydinucleoside monophosphate conformational building blocks of DNA was 1944. As a test case, the minimum energy conformations of d(GpC) and d(CpG) to 5.5 kcal/mole were then combined to generate energy-minimized structures for d(CpGpC). The number of trials that were made for d(CpGpC) was 3752. Minima for this single-stranded trimer to 15 kcal/mole were then employed to search for minimum energy conformations of the duplex d(CpGpC).d(GpCpG). The number of starting conformations that were utilized at this stage was 1514. The lowest energy duplex had a Z-II-DNA conformation, followed by a B-DNA form at 1.2 kcal/mole. The A- and Z-I-forms as well as many novel Watson-Crick base-paired structures were found at higher energy. Finally, energy-minimized structures of d(CG)6.d(CG)6 in Z-II and B-DNA conformations were computed using torsion angles from the analogous duplex trimer minima.

Single adduct mutagenesis: strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot

2-Acetylaminofluorene (AAF), a potent rat liver carcinogen that binds covalently to the C-8 position of guanine residues in DNA, is an effective frameshift mutagen. The mutations are distributed nonrandomly, in that most are located at a few specific DNA sequences (i.e., mutation hot spots). Among these hot spots, the Nar I sequence (GGCGCC) is especially susceptible to the induction of -2 frameshift mutations (GGCGCC----GGCC). Due to the nature of the Nar I sequence, G1G2CG3CC, three different molecular events, each involving the deletion of two contiguous base pairs (i.e., G2C, CG3, G3C), can give rise to the observed end point (GGCC). To compare the potential role of each of the three possible guanine-AAF adducts in the Nar I site to induce the -2 frameshift mutation, we constructed double-stranded plasmid molecules containing a single-AAF adduct bound to one of the three guanine positions. Using these plasmids, we found that only the adduct in the G3 position induces the -2 frameshift mutation. This strong effect of the position of the -AAF adduct within the Nar I site is discussed in relation to the possible involvement of an unusual DNA conformation in the mutagenic processing.

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.

Targeted mutations induced by a single acetylaminofluorene DNA adduct in mammalian cells and bacteria

Mutagenic specificity of 2-acetylaminofluorene (AAF) has been established in mammalian cells and several strains of bacteria by using a shuttle plasmid vector containing a single N-(deoxyguanosin-8-yl)acetylaminofluorene (C8-dG-AAF) adduct. The nucleotide sequence of the gene conferring tetracycline resistance was modified by conservative codon replacement so as to accommodate the sequence d(CCTTCGCTAC) flanked by two restriction sites, Bsm I and Xho I. The corresponding synthetic oligodeoxynucleotide underwent reaction with 2-(N-acetoxy-N-acetylamino)-fluorene (AAAF), forming a single dG-AAF adduct. This modified oligodeoxynucleotide was hybridized to its complementary strand and ligated between the Bsm I and Xho I sites of the vector. Plasmids containing the C8-dG-AAF adduct were used to transfect simian virus 40-transformed simian kidney (COS-1) cells and to transform several AB strains of Escherichia coli. Colonies containing mutant plasmids were detected by hybridization to 32P-labeled oligodeoxynucleotides. Presence of the single DNA adduct increased the mutation frequency by 8-fold in both COS cells and E. coli. Over 80% of mutations detected in both systems were targeted and represented G.C----C.G or G.C----T.A transversions or single nucleotide deletions. We conclude that modification of a deoxyguanosine residue with AAF preferentially induces mutations targeted at this site when a plasmid containing a single C8-dG-AAF adduct is introduced into mammalian cells or bacteria.

Visualization of an AAF induced frameshift mutation: molecular views of base displacement in B-DNA from minimized potential energy calculations

Energy minimized structures of base displacement in an AAF modified B-DNA dodecamer are presented. A rational search strategy, beginning with a global search of the conformation space of the modified deoxydinucleoside monophosphate, together with model building by computer graphics, has been employed. A number of different minimum energy conformations have been located which reveal base displaced structures. These show fluorene interstrand stacking, fluorene inter- and intrastrand stacking, and non-stacked fluorene situated in the denatured bulge. The local helix axis is bent to various extents in the different forms, and one or two base pairs are fully denatured. One structure of special interest offers a molecular view that suggests how AAF can induce the -2 deletion mutation observed in AAF modified E. coli.

Specific strand loss in N-2-acetylaminofluorene-modified DNA

N-2-Acetylaminofluorene (AAF), a well-known chemical carcinogen, when covalently linked to guanine residues constitutes a premutagenic lesion that is converted in vivo into frameshift mutations. In Escherichia coli, it is thought that -AAF adducts block the replication fork and that the mutagenic processing of the -AAF adducts is mediated by the SOS response. The construction in vitro of plasmids containing -AAF adducts in one strand only of a double-stranded DNA molecule enabled us to investigate the segregation of the strands and the mutagenicity of the lesions in vivo. The two DNA strands were "genetically labelled" by means of a single base-pair mismatch in the tetracycline-resistance gene, one strand carrying the wild-type allele and the other strand a mutant tetracycline-sensitive allele. The two strands contained either no -AAF adducts, -AAF adducts in one strand or -AAF adducts in both strands. When such constructions are used to transform bacterial cells the following are found. When no -AAF adducts are present on either strand of the DNA, a mixture of plasmids having information from both parent strands is found in 80% of the transformed bacterial clones. With -AAF adducts present in one strand only, in 90% of the transformants there is a consistent loss of the parent strand information that contained the -AAF adducts. In the constructions having -AAF adducts in both strands, the transformed bacteria carry either one or the other allele in a pure form. Our results suggest that when blocking lesions (-AAF adducts) are present in one strand only, they trigger the specific loss of that strand. The forward mutation frequency (i.e. the tetracycline-resistance gene inactivation frequency) was found to be more than ten times lower when the -AAF adducts are bound to one strand only compared with the situation where both strands carry the premutagenic lesions. Moreover, when the isolated mutants were sequenced, the mutations were found to consist of a mixture of true -AAF-induced mutations (i.e. -1 or -2 frameshift mutation at previously determined mutation hot spots) and of mutations that are not targeted at -AAF adducts. We suggest that these "background" mutants arose from the mutagenic processing of cryptic lesions present in our DNA. The low mutagenic efficiency of -AAF adducts, when present in one strand only of a duplex DNA, most probably results from the above-described loss of the damaged strand.(ABSTRACT TRUNCATED AT 400 WORDS)

Energy minimized structures of carcinogen-DNA adducts: 2-acetylaminofluorene and 2-aminofluorene

Energy minimized structures of DNA modified by the aromatic amines 2-acetylaminofluorene (AAF) and 2-aminofluorene (AF), for which no experimental atomic resolution data exist, are presented. These have been computed with a new molecular mechanics program specifically designed to define distortions imposed by such adducts, and employing a rational strategy for searching the conformation space of a DNA molecule with covalently linked carcinogen. In alternating G-C sequences, the AAF adduct prefers to reside at the exterior of an undeformed Z-helix. It can also induce base displacement with attendant denaturation and helix bending in sequences that disfavor the Z form, but undeformed B helices are excluded. The AF adduct, by contrast, prefers the major groove of an unperturbed B-helix, but can also induce carcinogen-base stacking in single stranded regions of the DNA, such as at the replication fork. The different biological properties of these two adducts may be related to their distinct

N-hydroxyaminofluorene: a chemical probe for DNA conformation

The importance of the polymorphism of DNA in the reaction with the chemical carcinogen N-hydroxyaminofluorene is studied by means of a supercoiled plasmid containing an insert of (dC-dG). Immunochemical titration and the determination of the binding spectrum of -aminofluorene adducts show that the carcinogen reacts with B-DNA but not with Z-DNA and that conformational changes of the B-DNA-Z-DNA junctions occur as a function of the superhelical density.

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.

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.

DNA binding and mutation spectra of the carcinogen N-2-aminofluorene in Escherichia coli. A correlation between the conformation of the premutagenic lesion and the mutation specificity

When the chemical carcinogen N-2-acetylaminofluorene binds to DNA in vivo, two major adducts are formed, both at position C-8 of the guanine residue. One of these (the acetylaminofluorene adduct) retains the acetyl group, while the other (the aminofluorene adduct) is the corresponding deacetylated form. Unlike -AAF adducts, which trigger important structural changes of the DNA secondary structure (either the insertion-denaturation model or the induction of a Z-DNA structure, depending upon the local nucleotide sequence), -AF adducts bind to the C-8 of guanine residues without causing any major conformational change of the B-DNA structure. Well-defined adducts (either -AF or -AAF) can be formed in vitro by reacting DNA with either N-hydroxy-N-2-aminofluorene or N-acetoxy-N-2-acetylaminofluorene. Specific cleavage of the phosphodiester backbone at -AF adducts can be achieved by treating -AF-modified DNA in 1 M-piperidine at 90 degrees C. This observation led us to construct the spectrum for -AF binding to a defined DNA restriction fragment. It is found that only guanine residues react to form alkali-labile lesions and that the reactivity among the different guanines is similar. In a forward mutation assay, namely the inactivation of the tetracycline resistance gene, we found previously that more than 90% of mutations induced by -AAF adducts are frameshift mutations. Using the same assay, we show here that -AF adducts induce primarily base substitution mutations (85%), mainly of the G to T transversion type. There is therefore a strong correlation between the nature of the carcinogen-induced conformational change of the DNA structure and the corresponding mutation specificity. The -AF-induced base substitution mutations depend upon the umuC gene function(s). The data obtained in our forward mutation assay are compared to the data previously obtained in the histidine reversion assay (Ames test).

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.

A role for DNA polymerase in the specificity of nucleotide incorporation opposite N-acetyl-2-aminofluorene adducts

Escherichia coli DNA polymerase I (Klenow fragment), DNA polymerase alpha from both calf thymus and human lymphoma cells and DNA polymerase beta from calf thymus and Novikoff hepatoma cells can incorporate nucleotides opposite N-guanin-8-yl-acetyl-2-aminofluorene in DNA. The polymerases incorporate dCTP opposite some AAF-dG lesions when Mg2+ is the divalent cation. Substitution of Mn2+ for Mg2+ broadens the specificity of insertion: E. coli DNA polymerase I (Klenow fragment) also inserts A, and at specific sites G or T; DNA polymerase alpha inserts any of the four dNTPs with A and C incorporated preferentially to G and T. Polymerase beta is specific, inserting mainly C even in the presence of Mn2+. The Km for addition of dATP opposite a lesion by E. coli polymerase I (Klenow fragment) in the presence of Mn2+ is about 0.5 mM. dNMPs increase the insertion of nucleotides opposite AAF-dG in the presence of Mg2+ and increase both the rate and number of sites at which incorporation occurs in the presence of Mn2+. dNTP alpha S and recA protein increase only the insertion of C. We suppose that the incorporation of dCTP reflects normal base-pairing with the AAF-deoxyguanine in the anti conformation, whereas insertion of the other nucleotides (including some of the C) reflects insertion opposite the AAF adduct in its preferred syn conformation. The fact that the DNA polymerase plays a role in determining the specificity of insertion opposite a lesion terminating DNA synthesis suggests that the spectrum of base substitution mutagenesis seen in vivo may reflect the properties of the protein components, including the polymerase, involved in bypass synthesis.

Preferential reaction of the carcinogen N-acetoxy-2-acetylaminofluorene with satellite DNA

The carcinogens N-acetoxy-2-acetylaminofluorene (N-acetoxy-AAF) and N-hydroxy-2-aminofluorene (N-hydroxy-AF) were incubated with calf thymus DNA to determine if reaction occurred preferentially with discrete regions within the DNA. Derivative melting profiles indicated that both compounds decreased satellite transitions and that N-acetoxy-AAF depressed the melting of higher temperature regions. These data suggest that N-acetoxy-AAF reacted to a greater extent with G + C-rich regions and, because the resulting adduct disrupted the helix, the cooperativity of melting decreased. Reaction of N-acetoxy-AAF with purified satellite III DNA confirmed the preferential interaction of this carcinogen with G + C-rich regions as compared to main component DNA. The derivative melting profile of lambda DNA in the presence of actinomycin D further demonstrated that this type of analysis can detect preferential interactions with specific DNA sequences.

A conformational analysis of the (+) anti BPDE adduct to the guanine amino group of dCpdG

The (+) anti isomer of benz[a]pyrene diol epoxide (BPDE), 7 beta, 8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenz [a] pyrene has been identified as the probable tumorigenic lesion in mammalian systems. It forms a predominant adduct with DNA at N2 of guanine. In order to elucidate its conformation in atomic resolution detail, minimized conformational potential energy calculations were performed for the adduct with dCpdG. A global conformation search involving about 1000 trials was made. The lowest energy conformation had stacking between the hydrocarbon and the adjacent cytidine, in agreement with CD studies on modified GpU and UpG. This conformer differed from the B form most notably in the guanine glycosidic torsion, which is high anti. The next lowest energy form had torsion angles like the B form, with guanine-cytidine stacking. These two conformers differ in energy by only 2.1 kcal./mole, suggesting that their relative stability could easily be reversed in larger polymers, or under specific environmental conditions. Other conformations, with base-hydrocarbon or base-base stacking are also found, at somewhat higher energies. The Z form is at 7.8 kcal./mole. Thus, this adduct stabilizes the B form, in contrast with the N2 linked AAF adduct, which stabilizes the Z conformation.

Interactions of molecules with nucleic acids. X. Covalent intercalative binding of the carcinogenic BPDE I(+) to kinked DNA

A theoretical model is proposed for the covalent binding of (+) 7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene denoted by BPDE I(+), to N2 on guanine. The DNA must kink a minimum of 39 degrees to allow proper hybrid configurations about the C10 and N2 atoms involved in bond formation and to allow stacking of the pyrene moiety with the non-bonded adjacent base pair. Conservative (same sugar puckers and glycosidic angles as in B-DNA) and non-conservative (alternating sugar puckers as in intercalation sites) conformations are found and they are proposed structures in pathways connecting B-DNA, an intercalation site, and a kink site in the formation of a covalently intercalative bound adduct of BPDE I(+) to N2 on guanine. Stereographic projections are presented for (3') and (5') binding in the DNA. Experimental data for bending of DNA by BPDE, orientation of BPDE in DNA and unwinding of superhelical DNA is explained. The structure of a covalent intercalative complex is predicted to result from the reaction. Also, an anti----syn transition of guanine results in a structure which allows the DNA to resume its overall B-form. The only change is that guanine has been rotated by 200 degrees about its glycosidic bond so that the BPDE I(+) is bound in the major groove. The latter step may allow the DNA to be stored with an adduct which may produce an error in the genetic code.

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.

AAF linked to the guanine amino group: a B-Z junction

Minimized conformational potential energy calculations have been performed for AAF linked to dCpdG at the guanine amino group. This is a model for the minor AAF adduct observed in DNA, whose conformational influence has been difficult to ascertain. A global minimum energy conformation was computed with torsion angles like those of the dCpdG residue of Z-DNA. This conformation was incorporated into a larger polymer model at a B-Z junction, with the carcinogen residing in the groove in the Z direction. Local minimum energy conformations of the B type were also computed. In addition, two minima were found with fluorenecytidine stacking. These results suggest that existing B-Z junctions may be vulnerable to modification by AAF at the guanine amino group, or that such junctions may be induced by the carcinogen if the base sequence is appropriate. Otherwise the carcinogen can be located in the minor groove of the B helix (5, 10, 11) or covalently intercalated (13-15).

Effect of acetylated and deacetylated 2-aminofluorene adducts on in vitro DNA synthesis

We have constructed primed phi X174 DNA templates containing either acetylated or deacetylated aminofluorene adducts at the C-8 position of guanine. T4 DNA polymerase terminates synthesis one nucleotide before the acetylated adducts but incorporates an additional nucleotide opposite the deacetylated guanylaminofluorene. These observations can be explained by the known preferred conformations of the acetylated and deacetylated guanosinylaminofluorene nucleosides--the former favoring the syn conformation (so that in DNA the guanine is displaced from the helix by the fluorene ring) and the latter preferring the anti conformation (which allows normal base pairing of the guanine with cytosine). A similar differentiation between the two adducts was found with Escherichia coli DNA polymerase I. In contrast, avian myeloblastosis virus (AMV) reverse transcriptase, which terminated with a nucleotide inserted opposite the acetylated adducts, was less able to do so at the deacetylated adducts. The nucleoside incorporated by AMV reverse transcriptase opposite the acetylated adduct was exclusively cytidine, which suggests regular base pairing with the reacted guanosine nucleoside in the anti conformation; however, synthesis was completely blocked and unable to continue beyond this point. The differences between the termination patterns of the prokaryotic enzymes and AMV reverse transcriptase indicates that specific properties of a replicating polymerase can influence the conformation of a reacted nucleoside in the DNA, thus altering its recognition and possibly its mutagenic activity.