GC-rich regions in genomes as targets for DNA alkylation

Sequence variants affecting the genome-wide rate of germline microsatellite mutations

Microsatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and are some of the most polymorphic variants in the genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9-65.4) microsatellite de novo mutations (mDNMs) per offspring per generation, excluding one bp repeats motifs (homopolymers) the estimate is 48.2 mDNMs (95% CI: 46.7-49.6). Paternal mDNMs occur at longer repeats than maternal ones, which are in turn larger with a mean size of 3.4 bp vs 3.1 bp for paternal ones. mDNMs increase by 0.97 (95% CI: 0.90-1.04) and 0.31 (95% CI: 0.25-0.37) per year of father's and mother's age at conception, respectively. Here, we find two independent coding variants that associate with the number of mDNMs transmitted to offspring; The minor allele of a missense variant (allele frequency (AF) = 1.9%) in MSH2, a mismatch repair gene, increases transmitted mDNMs from both parents (effect: 13.1 paternal and 7.8 maternal mDNMs). A synonymous variant (AF = 20.3%) in NEIL2, a DNA damage repair gene, increases paternally transmitted mDNMs (effect: 4.4 mDNMs). Thus, the microsatellite mutation rate in humans is in part under genetic control.

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G₁G₂C₃G₄C₅C₆)₂, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)₂ sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O₆/N₇ of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N₉-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C₁G₂G₃G₄C₅G₆C₇C₈C₉G₁₀)₂. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.

Host translesion polymerases are required for viral genome integrity

Human cells encode up to 15 DNA polymerases with specialized functions in chromosomal DNA synthesis and damage repair. In contrast, complex DNA viruses, such as those of the herpesviridae family, encode a single B-family DNA polymerase. This disparity raises the possibility that DNA viruses may rely on host polymerases for synthesis through complex DNA geometries. We tested the importance of error-prone Y-family polymerases involved in translesion synthesis (TLS) to human cytomegalovirus (HCMV) infection. We find most Y-family polymerases involved in the nucleotide insertion and bypass of lesions restrict HCMV genome synthesis and replication. In contrast, other TLS polymerases, such as the polymerase ζ complex, which extends past lesions, was required for optimal genome synthesis and replication. Depletion of either the polζ complex or the suite of insertion polymerases demonstrate that TLS polymerases suppress the frequency of viral genome rearrangements, particularly at GC-rich sites and repeat sequences. Moreover, while distinct from HCMV, replication of the related herpes simplex virus type 1 is impacted by host TLS polymerases, suggesting a broader requirement for host polymerases for DNA virus replication. These findings reveal an unexpected role for host DNA polymerases in ensuring viral genome stability.

Sequence Selective Molecular Recognition of Long DNA Sequences by Oligomethylene-Linked Oligoimidazole Analogs of Distamycin

We have studied a series of homologous N-to-N oligomethylene linked bis(diimidazole) analogs 4a-f (number of methylene groups = 1 to 6, re spectively) and a dipicolinamide congener 4g that bind to long GC-containing sequences of DNA. Results from an ethidium binding assay reveal that, for 4a-f, the compounds with an even number of methylene groups have larger ap parent binding constants, Kapp, than those with an odd number. The Kapp values of the compounds with an odd number of methylene groups are close to that of their monomeric analog 3 suggesting that they may be binding to DNA in a monodentate fashion. The binding of these compounds to T4 DNA and their larger binding constants for poly(dG-dC) over poly(dA-dT) indicated minor groove binding selectivity and tolerance for GC sequences. The ability of com pounds 4b-f to bind selectively to DNA was illustrated by an MPE-Fe(II) foot printing study which showed that compound 4f gave the most distinct foot prints. CD titration studies on compounds 4b, d, and f further demonstrated the GC tolerance of these compounds and that they can bind to 7 ~ 8 base pairs of DNA in a bidentate fashion. The minor groove and bidentate bind ing of the ethylene linked compound 4b on the underlined sequence of

The application of mass spectrometry in molecular dosimetry: ethylene oxide as an example

Mass spectrometry plays an increasingly important role in the search for and quantification of novel chemically specific biomarkers. The revolutionary advances in mass spectrometry instrumentation and technology empower scientists to specifically analyze DNA and protein adducts, considered as molecular dosimeters, derived from reactions of a carcinogen or its active metabolites with DNA or protein. Analysis of the adducted DNA bases and proteins can elucidate the chemically reactive species of carcinogens in humans and can serve as risk-associated biomarkers for early prediction of cancer risk. In this article, we review and compare the specificity, sensitivity, resolution, and ease-of-use of mass spectrometry methods developed to analyze ethylene oxide (EO)-induced DNA and protein adducts, particularly N7-(2-hydroxyethyl)guanine (N7-HEG) and N-(2-hydroxyethyl)valine (HEV), in human samples and in animal tissues. GC/ECNCI-MS analysis after HPLC cleanup is the most sensitive method for quantification of N7-HEG, but limited by the tedious sample preparation procedures. Excellent sensitivity and specificity in analysis of N7-HEG can be achieved by LC/MS/MS analysis if the mobile phase, the inlet (split or splitless), and the collision energy are properly optimized. GC/ECNCI-HRMS and GC/ECNCI-MS/MS analysis of HEV achieves the best performance as compared with GC/ECNCI-MS and GC/EI-MS. In conclusion, future improvements in high-throughput capabilities, detection sensitivity, and resolution of mass spectrometry will attract more scientists to identify and/or quantify novel molecular dosimeters or profiles of these biomarkers in toxicological and/or epidemiological studies.

Phosphorylation of Sp1 in response to DNA damage by ataxia telangiectasia-mutated kinase

Sp1, a transcription factor that regulates expression of a wide array of essential genes, contains two SQ/TQ cluster domains, which are characteristic of ATM kinase substrates. ATM substrates are transducers and effectors of the DNA damage response, which involves sensing damage, checkpoint activation, DNA repair, and/or apoptosis. A role for Sp1 in the DNA damage response is supported by our findings: Activation of ATM induces Sp1 phosphorylation with kinetics similar to H2AX; inhibition of ATM activity blocks Sp1 phosphorylation; depletion of Sp1 sensitizes cells to DNA damage and increases the frequency of double strand breaks. We have identified serine 101 as a critical site phosphorylated by ATM; Sp1 with serine 101 mutated to alanine (S101A) is not significantly phosphorylated in response to damage and cannot restore increased sensitivity to DNA damage of cells depleted of Sp1. Together, these data show that Sp1 is a novel ATM substrate that plays a role in the cellular response to DNA damage.

A study of 7-deaza-2'-deoxyguanosine 2'-deoxycytidine base pairing in DNA

The incorporation of 7-deazaguanine modifications into DNA is frequently used to probe protein recognition of H-bonding information in the major groove of DNA. While it is generally assumed that 7-deazaguanine forms a normal Watson–Crick base pair with cytosine, detailed thermodynamic and structural analyses of this modification have not been reported. The replacement of the 7-N atom on guanine with a C–H, alters the electronic properties of the heterocycle and eliminates a major groove cation-binding site that could affect the organization of salts and water in the major groove. We report herein the characterization of synthetic DNA oligomers containing 7-deazaguanine using a variety of complementary approaches: UV thermal melting, differential scanning calorimetry (DSC), circular dichroism (CD), chemical probing and NMR. The results indicate that the incorporation of a 7-deazaguanine modification has a significant effect on the dynamic structure of the DNA at the flanking residue. This appears to be mediated by changes in hydration and cation organization.

A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns

Alkylating agents, including environmental and endogenous carcinogens and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA.

Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context

The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N²-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5′- ··· GG ··· dinucleotide sequences, but their origins are poorly understood. Here we used high resolution NMR and molecular dynamics simulations to investigate differences in G* adduct conformations in 5′- ··· CG*GC ··· and 5′- ··· CGG* C··· sequence contexts in otherwise identical 12-mer duplexes. The BP rings are positioned 5′ along the modified strand in the minor groove in both cases. However, subtle orientational differences cause strong distinctions in structural distortions of the DNA duplexes, because the exocyclic amino groups of flanking guanines on both strands compete for space with the BP rings in the minor groove, acting as guideposts for placement of the BP. In the 5′- ··· CGG* C ··· case, the 5′-flanking G · C base pair is severely untwisted, concomitant with a bend deduced from electrophoretic mobility. In the 5′- ··· CG*GC ··· context, there is no untwisting, but there is significant destabilization of the 5′-flanking Watson–Crick base pair. The minor groove width opens near the lesion in both cases, but more for 5′- ··· CGG*C···. Differential sequence-dependent removal rates of this lesion result and may contribute to the mutation hotspot phenomenon.

Targeting critical regions in genomic DNA with AT-specific anticancer drugs

Cellular DNA is not a uniform target for DNA-reactive drugs. At the nucleotide level, drugs recognize and bind short motifs of a few base pairs. The location of drug adducts at the genomic level depends on how these short motifs are distributed in larger domains. This aspect, referred to as region specificity, may be critical for the biological outcome of drug action. Recent studies demonstrated that certain minor groove binding (MGB) drugs, such as bizelesin, produce region-specific lesions in cellular DNA. Bizelesin binds mainly T(A/T)(4)A sites, which are on average scarce, but occasionally cluster in distinct minisatellite regions (200-1000 bp of approximately 85-100% AT), herein referred to as AT islands. Bizelesin-targeted AT islands are likely to function as strong matrix attachment regions (MARs), domains that organize DNA loops on the nuclear matrix. Distortion of MAR-like AT islands may be a basis for the observed inhibition of new replicon initiation and the extreme lethality of bizelesin adducts (<10 adducts/cell for cell growth inhibition). Hence, long AT-islands represent a novel class of critical targets for anticancer drugs. The AT island paradigm illustrates the potential of the concept of regional targeting as an essential component of the rational design of new sequence-specific DNA-reactive drugs.

Alkylation of nucleic acids by the antitumor agent COMC

[reaction: see text]. Mass spectral data are presented indicating that the antitumor agent 2-crotonyloxymethyl-2-cyclohexenone (COMC) is capable of alkylating oligonucleotides via a mechanism involving an electrophilic exocyclic enone intermediate. Under physiological conditions, the exocyclic enone is likely the glutathionylated 2-exomethylenecyclohexenone. This supports a recent hypothesis that the antitumor activity of COMC arises from alkylation of nucleic acids and/or proteins critical to cell function and not from competitive inhibition of glyoxalase I by an adduct of COMC and glutathione.

Development of distamycin-related DNA binding anticancer drugs

The relatively low therapeutic index of the clinically used alkylating agents is probably related to the fact that these compounds cause DNA damage in a relatively unspecific manner, mainly involving guanine-cytosine rich stretches of DNA present in virtually all genes, therefore inducing unselective growth inhibition and death, both in neoplastic and in highly proliferative normal tissues. These considerations explain why in the last twenty years there has been an increasing interest in the identification of compounds which can target DNA with a much higher degree of sequence specificity than that of conventional alkylators. Minor groove binders (MGBs) are one of the most widely studied class of alkylating agents characterised by a high level of sequence specificity. The prototype of this class of drugs is distamycin A which is an antiviral compound able to interact, non-covalently, in theminor groove of DNA in A-T rich regions. It is not cytotoxic against tumour cells and thus has been used as a carrier for targeting cytotoxic alkylating moieties in theminor groove of DNA. The benzoyl mustard derivative of distamycin A, tallimustine, was found to be able to alkylate the N(3) of adenine in theminor groove of DNA only in the target hexamer 5'-TTTTGA or 5'-TTTTAA. Tallimustine was investigated in the clinic and was not successful because it causes severe bone marrow toxicity. The screening of other distamycin derivatives, which maintain antitumour activity and exhibit much lower toxicity against human bone marrow cells than tallimustine led to the identification of brostallicin (PNU-166196) which is currently under early clinical investigation. Although MGBs which bind DNA in A-T rich regions have not fulfilled the expectations, it is too early to draw definitive conclusions on this class of compounds. The peculiar bone-marrow toxicity observed in the clinic both with tallimustine or with CC-1065 derivatives is not necessarily a feature of all MGBs, as indicated by recent evidence obtained with brostallicin and other structurally unrelated MGBs (e.g., ET-743).

DNA damage by nitrogen mustard in a gene containing multiple Sp1-binding sites

The human cytochrome c(1) gene TATA-less promoter contains 10 Sp1-binding elements that regulate the activation of transcription of this gene. Quantitative PCR was used to show that nitrogen mustard induces DNA lesions within this Sp1-binding region following exposure of HeLa cells to clinical levels of the drug. Alkylation of the cytochrome c(1) gene in HeLa cells increased with reaction time up to 4 h following exposure to nitrogen mustard, with 50% of the lesions (approximately 0.8/kb) forming within 1 h. An Sp1 competition assay showed that nitrogen mustard inhibited the binding of Sp1 to the promoter region of the cytochrome c(1) gene in HeLa cells. These results show that nitrogen mustard-induced damage to Sp1-binding sites may contribute to the toxicity of this compound by interfering with the activation of specific genes.

Theoretical studies employing an ab initio and molecular modeling combination method on the DNA binding of bis-benzimidazoles designed for bioreductive activation

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on synthetic analogues of the minor groove binding bis-benzimidazole Hoechst 33258 designed to be subject to bioreductive activation. Such compounds have been shown experimentally to react with DNA to exhibit sequence dependent inhibition of human placental helicase and display significant anticancer properties. Geometry optimized conformations and energies were derived. The binding of the optimized conformations of the drugs to both alternating and non-alternating (AT)n and to (G)n-(C)n sequences were studied. The energetics of reaction at alternative DNA base sites are calculated and compared.

AF64A-induced changes in N-myc expression in the LA-N-2 human neuroblastoma cell line are modulated by choline and hemicholinium-3

Due to AF64A's structural similarity to choline, AF64A can selectively affect cholinergic neurons, which possess a high affinity choline transport system for acetylcholine synthesis. The mechanism by which AF64A selectively produces its cytotoxic effect is unknown. However, based on previous studies that demonstrate that DNA lesions produced by AF64A caused premature termination of N-myc transcription in vitro, it is possible that AF64A may affect the transcription of genes necessary for developmental maintenance in cholinergic cells. Using the LA-N-2 cells as a model to study the effects of AF64A in a purely cholinergic system, we investigated the effects of AF64A on the expression of the N-myc gene and monitored cell growth. AF64A produced a maximal decrease in N-myc mRNA with a return to steady state levels at later time points. Moreover, a decrease in cell numbers in AF64A-treated cells was observed, and these cells did not double in number at their respective doubling time as compared to control. In other studies, a causal relationship between a reduction in N-myc and an inhibition of cell growth and replication has been reported. While these studies do not allow us to conclude that AF64A is specific for N-myc, the data do, nevertheless, suggest that AF64A affects cell growth and/or replication by down-regulating the expression of N-myc which is involved in differentiation and cell growth in neuroblastomas. Presence of choline or hemicholinium-3 prevented the AF64A-induced decrease of N-myc levels by competing with, or inhibiting the choline transport mechanism by which AF64A enters the cell, respectively.

Somatic mutation theory, DNA repair rates, and the molecular epidemiology of p53 mutations

The theory of somatic mutagenesis predicts that the frequency pattern of induced selectable mutations along a gene is the product of the probability patterns of the several sequential steps of mutagenesis, e.g., damage, repair, polymerase misreading, and selection. Together, the variance of these component steps is propagated to generate a mutagen's induced mutational spectrum along a gene. The step with the greatest component of variance will drive most of the variability of the mutation frequency along a gene. This most variable step, for UV-induced mutations, is the cyclobutyl pyrimidine dimer repair rate. The repair rate of cyclopyrimidine dimers is quite variable from nucleotide position to nucleotide position and we show that this variation along the p53 gene drives the C-->T transition frequency of non-melanocytic skin tumors. On showing that the kinetics of cyclopyrimidine dimer repair at any one nucleotide position are first order, we use this kinetic and the somatic mutation theory to derive Leq, the adduct frequency along a gene as presented to a DNA polymerase after a cell population reaches damage-repair equilibrium from a chronic dose of mutagen. Leq is the product of the first two sequential steps of mutagenesis, damage and repair, and the frequency of this product is experimentally mapped using ligation-mediated PCR. The concept of Leq is applied to mutagenesis theory, chronic dose genetic toxicology, genome evolution, and the practical problems of molecular epidemiology.

Enhanced DNA alkylation activities of Hoechst 33258 analogues designed for bioreductive activation

A series of analogues of Hoechst 33258, designed to be subject to bioreductive activation, were synthesized, and interactions between these compounds and pBR322 DNA were investigated. Compounds containing a quinone group reacted with DNA via two possible pathways in the presence of reductants NADH or NADPH: radical cleavage and DNA alkylation. The corresponding dimethoxy compounds, which are not subject to reduction, showed very weak DNA binding ability. The strength of alkylation reaction of the quinone derivatives is related to leaving group ability. Furthermore, the quinone compounds preferentially alkylate DNA at 5'-CG and TG sequences rather than at the AT sites preferred as binding sites of Hoechst 33258.

Adriamycin-induced DNA adducts inhibit the DNA interactions of transcription factors and RNA polymerase

Adriamycin is known to specifically induce DNA interstrand cross-links at 5'-GC sequences. Because 5'-GC sequences are a predominant feature of 5'-untranslated regions (transcription factor-binding sites, promoter, and enhancer regions), it is likely that adriamycin adducts at GC sites would affect the binding of DNA-interacting proteins. Two model systems were chosen for the analysis: the octamer-binding proteins Oct-1, N-Oct-3 and N-Oct-5, which bind to ATGCAAAT and TAATGARAT recognition sites, and Escherichia coli RNA polymerase binding to the lac UV5 promoter. Electrophoretic mobility shift studies showed that adriamycin adducts at GC sites inhibited the binding of octamer proteins to their consensus motifs at drug levels as low as 1 micoM, but no effect was observed with a control sequence lacking a GC site. Adriamycin adducts at GC sites also inhibited the binding of RNA polymerase to the lac UV5 promoter. Adriamycin may therefore function by down-regulating the expression of specific genes by means of inactivation of short but critical motifs containing one or more GC sites.

Backbone and benzoyl mustard carrying moiety modifies DNA interactions of distamycin analogues

Alkylating distamycin derivative FCE-24517 (l) is the prototype of a novel class of alkylating agents. In the present study we have investigated the effect of further chemical modifications introduced in the alkylating distamycin-derived molecule with the aim of improving their ability to bind DNA. The new compound, MEN 10710 (II), has a four pyrrolecarboxamide backbone linked at its N-terminus and through a butanamido residue to a 4-[bis(chloroethyl)amino]phenyl moiety. We have demonstrated that the presence of the flexible trimethylene chain confers to the novel distamycin derivative a peculiar mode of interaction with DNA as compared with I or melphalan. In fact, interstrand cross-links are detected in DNA samples treated even with low concentrations of II (being 200-fold more efficient than melphalan) but not with I. Similar results were obtained with a related compound of II containing a three pyrrole ring backbone. Compound II induces a conformational change in the DNA structure as deduced from the inhibition of T4 DNA ligase activity. In alkylation experiments, unlike melphalan, both I and II induce DNA breaks at bases closely located to AT-rich tracts, however II was more potent than I in producing greater amount of covalent adducts. These data suggest that the new compound shows a different and peculiar mechanism of interaction with DNA.

A search for specificity in DNA-drug interactions

The GRID force field and a principal component analysis have been used in order to predict the interactions of small chemical groups with all 64 different triplet sequences of B-DNA. Factors that favor binding to guanine-cytosine base pairs have been identified, and a dictionary of ligand groups and their locations is presented as a guide to the design of specific DNA ligands.

Intragenomic heterogeneity of DNA damage formation and repair: a review of cellular responses to covalent drug DNA interaction

Chemical DNA interaction and its processing can now be studied at the level of specific genomic regions. Such investigations have revealed important new information about the molecular biology of the cellular responses to genomic insult and especially of the repair processes. They also have demonstrated that both the formation and repair of DNA damage display patterns of intragenomic heterogeneity. Therefore, mechanistic studies should involve examination of DNA damage formation and repair in specific genomic sequences besides in the overall genome to provide clues to the way in which specific modifications of DNA or chromatin could have specific biological effects. This review primarily focuses on studies done to elucidate the nature of DNA damage induction and intragenomic processing provoked by covalent drug-DNA modification in mammalian cells. The involvement of DNA damage formation and cellular processing as critical factors for genomic injury is exemplified by studies of the novel alkylating morpholinyl anthracyclines and the bifunctional alkylating agent nitrogen mustard as a prototype agent for covalent drug DNA interaction.

Studies of chlorambucil-DNA adducts

Chlorambucil (CLB) is a bifunctional nitrogen mustard whose therapeutic and major side-effects are thought to be caused by binding to DNA. HPLC analysis of hydrolyzed DNA from L1210 cells incubated with [14C]CLB generated two peaks of radioactivity, indicating the formation of two or more major adducts. Since DNA incubated with [14C]CLB in a cell-free system gave rise to the same profile, experiments were conducted with DNA from cells exposed to radiolabeled DNA precursors, which was then reacted with CLB. DNA containing [8-14C]guanine gave rise to one peak of radioactivity, while DNA containing [2,8-3H]adenine gave rise to two peaks. These peaks corresponded to the peaks seen in the experiment with intact L1210 cells treated with [14C]CLB. Experiments with DNA containing [5-3H]cytosine indicated that no cytosyl adducts were formed. No adducts were seen in hydrolysates prepared from labeled DNA incubated with drug solvent alone. These data indicate that the majority of adducts induced by CLB are guanyl adducts, but a substantial quantity of adenyl adducts has also been identified.

Evolutionary consequences of nonrandom damage and repair of chromatin domains

Some evolutionary consequences of different rates and trends in DNA damage and repair are explained. Different types of DNA damaging agents cause nonrandom lesions along the DNA. The type of DNA sequence motifs to be preferentially attacked depends upon the chemical or physical nature of the assaulting agent and the DNA base composition. Higher-order chromatin structure, the nonrandom nucleosome positioning along the DNA, the absence of nucleosomes from the promoter regions of active genes, curved DNA, the presence of sequence-specific binding proteins, and the torsional strain on the DNA induced by an increased transcriptional activity all are expected to affect rates of damage of individual genes. Furthermore, potential Z-DNA, H-DNA, slippage, and cruciform structures in the regulatory region of some genes or in other genomic loci induced by torsional strain on the DNA are more prone to modification by genotoxic agents. A specific actively transcribed gene may be preferentially damaged over nontranscribed genes only in specific cell types that maintain this gene in active chromatin fractions because of (1) its decondensed chromatin structure, (2) torsional strain in its DNA, (3) absence of nucleosomes from its regulatory region, and (4) altered nucleosome structure in its coding sequence due to the presence of modified histones and HMG proteins. The situation in this regard of germ cell lineages is, of course, the only one to intervene in evolution. Most lesions in DNA such as those caused by UV or DNA alkylating agents tend to diminish the GC content of genomes. Thus, DNA sequences not bound by selective constraints, such as pseudogenes, will show an increase in their AT content during evolution as evidenced by experimental observations. On the other hand, transcriptionally active parts may be repaired at rates higher than inactive parts of the genome, and proliferating cells may display higher repair activities than quiescent cells. This might arise from a tight coupling of the repair process with both transcription and replication, all these processes taking place on the nuclear matrix. Repair activities differ greatly among species, and there is a good correlation between life span and repair among mammals. It is predicted that genes that are transcriptionally active in germ-cell lineages have a lower mutation rate than bulk DNA, a circumstance that is expected to be reflected in evolution. Exception to this rule might be genes containing potential Z-DNA, H-DNA, or cruciform structures in their coding or regulatory regions that appear to be refractory to repair.(ABSTRACT TRUNCATED AT 400 WORDS)

DNA damage by drugs and radiation: what is important and how is it measured?

DNA is the most important target for drug and radiation induced cell killing. The mode of cell killing by cytotoxic drugs and radiation has been derived by correlating the type and quantity of DNA damage induced with lethality. Cytotoxic drugs can be classified by their main mode of action, while ionising radiation causes a range of lesions with the DNA double-strand break (dsb) being the most significant. Strand-breaks are measured from the reduction in the size of DNA molecules following treatment. Molecule size can be derived from the rate that DNA fragments sediment when centrifuged, elute through filters or migrate under electrophoresis. The effect of strand-breaks on DNA loop supercoiling allow a sensitive assay of DNA damage. Specific assays for base damage and drug adducts include changes in chromatographic mobility or binding by specific antibodies. By comparing the levels of damage in the genome overall with damage in specific gene targets, regions susceptible to damage induction, and varying in repair efficiency, have been revealed.

Activated protooncogenes in human lung tumors from smokers

Fourteen primary human lung tumor DNAs from smokers were analyzed for transforming activity by two DNA transfection assays. Activated protooncogenes were detected in 3 of 11 tumor DNAs by the NIH 3T3 focus assay, whereas activated protooncogenes were detected in 11 of 13 tumor DNAs by the NIH 3T3 cotransfection-nude mouse tumorigenicity assay. K- or NRAS genes activated by point mutation at codons 12 or 61 were detected in a large cell carcinoma, a squamous cell carcinoma, and 5 adenocarcinomas. An HRAS oncogene activated by a different mechanism was detected in an epidermoid carcinoma. One adenocarcinoma was found to contain an activated RAF gene. Two unidentified transforming genes were detected in a squamous cell carcinoma DNA and two adenocarcinoma DNAs. Eight of 10 lung adenocarcinomas that had formed metastases at the time of surgery were found to contain RAS oncogenes. No significant increase in metastasis was observed in the lung adenocarcinomas that contained one or more 6-kilobase EcoRI alleles of the LMYC gene. Overall, 12 of 14 (86%) of the lung tumor DNAs from smokers were found to contain activated protooncogenes. RAS oncogenes appear to play a role in the development of metastases in lung adenocarcinomas.

Sequence preferences of DNA interstrand cross-linking agents: dG-to-dG cross-linking at 5'-CG by structurally simplified analogues of mitomycin C

The nucleotide sequence preferences of the DNA interstrand cross-linking agents dehydroretronecine diacetate (DHRA), 2,3-bis(acetoxymethyl)-1-methylpyrrole (BAMP), dehydromonocrotaline, and dehydroretrorsine were studied by using synthetic DNA duplex fragments and polyacrylamide gel electrophoresis (PAGE). These agents have structural features in common with the reductively activated aziridinomitosene of mitomycin C (MC). Like MC, they preferentially cross-linked DNA duplexes containing the duplex sequence 5'-CG. For DHRA and BAMP interstrand cross-linked DNA duplexes, PAGE analysis of iron(II)-EDTA fragmentation reactions revealed the interstrand cross-links to be deoxyguanosine to deoxyguanosine (dG-to-dG), again analogous to DNA cross-links caused by MC. Unlike MC, DHRA could be shown to dG-to-dG cross-link a 5'-GC sequence. Furthermore, the impact of flanking sequence on the efficiency of interstrand cross-linking at 5'-CG was reduced for BAMP, with 5'-TCGA and 5'-GCGC being equally efficiently cross-linked. Possible origins of the 5'-CG sequence recognition common to all of the agents are discussed. A model is presented in which the transition state for the conversion of monoadducts to cross-links more closely resembles ground-state DNA at 5'-CG sequences.

Base sequence specificity of three 2-chloroethylnitrosoureas

Chemical modifications of guanine are some of the most common results of interactions of DNA with many carcinogens and anti-cancer drugs, including nitrosoureas, nitrogen mustards, triazenes, polycyclic aromatics, and aflatoxins. The base sequence specificity for alkylation of guanines by three 2-chloroethylnitrosoureas has been determined. Guanines in the midst of a run of guanines are more susceptible than guanines in other base sequences. We have shown that certain 2-chloroethylnitrosoureas (BCNU, CCNU and methyl-CCNU) follow this same pattern. However, the quantitative degree of higher specificity for guanine with guanines as nearest neighbors depended on both the guanine position alkylated and the structure of the alkyl group attached. For example, when hydroxyethylation of runs of guanine occurred at N-7, a 6- to 11-fold increase of alkylation occurred compared to that found in the random base sequences of DNA, while hydroxyethylation at O-6 increased 1.2 to 3.5-fold and chloroethylation at N-7 was 2-to 4-fold higher than in DNA. Guanines with thymines on both the 3' and 5' sides were much less susceptible, most notably in N-7-hydroxyethylation and N-7-chloroethylation. Since guanine-rich regions are found in regulatory regions of the genome, knowledge concerning the effect of base sequence upon the production of each of the potential DNA lesions is vital to gaining an understanding of the roles of these lesions in the anti-tumor activity of a drug.

Lesion selectivity in blockage of lambda exonuclease by DNA damage

Various kinds of DNA damage block the 3' to 5' exonuclease action of both E. coli exonuclease III and T4 DNA polymerase. This study shows that a variety of DNA damage likewise inhibits DNA digestion by lambda exonuclease, a 5' to 3' exonuclease. The processive degradation of DNA by the enzyme is blocked if the substrate DNA is treated with ultraviolet irradiation, anthramycin, distamycin, or benzo[a]-pyrene diol epoxide. Furthermore, as with the 3' to 5' exonucleases, the enzyme stops at discrete sites which are different for different DNA damaging agents. On the other hand, digestion of treated DNA by lambda exonuclease is only transiently inhibited at guanine residues alkylated with the acridine mustard ICR-170. The enzyme does not bypass benzo[a]-pyrene diol epoxide or anthramycin lesions even after extensive incubation. While both benzo[a]-pyrene diol epoxide and ICR-170 alkylate the guanine N-7 position, only benzo[a]-pyrene diol epoxide also reacts with the guanine N-2 position in the minor groove of DNA. Anthramycin and distamycin bind exclusively to sites in the minor groove of DNA. Thus lambda exonuclease may be particularly sensitive to obstructions in the minor groove of DNA; alternatively, the enzyme may be blocked by some local helix distortion caused by these adducts, but not by alkylation at guanine N-7 sites.

Cisplatin resistance and mechanism in a viral test system: SV40 isolates that resist inhibition by the antitumor drug have lost regulatory DNA

Isolates of SV40 that have enhanced ability to survive inhibition by the antitumor drug cisplatin were selected by serial drug challenge in vivo. These mutant viruses have acquired specific deletions within the repeated regulatory motif (GGGCGG)6 or GC box. This DNA element was shown previously to be a strong target of drug attack by cisplatin and other anticancer drugs in vitro and is an important viral and cellular DNA control sequence. Thus, drug resistance in this viral test system is dependent on the loss of important target DNA sequences. The results also indicate that drug efficacy may be related to the ability of certain anticancer drugs to attack regulatory DNA sequences containing strings of guanosines.

Effect of ionic strength and cationic DNA affinity binders on the DNA sequence selective alkylation of guanine N7-positions by nitrogen mustards

Large variations in alkylation intensities exist among guanines in a DNA sequence following treatment with chemotherapeutic alkylating agents such as nitrogen mustards, and the substituent attached to the reactive group can impose a distinct sequence preference for reaction. In order to understand further the structural and electrostatic factors which determine the sequence selectivity of alkylation reactions, the effect of increased ionic strength, the intercalator ethidium bromide, AT-specific minor groove binders distamycin A and netropsin, and the polyamine spermine on guanine N7-alkylation by L-phenylalanine mustard (L-Pam), uracil mustard (UM), and quinacrine mustard (QM) was investigated with a modification of the guanine-specific chemical cleavage technique for DNA sequencing. For L-Pam and UM, increased ionic strength and the cationic DNA affinity binders dose dependently inhibited the alkylation. QM alkylation was less inhibited by salt (100 mM NaCl), ethidium (10 microM), and spermine (10 microM). Distamycin A and netropsin (100 microM) gave an enhancement of overall QM alkylation. More interestingly, the pattern of guanine N7-alkylation was qualitatively altered by ethidium bromide, distamycin A, and netropsin. The result differed with both the nitrogen mustard (L-Pam less than UM less than QM) and the cationic agent used. The effect, which resulted in both enhancement and suppression of alkylation sites, was most striking in the case of netropsin and distamycin A, which differed from each other. DNA footprinting indicated that selective binding to AT sequences in the minor groove of DNA can have long-range effects on the alkylation pattern of DNA in the major groove.

Characterization of c-Ki-ras and N-ras oncogenes in aflatoxin B1-induced rat liver tumors

c-Ki-ras and N-ras oncogenes have been characterized in aflatoxin B1-induced hepatocellular carcinomas. Detection of different protooncogene and oncogene sequences and estimation of their frequency distribution were accomplished by polymerase chain reaction, cloning, and plaque screening methods. Two c-Ki-ras oncogene sequences were identified in DNA from liver tumors that contained nucleotide changes absent in DNA from livers of untreated control rats. Sequence changes involving G.C to T.A or G.C to A.T nucleotide substitutions in codon 12 were scored in three of eight tumor-bearing animals. Distributions of c-Ki-ras sequences in tumors and normal liver DNA indicated that the observed nucleotide changes were consistent with those expected to result from direct mutagenesis of the germ-line protooncogene by aflatoxin B1. N-ras oncogene sequences were identified in DNA from two of eight tumors. Three N-ras gene regions were identified, one of which was shown to be associated with an oncogene containing a putative activating amino acid residing at codon 13. All three N-ras sequences, including the region detected in N-ras oncogenes, were present at similar frequencies in DNA samples from control livers as well as liver tumors. The presence of a potential germ-line oncogene may be related to the sensitivity of the Fischer rat strain to liver carcinogenesis by aflatoxin B1 and other chemical carcinogens.

Streptozotocin interactions with pancreatic beta cells and the induction of insulin-dependent diabetes

The MSZ diabetic male mouse represents one of the most useful tools available to researchers interested in analyzing the consequences of insulin dependent diabetes in male mice. In contrast to the high mortality induced by single high doses of SZ, protracted administration of smaller SZ dosages yields a more stable diabetic condition. Moreover, in insulitis prone strains such as BKs, the model allows "synchronization" of beta cell destruction such that the inflammatory events occur on a predictable timescale. The MSZ-diabetic mouse represents a diabetic condition in which the primary etiopathologic effect is produced by an environmental toxin, and not by a genetically programmed loss of tolerance to beta cell specific antigens. In this regard, etiopathogenesis in the MSZ model is quite distinct from that underlying autoimmune type I diabetes in humans, NOD mice, and BB rats, and it is probably not appropriate to refer to pathogenesis in the MSZ model as one of "autoimmune insulitis" as has sometimes been done. The fact that insulitis in the MSZ model may not be "autoimmune," but may actually be a normal response to either tissue damage or to beta cells that have been structurally modified by a chemical, makes the model of special interest. Clearly, there is no single cause of insulin dependent diabetes, with disease induction representing a genetic susceptibility interacting with environmental triggers, such as toxins in the diet (including nitrosamines and fungal metabolites) as well as pathogenic viruses. The MSZ model will continue to be actively investigated because of insights it will afford regarding the genetic bases for susceptibility and resistance to diabetogenic environmental toxins. The model will be of further value by contributing to knowledge of the complicated interactions between pancreatic islet cells, other endocrine cells, and leukocytes in maintenance of glucose homeostasis.

Sequence specificity in the reaction of benzopyrene diol epoxide with DNA

Benzopyrene diol epoxide (BPDE; (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene), the ultimate carcinogen derived from the polycyclic hydrocarbon benzo[a]pyrene, reacts principally with the guanine bases in DNA. Nineteen double stranded, self-complementary oligonucleotides, containing deoxyguanosine in various sequence contexts, were each treated with tritium labelled BPDE. The extent of reaction was determined by releasing the BPDE-guanine adduct with acid, isolating it by chromatography on a reverse-phase column, and estimating it by its radioactivity. Oligonucleotides containing an isolated guanine, such as AAGTACTT, were little affected by BPDE. Reactivity was increased where the guanine was flanked by another guanine on the same strand (e.g. TACCTAGGTA) or on the complementary strand (e.g. TATTCGAATA), and was highest in mixed G-C sequences such as ATCCGGAT. The results should help predict major sites of attack of BPDE on cellular proto-oncogenes.