N3 Of Adenine Research Articles

Molecular basis for sequence selective DNA alkylation by (+)- and ent-(−)-CC-1065 and related agents: Alkylation site models that accommodate the offset AT-rich adenine N3 alkylation selectivity

A detailed evaluation of the DNA alkylation selectivity of (+)-CC-1065, ent-(−)-CC-1065 and a series of aborted and extended analogs possessing the CPI alkylation subunit is detailed and the refinement of a model that accommodates the offset AT-rich adenine N3 alkylation selectivity of the enantiomeric agents is presented. The natural enantiomers bind in the minor groove in the 3′→5′ direction starting from the adenine N3 alkylation site across a 2 base ( N-BOC-CPI; i.e. 5′-A A ), 3.5 base (CPI-CDPI 1/CPI-PDE-I 1; i.e. 5′-AA A ), 5 base (CC-1065/CPI-CDPI 2; i.e. 5′-AAAA A ) or 6.5 base (CPI-CDPI 3; i.e. 5′-AAAAA A ) AT-rich site. In contrast, the unnatural enantiomers bind in the reverse 5′→3′ direction in the minor groove and the binding site necessarily starts at the first 5′ base preceding the adenine N3 alkylation site and extends across the alkylation site to the adjacent 3′ bases covering an AT-rich site of 2 bases ( N-BOC-CPI; e.g., 5′-A A ), 5 bases (CC-1065/CPI-CDPI 2; eg. 5′-A A AAA), or 6.5 bases (CPI-CDPI 3; e.g. 5′-A A AAAA). Notably, the model accommodates the unusual observation that both enantiomers of N-BOC-CPI alkylate the same sites within duplex DNA (5′-A A > 5′-T A ) and the required reversed binding orientation of the enantiomeric agents. The reversed binding orientation is required to permit access to the electrophilic cyclopropane and the resulting offset AT-rich alkylation selectivity is the natural consequence of the diastereomeric relationship of the adducts. Three dimensional models of the natural and unnatural enantiomer alkylations are presented which clearly illustrate the offset binding sites. A fundamentally simple model for the CC-1065 DNA alkylation reaction, that accommodates the behavior of both enantiomers, is provided in which the sequence selectivity is derived from the noncovalent binding selectivity of the agents preferentially in the narrower, sterically more accessible AT-rich minor groove, the inherent steric accessibility to the adenine N3 alkylation site that accompanies deep penetration of the agent into the minor groove within an AT-rich site, and the 2 base-pair ( N-BOC-CPI), 3.5 base-pair (CPI-PDE-I 1/CPI-CDPI 1), 5 base-pair (CC-1065/CPI-CDPI 2), or 6.5 base-pair (CPI-CDPI 3) site size required to permit agent binding in the minor groove at the alkylation site. Using the models, a simple explanation for the distinguishing DNA alkylation rate, efficiency, and biological potency of enantiomeric pairs of agents is detailed based on the unnatural enantiomer sensitivity to steric bulk at the CPI C7 center.

Mutation spectra of 1,2-dibromoethane, 1,2-dichloroethane and 1-bromo-2-chloroethane in excision repair proficient and repair deficient strains of Drosophila melanogaster.

DNA sequence changes produced by 1,2-dibromoethane (DBE), 1,2-dichloroethane (DCE) and 1-bromo-2-chloroethane (BCE) were analyzed using the vermilion locus of Drosophila melanogaster. Under excision repair proficient (exr+) conditions (mutagenized exr+ males mated with exr+ females) all mutants isolated from the first generation (F1) after DBE and DCE exposure represented DNA rearrangements (multi-locus deletions, small deletions with tandem repeats, duplicate insertions). By contrast, mutants expressing a vermilion phenotype only in the F2 (F1 mosaics) all carried single bp changes. When exr+ males, after exposure to DBE, were mated to excision repair deficient (exr-) mus 201 females 11 of 14 mutational events isolated from either F1 or F2 progeny were single bp changes. In general the mutation spectra for the three dihaloalkanes were similar to the spectrum obtained at the same locus for the direct-acting monofunctional agent methylmethanesulfonate (MMS). The data lend support to the conclusions that these 1,2-dihaloalkanes are genotoxic through modification at ring nitrogens in DNA, primarily at the N7 of guanine and, to a lesser extent, at the N1 of adenine. These N-adducts could be directly miscoding. However, more important for the mutagenic action of the chemicals seems to be the formation of non-coding lesions and/or misrepair.

Identification of the major lesion from the reaction of an acridine-targeted aniline mustard with DNA as an adenine N1 adduct.

DNA adducts of two acridine-linked aniline half-mustards have been isolated and identified. The compound where the half-mustard is attached to the DNA-targeting acridine moiety by a short linker chain alkylates both double- and single-stranded DNA exclusively at guanine N7, as do the majority of known aromatic and aliphatic nitrogen mustards. The longer-chain analogue, also containing a more reactive half-mustard, shows a strikingly different pattern, alkylating double-stranded DNA to yield primarily (> 90%) the adenine N1 adduct, together with < 10% of the adenine N3 adduct and only trace amounts of the guanine N7 adduct. In the presence of MgCl2 (which is known not to inhibit the interaction of drugs at minor groove sites), the adenine N3 adduct is the major product. The latter compound is the first known aniline mustard (and apparently the first known alkylating agent of any type) to preferentially alkylate adenine at the N1 position in duplex DNA. These results are consistent with previous work [Prakash et al. (1990) Biochemistry 29, 9799-9807], which showed that the preferred site of DNA alkylation by the corresponding long-chain acridine-linked aniline bis-mustards in general was at major groove sites of adenines and identifies the major site of alkylation as adenine N1 and not N7. This selectivity for adenine N1 alkylation is suggested to result from a preference for the acridine mustard side chain of these compounds to project into the major groove following intercalation of the acridine, coupled with structural distortion of the DNA helix to make the N1 positions of adenines adjacent to the intercalation sites more accessible.

3T3 NIH murine fibroblasts and B78 murine melanoma cells expressing the Escherichia coli N3-methyladenine-DNA glycosylase I do not become resistant to alkylating agents.

The role of alkylation of the N3 position of adenine in the cytotoxicity of alkylating agents in mammalian cells is still undefined. By co-transfecting NIH3T3 murine fibroblast and murine B78 H1 melanoma cells with pSG5tag and pSV2neo, we obtained clones expressing the mRNA of the bacterial tag gene coding for N3-methyladenine-DNA glycosylase I (Gly I), which specifically repairs N3-methyladenine. The levels of Gly I were 400 times higher in NIH3T3 pSG5tag (clone 3.9.4) and 12-33 times higher in B78 H1 tag clones (2A4, 2A6, 2C3 and 2D1) than in the respective control cells. The sensitivity to alkylating agents was evaluated in tag-expressing cells in comparison with pSG5, pSV2neo co-transfected control cells. As regards the cytotoxic activity of methylating agents (N-methylnitrosourea, N-methyl-N'-nitro-N-nitrosoguanidine, dimethylsulfate and temozolomide) and other alkylators with different structure and different interactions with DNA such as CC-1065 and FCE-24517 (minor groove binders known to bind to N3 of adenine), 4-[bis(2-chloroethyl)amino]-L-phenylalanine and cis-diamminedichloroplatinum II, cytotoxicity was the same for tag-expressing and non-expressing cells. These results suggest that the increased expression of N3-methyladenine-DNA glycosylase is not necessarily a crucial mechanism for the resistance of cells to alkylating agents.

Design, synthesis, and evaluation of DNA minor groove binding agents: the duocarmycins

Abstract

The replication fate of R- and S-styrene oxide adducts on adenine N6 is dependent on both the chirality of the lesion and the local sequence context.

In order to deduce the biological fate of adducts formed by the reaction of styrene oxide, a suspected carcinogen, with DNA, four oligodeoxynucleotides were synthesized which contained either R- or S-styrene oxide lesions on the N6 position of neighboring adenines within the human N-ras codon 61. When these adducted oligodeoxynucleotides were ligated into the single-stranded vector M13mp7L2 and the modified DNA used to transform repair-deficient Escherichia coli, the resultant plaque-forming abilities were found to vary as much as 300-fold, depending on the stereochemical configuration of the styrene oxide lesion and the sequence context in the vicinity of the damage. The frequency of mutations caused by the various styrene oxide adducts were similarly dependent on both their chirality and local sequence context. Oligodeoxynucleotide templates bearing these same four adducts were also constructed in order to evaluate their replication in vitro by the Klenow fragment. Three of the four styryl-modified templates yielded significant levels of fully extended primer upon polymerization. In contrast, the template containing R-styrene oxide at the second position of N-ras 61 was a very poor substrate for replication, a result which correlates well with the observed lethality of this lesion in vivo.

DNA interstrand cross-links induced by the cyclopropylpyrroloindole antitumor agent bizelesin are reversible upon exposure to alkali.

Bizelesin, a cyclopropylpyrroloindole (CPI) antitumor agent, has been shown to alkylate and cross-link DNA within A/T-rich tracts. Previous studies have shown that covalent reaction of the CPI adozelesin with DNA was reversible [Warpehoski, M. A., Harper, D. E., Mitchell, M. A., & Monroe, T. J. (1992) Biochemistry 31, 2502-2508]. That is, the monofunctional adduct could be lost from DNA, thus restoring the fidelity of DNA. In this study, we demonstrate that covalent DNA adducts induced by bizelesin at the adenine N3 position undergo two subsequent competing reactions: one which causes DNA strand cleavage, via depurination, and one which proceeds through loss of the DNA adduct (adduct reversal with restoration of DNA integrity). Our results were obtained by studying the chemical stability of synthetic DNA oligonucleotides which contained either a distinct DNA monofunctional adduct or DNA interstrand cross-links. Quantification of adduct reversal was performed on the basis that drug-modified DNA, upon exposure to heat followed by hot piperidine treatment, was resistant to strand cleavage at the site of alkylation. The rate of adduct reversal was found to increase with increasing temperature and was found to be maximum at 70-80 degrees C. The rate of adduct reversal was also found to increase with increasing pH and ionic strength. In contrast, the rate of depurination and subsequent DNA strand cleavage decreased as pH and ionic strength were increased. Adduct reversal was favored in DNA containing interstrand cross-links, whereas rapid depurination occurred preferentially within monofunctionally alkylated DNA.

Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin.

The molecular structure of the complex between the minor groove binding drug netropsin and the dodecamer d(CGCAAATTTGCG) has been solved and refined by X-ray diffraction analysis to an R-factor of 19.8% and 2.2-A resolution. The drug lies in the narrow minor groove of the B-DNA fragment, covering five of the six A.T base pairs (from A5.T20 to T9.A16). The long six A.T base pair tract allows the drug to bind in a position that optimizes its contacts with the DNA, establishing hydrogen bonds with O2 of thymines and N3 of adenines. The DNA molecule shows a high propeller twist only at the A6.T19 step of the A-tract. Two three-centered hydrogen bonds are observed in the major groove at half of the A-tract.

Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition.

We have measured the binding of EcoRI endonuclease to a complete set of purine-base analogue sites, each of which deletes one functional group that forms a hydrogen bond with the endonuclease in the canonical GAATTC complex. For five of six functional group deletions, the observed penalty in binding free energy is +1.3 to +1.7 kcal/mol. For two of these cases (replacement of adenine N7 with carbon) a single protein-base hydrogen bond is removed without deleting an interstrand Watson-Crick hydrogen bond or causing structural "adaptation" in the complex. This observation establishes that the incremental energetic contribution of one protein-base hydrogen bond is about -1.5 kcal/mol. By contrast, deletion of the N6-amino group of the inner adenine in the site improves binding by -1.0 kcal/mol because the penalty for deleting a protein-base hydrogen bond is outweighed by facilitation of the required DNA distortion ("kinking") in the complex. This result provides direct evidence that the energetic cost of distorting a DNA site can make an unfavorable contribution to protein-DNA binding.

Analysis of the monoalkylation and cross-linking sequence specificity of bizelesin, a bifunctional alkylation agent related to (+)-CC-1065

The sequence specificity of bizelesin, an interstrand DNA-DNA cross-linker related to the monoalkylating compound (+)-CC-1065, was studied using restriction enzyme fragments. Bizelesin, like (+)-CC-1065, forms monoalkylation adducts through N3 of adenine but can also form DNA-DNA cross-links six base pairs apart on opposite strands. Compared to many other minor groove cross-linking compounds, bizelesin is very efficient at cross-linking DNA. There is a higher than expected proportion of cross-linked adducts based upon the relative number of cross-linked vs monoalkylated adducts. This is rationalized based upon the relative thermodynamic stability of the cross-linked vs monoalkylated species

Evaluation of functional Analogs of CC-1065 and the Duocarmycins incorporating the cross-linking 9a-chloromethyl-1,2,9,9a-tetrahydrocyclopropa[ c]benz[ e]indol-4-one (C 2BI) alkylation subunit

The DNA alkylation properties and in vitro cytotoxic activity of a series of analogs of CC-1065 and the duocarmycins incorporating the 9a-chloromethyl-1,2,9,9a-tetrahydrocyclopropa[ c]benz[ e]inol-4-one (C 2BI) alkylation subunit are detailed. The C 2BI-based agents have been shown to alkylate DNA within the minor groove in a fashion analogous to CC-1065 or duocarmycin. The stereoelectronically-controlled adenine N3 addition to the least substituted cyclopropane carbon occurs with a selectivity that represents a composite of the two enantiomers of the corresponding CBI-based agents. Additional high affinity alkylation sites were detected which were not prominent alkylation sites for either enantiomer of the CBI-based agents. Such sites may represent induced high affinity alkylation sites resulting from DNA cross-linking following complementary strand alkylation at a high affinity alkylation site and each such site detected proved consistent with predicted models of an adenine-adenine cross-linking event. Further, consistent with this interpretation, the C 2BI agents were shown to constitute efficient cross-linking agents with DNA cross-linking being observed at the same concentrations as DNA alkylation. In comparison to the parent CBI-based agents, the C 2BI-based agents proved to be approximately 100–10.000x less effective at DNA alkylation and 100–10,000x less potent in cytotoxic assays. This is suggested to be the consequence of a significant steric deceleration of the adenine N3 alkylation reaction attributable to the additional 9a-chloromethyl substituent. Consistent with this interpretation, the noncovalent binding constant of C 2BICDPI 2 for poly[dA]-poly[dT] proved nearly identical to that of CDPI 3 under kinetic binding conditions, and prolonged incubation of C 2BICDPI 2 with poly[dA]-poly[dT] (72 h, 25°C) provided covalent complexes with a helix stabilization comparable to that observed with (+)- or (−)-CPI-CDPI 2 indicating that the size of the C 2BI subunit inhibits but does not preclude productive DNA alkylation.

Chemistry of drug-induced DNA lesions

Recent results on the action mechanisms of naturally occurring DNA-damaging antitumor antibiotics have been described. These antibiotics include neocarzinostatin (NCS) and DNA alkylating, duocarmycin A and kapurimycin A3. A series of duplex hexanucleotides of modified bases were prepared and their selectivity for C5' and C4' oxidation in the NCS-mediated degradation was investigated. Based on the cleavage data, a new binding model that permits competitive hydrogen abstraction from C5' and C4' of the DNA deoxyribose moiety has been described. Chemistry of alkylation of self complementary octanucleotide d(CGTATACG) 2 by antitumor antibiotic duocarmycin A was described. It was demonstrated that N3 of adenine 6 attacks the cyclopropane subunit of duocarmycin A to produce the covalently alkylated adduct. In contrast, antibiotic kapurimycin A3 alkylate N7 of guanine 4 ofd(CGCG) 2 to provide the corresponding covalent adduct. Heating at 90°C degraded the adduct to kapurimycin A3-guanine adduct and the respective abasic site-containing oligonucleotide. The structures of heat-induced abasic sites were unambiguously characterized.

Design, synthesis, and evaluation of DNA minor groove binding agents

Abstract

(+)-CC-1065 as a structural probe of Mu transposase-induced bending of DNA: overcoming limitations of hydroxyl-radical footprinting

Phage Mu transposase (A-protein) is primarily responsible for transposition of the Mu genome. The protein binds to six att sites, three at each end of Mu DNA. At most att sites interaction of a protein monomer with DNA is seen to occur over three minor and two consecutive major grooves and to result in bending up to about 90 degrees. To probe the directionality and locus of these A-protein-induced bends, we have used the antitumor antibiotic (+)-CC-1065 as a structural probe. As a consequence of binding within the minor groove, (+)-CC-1065 is able to alkylate N3 of adenine in a sequence selective manner. This selectivity is partially determined by conformational flexibility of the DNA sequence, and the covalent adduct has a bent DNA structure in which narrowing of the minor groove has occurred. Using this drug in experiments in which either gel retardation or DNA strand breakage are used to monitor the stability of the A-protein--DNA complex or the (+)-CC-1065 alkylation sites on DNA (att site L3), we have demonstrated that of the three minor grooves implicated in the interaction with A-protein, the peripheral two are 'open' or accessible to drug bonding following protein binding. These drug-bonding sites very likely represent binding at at least two A-protein-induced bending sites. Significantly, the locus of bending at these sites is spaced approximately two helical turns apart, and the bending is proposed to occur by narrowing of the minor groove of DNA. The intervening minor groove between these two peripheral sites is protected from (+)-CC-1065 alkylation. The results are discussed in reference to a proposed model for overall DNA bending in the A-protein att L3 site complex. This study illustrates the utility of (+)-CC-1065 as a probe for protein-induced bending of DNA, as well as for interactions of minor groove DNA bending proteins with DNA which may be masked in hydroxyl radical footprinting experiments.

A base-triple structural domain in RNA.

An oligonucleotide modeled on a proposed base-triple domain of the Tetrahymena group I intron has been characterized by NMR. The oligonucleotide contains two double-helix regions with adjacent single-stranded nucleotides. The NMR data show that the two helices stack coaxially, although the rotation between the two helices is approximately twice as large as the rotation between normal base pairs. The rotation between the two helices allows the single-stranded nucleotides to form U.U.G and A.G.C base triples in the minor groove. The A.G.C base triple contains a hydrogen bond between the adenine N1 and a 2'-hydroxyl in the minor groove of the G.C pair. A similar hydrogen bond between an adenine and a 2'-hydroxyl in transfer RNA suggests that this could be a recurring tertiary interaction in RNA.

Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.

The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.

Sequence-specific interaction of the Salmonella Hin recombinase in both major and minor grooves of DNA.

The Hin recombinase of Salmonella catalyzes a site-specific recombination event which leads to flagellar phase variation. Starting with a fully symmetrical recombination site, hixC, a set of 40 recombination sites which vary by pairs of single base substitutions was constructed. This set was incorporated into the Salmonella-specific bacteriophage P22 based challenge phage selection and used to define the DNA sequence determinants for the binding of Hin to DNA in vivo. The critical sequence-specific contacts between a Hin monomer and a 13 bp hix half-site are at two T:A base pairs in the major groove of the DNA which are separated by one base pair, and two consecutive A:T contacts in the minor groove. The base substitutions in the major groove recognition portion which were defective in binding Hin still retained residual binding capability in vivo, while the base pair substitutions affecting the minor groove recognition region lost all in vivo binding. Using in vitro binding assays, Hin was found to bind to hix symmetrical sites with A:T base pairs or I:C base pairs in the minor groove recognition sequences, but not to G:C base pairs. In separate in vitro binding assays, Hin was equally defective in binding to either a G:C or a I:C contact in a major groove recognition sequence. Results from in vitro binding assays to hix sites in which 3-deazaadenine was substituted for adenine are consistent with Hin making a specific contact to either the N3 of adenine or O2 of thymine in the minor groove within the hix recombination site on each symmetric half-site. These results taken with the results of previous studies on the DNA binding domain of Hin suggest a sequence-specific minor groove DNA binding motif.

Interactions between the trp repressor and its operator sequence as studied by base analogue substitution.

A series of modified trp operator sequences has been prepared by the incorporation of seven different base analogues. Four of the analogues allow the site-specific deletion of functional groups present on the dA-dT and dT-dA base pairs at positions -4/+4 and -5/+5 in the trp operator. The remaining three analogues permit the incorporation of structural analogues of the native dA-dT or dG-dC base pairs. The duplex operator sequences all exhibit Tm values well above ambient temperature (48-70 degrees C), and these values generally correlate very well with the number of interstrand hydrogen bonds present. The affinity between the trp repressor and 14 modified operator sequences was examined using a recently developed alkaline phosphatase protection assay. The results from the analogue sequences used in this study suggest that the structure of the dA-dT or dT-dA base pairs at positions -4/+4 and -5/+5, respectively, has relatively little effect upon the solution binding by the trp repressor, but the protein is very sensitive to the orientation of the amino and carbonyl functional groups at the -4/+4 positions, which are involved in the formation of an interbase hydrogen bond present in the major groove. (The term structure in this case refers to the hydrogen bonding structure of the base pairs. We recognize that the introduction of conservative functional group deletions or reversals may affect other structural criteria such as hydration.) The deletion of individual functional groups from the operator sequence suggests that the carbonyl at dT+4 is critical for formation of the high-affinity sequence-specific complex. Additionally, the thymine methyl group at dT+4 and the N7 nitrogen of dA+5 appear to be critical contacts necessary for high-affinity binding by the repressor. The thymine carbonyl and the adenine N7 nitrogen are each responsible for approximately -1.5 kcal/mol of apparent free energy of binding. The thymine methyl provides a somewhat smaller contribution of -0.7 kcal/mol. Deletion of either of the adenine amino groups at dA-4 or dA+5 results in a sequence that binds to the repressor with a higher affinity than observed with the native sequence; this can be explained in that the functional groups lost are not critical for binding, and the resulting increased flexibility of the operator, or the creation of a more hydrophobic surface at these sites, enhances van der Waals contacts between the protein and the nucleic acid.

The antitumor agent CC-1065 inhibits helicase-catalyzed unwinding of duplex DNA.

The antitumor drug CC-1065 is thought to exert its effects by covalent bonding to N3 of adenine in DNA and interfering with some aspect of DNA metabolism. Therefore, it is of interest to determine what effect this drug has on enzymes involved in various aspects of DNA metabolism. In this report, we examine the ability of two DNA helicases, the dda protein of phage T4 and helicase II of Escherichia coli, to unwind CC-1065-adducted, tailed, oligonucleotides. It is shown that the presence of the drug on DNA strongly inhibits unwinding catalyzed by the T4 and E. coli proteins. A significant difference between the results obtained with the two helicases is that DNAs containing drug on either the tailed or the completely duplex strands are poor substrates for helicase II but dda protein-mediated unwinding is inhibited only when the drug is on the tailed strand. The drug-modified, helicase-released, strands migrate abnormally through a native gel, suggesting that the drug traps an unusual secondary structure generated in the course of protein-mediated unwinding. A kinetic analysis of the drug-inhibited reactions reveals that the helicases are trapped by the DNA-drug complex. This is evidenced by a decrease in the rate of helicase exchange between drug-bound substrate and drug-free duplex. The implications of these results with respect to the mechanism of action of CC-1065 in vivo are discussed.

Specific binding of arginine to TAR RNA.

A single arginine residue within the basic region of the human immunodeficiency virus Tat protein mediates specific binding of Tat peptides to a three-nucleotide bulge in TAR RNA. It has been proposed that arginine recognizes TAR by forming a network of hydrogen bonds with two structurally distinct phosphates, an interaction termed the "arginine fork." Here it is shown that L-arginine blocks the Tat peptide/TAR interaction, whereas L-lysine and analogs of arginine that remove specific hydrogen bond donors do not. Experiments using an L-arginine affinity column demonstrate that arginine and the Tat peptides bind to the same site in TAR. Modification of two phosphates located at the junction of the double-stranded stem and bulge and modification of two adenine N7 groups in base-paired regions of TAR interfere with specific arginine binding. The results emphasize the importance of RNA structure in RNA-protein recognition and provide methods to identify arginine-binding sites in RNAs.