N7 Position Of Guanine Research Articles

Ab Initio Study of Alkylation of Guanine-Cytosine Base Pair by Sulfur and Nitrogen Mustards

Quantum modeling of the N7(G) alkylation of guanine-cytosine (G-C) base pair by sulfur (HD) and nitrogen mustard (HN2) was performed by using the Density Functional Theory (DFT) BPW91/6–31G++DP procedure. The vibrational IR and Raman spectra are discussed with regard to the N7 position of guanine when electrophilic HD+ episulfonium and HN2+ aziridinium attack the G-C base pair. Thermodynamic and polarizability considerations are also presented. The computed electronic chemical potential and the electrophilicity of the studied species indicate that an electronic transfer is produced from the nucleophile (G-C) base pair to the electrophile HD+ episulfonium or HN2+ aziridinium during the alkylation process.

Proteomic Analysis of DNA−Protein Cross-Linking by Antitumor Nitrogen Mustards

Nitrogen mustards are antitumor agents used clinically for the treatment of a variety of neoplastic conditions. The biological activity of these compounds is typically attributed to their ability to induce DNA-DNA cross-links. However, nitrogen mustards are able to produce a variety of other lesions, including DNA-protein cross-links (DPCs). DPCs induced by nitrogen mustards are not well-characterized because of their structural complexity and the insufficient specificity and sensitivity of previously available experimental methodologies. In the present work, affinity capture methodology in combination with mass spectrometry-based proteomics was employed to identify mammalian proteins that form covalent cross-links to DNA in the presence of a simple nitrogen mustard, mechlorethamine. Following incubation of 5'-biotinylated DNA duplexes with nuclear protein extracts, DPCs were isolated by affinity capture on streptavidin beads, and the cross-linked proteins were identified by high-performance liquid chromatography-electrospray tandem mass spectrometry of tryptic peptides. Mechlorethamine treatment resulted in the formation of DPCs with nuclear proteins involved in chromatin regulation, DNA replication and repair, cell cycle control, transcriptional regulation, and cell architecture. Western blot analysis was employed to confirm protein identification and to quantify the extent of drug-mediated cross-linking. Mass spectrometry of amino acid-nucleobase conjugates found in total proteolytic digests revealed that mechlorethamine-induced DPCs are formed via alkylation of the N7 position of guanine in duplex DNA and cysteine thiols within the proteins to give N-[2-[S-cysteinyl]ethyl]-N-[2-(guan-7-yl)ethyl]methylamine lesions. The results described herein suggest that cellular exposure to nitrogen mustards leads to cross-linking of a large spectrum of nuclear proteins to chromosomal DNA, potentially contributing to the cytotoxic and mutagenic effects of these drugs.

The formation and biological significance of N7-guanine adducts

DNA alkylation or adduct formation occurs at nucleophilic sites in DNA, mainly the N7-position of guanine. Ever since identification of the first N7-guanine adduct, several hundred studies on DNA adducts have been reported. Major issues addressed include the relationships between N7-guanine adducts and exposure, mutagenesis, and other biological endpoints. It became quickly apparent that N7-guanine adducts are frequently formed, but may have minimal biological relevance, since they are chemically unstable and do not participate in Watson Crick base pairing. However, N7-guanine adducts have been shown to be excellent biomarkers for internal exposure to direct acting and metabolically activated carcinogens. Questions arise, however, regarding the biological significance of N7-guanine adducts that are readily formed, do not persist, and are not likely to be mutagenic. Thus, we set out to review the current literature to evaluate their formation and the mechanistic evidence for the involvement of N7-guanine adducts in mutagenesis or other biological processes. It was concluded that there is insufficient evidence that N7-guanine adducts can be used beyond confirmation of exposure to the target tissue and demonstration of the molecular dose. There is little to no evidence that N7-guanine adducts or their depurination product, apurinic sites, are the cause of mutations in cells and tissues, since increases in AP sites have not been shown unless toxicity is extant. However, more research is needed to define the extent of chemical depurination versus removal by DNA repair proteins. Interestingly, N7-guanine adducts are clearly present as endogenous background adducts and the endogenous background amounts appear to increase with age. Furthermore, the N7-guanine adducts have been shown to convert to ring opened lesions (FAPy), which are much more persistent and have higher mutagenic potency. Studies in humans are limited in sample size and differences between controls and study groups are small. Future investigations should involve human studies with larger numbers of individuals and analysis should include the corresponding ring opened FAPy derivatives.

Structural consequences of a 3'-->3' DNA interstrand cross-link by a trinuclear platinum complex: unique formation of two such cross-links in a 10-mer duplex.

Combined multidimensional nuclear magnetic resonance spectroscopy and electrospray mass spectrometry was used to analyze the platinated DNA adduct of the phase II anticancer drug [[trans-PtCl(NH(3))(2)](2)-mu-[trans-Pt(NH(3))(2)(NH(2)(CH(2))(6)NH(2))(2)]](NO(3))(4) (BBR3464) with [5'-d(ACG*TATACG*T)-3'](2). Two 1,2-interstrand cross-links were formed by concomitant binding of two trinuclear moieties to the oligonucleotide. The four DNA-bound platinum atoms coordinated in the major groove at N7 positions of guanines in the 3' --> 3' direction and the central platinum unit is expected to lie in the DNA minor groove. This is the first report of such a DNA lesion. The melting temperature of the adduct is 76 degrees C and is 42 degrees C higher than that of the unplatinated DNA. The sugar residues of the platinated bases are in the N-type conformation and the G9 nucleoside is in the syn orientation, while the G3 nucleoside appears to retain the anti configuration. The secondary structure of DNA was significantly changed upon cross-linking of the two BBR3464 molecules. Base destacking occurs between A1/C2 and C2/G3 and weakened stacking is seen for the C8/G9 and G9/T10 bases. The lack of Watson-Crick base pairing is also seen for A1-T10 and C2-G9 base pairs, whereas Watson-Crick base pairs in the central sequence of the DNA (T4 --> A7) are well maintained. While DNA repair proteins may "see" different platinated adducts as bulky "lesions", the subtle differences involved in base pairing and stacking, as summarized here, may extend to their role as a substrate for repair enzymes. Thus, differences in protein recognition and repair efficiency among the various interstrand cross-links are likely and a subject worthy of detailed exploration.

Synthesis, spectroscopic studies of new water-soluble Co(II) and Cu(II) macrocyclic complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane: their interaction studies with calf thymus DNA and guanosine 5′ monophosphate

New water soluble Co(II) 1, Ni(II) 2 and Cu(II) 3 complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane Co(II) were synthesized and characterized by various techniques, viz. elemental analysis, conductivity measurements, infrared, electronic, ESI-MS, 1H and 13C NMR spectroscopy. Molar conductance measurements in aqueous solution showed that complexes 1, 2 and 3 are ionic in nature. On the basis of spectroscopic data, a square planar geometry was assigned to the complexes involving four N-atoms of the two cyclohexane moieties. Interaction studies of 1 and 3 with CT-DNA were carried using UV/Visible absorption spectroscopy, fluorescence spectrophotometry, cyclic voltammetry and viscosity measurements. Absorption spectral traces reveal 27.7 and 23.3% hyperchromism for complexes 1 and 3, respectively indicative of strong binding to CT-DNA. These results were authenticated by fluorescence quenching experiments and viscosity measurements. The intrinsic binding constants K b of 1 and 3 are 2.94 × 104 and 2.71 × 104 M−1, respectively. Early transition metals show preference for O6 position while later ones copper and cobalt prefer N7 position of DNA base guanine. To validate this hypothesis, interaction studies of copper (II) and cobalt (II) complexes were carried out with 5′GMP, which revealed electrostatic interactions are more favored along with hydrogen bonding than coordinate covalent interaction to N7 position of guanine.

Cross-Linking of the DNA Repair Protein O6-Alkylguanine DNA Alkyltransferase to DNA in the Presence of Antitumor Nitrogen Mustards

The antitumor activity of chemotherapeutic nitrogen mustards including chlorambucil, cyclophosphamide, and melphalan is commonly attributed to their ability to induce DNA-DNA cross-links by consecutive alkylation of two nucleophilic sites within the DNA duplex. DNA-protein cross-linking by nitrogen mustards is not well characterized, probably because of its inherent complexity and the insufficient sensitivity of previous methodologies. If formed, DNA-protein conjugates are likely to contribute to both target and off-target cytotoxicity of nitrogen mustard drugs. Here, we show that the DNA repair protein, O (6)-alkylguanine DNA alkyltransferase (AGT), can be readily cross-linked to DNA in the presence of nitrogen mustards. Both chlorambucil and mechlorethamine induced the formation of covalent conjugates between (32)P-labeled double-stranded oligodeoxynucleotides and recombinant human AGT protein, which were detected by SDS-PAGE. Capillary HPLC-electrospray ionization mass spectrometry (ESI-MS) analysis of AGT that had been treated with the guanine half-mustards of chlorambucil or mechlorethamine revealed the ability of the protein to form either one or two cross-links to guanine. C145A AGT (a variant containing a single point mutation in the protein's active site) was found capable of forming a single guanine conjugate, while cross-linking was virtually abolished upon treatment of the C145A/C150S AGT double mutant with the guanine half-mustards. HPLC-ESI (+)-MS/MS sequencing of tryptic peptides obtained from the wild-type AGT protein that had been treated with nitrogen mustards in the presence of DNA confirmed that the cross-linking took place between the N7 position of guanine in DNA and two active site residues within the AGT protein (Cys (145) and Cys (150)). The exact chemical structures of AGT-DNA cross-links induced by chlorambucil and mechlorethamine were identified as N-(2-[ S-cysteinyl]ethyl)- N-(2-[guan-7-yl]ethyl)- p-aminophenylbuyric acid and N-(2-[ S-cysteinyl]ethyl)- N-(2-[guan-7-yl]ethyl)methylamine, respectively, based upon HPLC-MS/MS analysis of protein hydrolysates in parallel with the corresponding amino acid conjugates prepared synthetically. Mechlorethamine-induced AGT-DNA conjugates were isolated from protein extracts of AGT-expressing CHO cells but not control cells, demonstrating that nitrogen mustards can cross-link the AGT protein to DNA in the presence of other nuclear proteins. Because AGT is overexpressed in many tumor types, further investigations of the potential role of AGT-DNA cross-linking in the antitumor and mutagenic activity of antitumor nitrogen mustards are warranted.

Structural Elucidation of a Novel DNA−DNA Cross-Link of 1,2,3,4-Diepoxybutane

DNA-DNA cross-linking by 1,2,3,4-diepoxybutane (DEB) is considered the molecular basis for its potent cytotoxic and genotoxic effects. DEB reactions with DNA initially lead to N7-(2'-hydroxy-3',4'-epoxybut-1'-yl)-guanine monoadducts, which can then alkylate neighboring DNA bases to form bifunctional lesions. We recently reported the structures of four regioisomeric guanine-adenine adducts of DEB involving the N7 position of guanine and the N1, N3, N6, and N7 positions of adenine (Park, S., et al. (2004) Chemical Research in Toxicology 17, 1638-1651). In the present work, a novel bifunctional DNA lesion of DEB was identified as 1-(hypoxanth-1-yl)-4-(guan-7-yl)-2,3-butanediol (N1HX-N7G-BD). An authentic standard of N1HX-N7G-BD was prepared and structurally characterized by proton NMR, UV, and mass spectrometry. HPLC-ESI-MS/MS analyses of acid hydrolysates of DEB-treated calf thymus DNA revealed a peak that had the same retention time, MS/MS fragmentation, and UV spectrum as the authentic standard of N1HX-N7G-BD. We propose that N1HX-N7G-BD is formed by the hydrolytic deamination of previously reported 1-(aden-1-yl)-4-(guan-7-yl)-2,3-butanediol. Although N1HX-N7G-BD adducts are less abundant in DEB-treated DNA than the corresponding guanine-guanine cross-links, they may play a role in the induction of both AT and GC base pair mutations.

Direct Reversal of DNA Alkylation Damage

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Direct reversal of DNA alkylation damage.

1.1. Overview of Direct Repair of DNA Alkylation Damage Cellular DNA is constantly subjected to modifications by intracellular and extracellular chemicals, which can result in covalent changes. 1,2 Alkylating agents are one group of such chemicals that can lead to DNA damage.3 These agents are prevalent in the environment and are used as anticancer compounds in the clinical setting.4–10 Alkylating agents also exist endogenously inside cells; for instance, S-adenosylmethionine, a methyl donor for many cellular reactions, has been shown to produce methylation damage.11,12 The attack on DNA by these alkylating agents can lead to various types of lesions on the heterocyclic bases or backbone.3,13–15 Most of these resulting adducts are mutagenic or toxic, and cells have evolved various proteins to detect and repair them.9,16,17 Interestingly, many of these alkylation lesions are repaired through the direct removal of the adduct. Other than the photolyase that catalyzes direct reversal of the thymine dimer created by UV light,18,19 all known direct DNA repair proteins are engaged in alkylation DNA damage repair. These are the N-terminal domain of the Escherichia coli (E. coli) Ada protein, the O6-alkylguanine-DNA alkyltransferase family, and the AlkB family.9 1.1.1. Alkylation of DNA Alkylating reagents can be divided into SN1 and SN2 types based on the mechanism of the alkylation attack. The alkylation susceptibility of each site on the bases or backbone varies depending on the reagent used (Figure 1); the resulting lesions also have different mutagenic and cytotoxic effects. The N7-position of guanine is the most vulnerable site on DNA; unsurprisingly, it also serves as the best ligand on the DNA for metal ions such as platinum(II).20 Treating double-stranded DNA (dsDNA) with methylating agents such as methylmethane sulfonate (MMS, an SN2 type methylating agent) or N-methyl-N′-nitrosourea (MNU, an SN1 type methylating agent) typically results in 70–80% of the methylation occurring on the N7-position of guanine. Despite being the most abundant product of alkylation damage, N7-methylguanine is relatively innocuous and is removed mostly through spontaneous depurination.21 The resulting abasic site is toxic and repaired enzymatically.22 The N3-methyladenine is the second most abundant alkylation lesion formed in dsDNA. This lesion can block DNA replication and is removed by AlkA in E. coli and 3-methyladenine-DNA-glycosylases.23–25 Figure 1 Methylation patterns of the DNA bases and phosphate backbone with MMS and MNU. The blue arrows indicate methylation sites that are repaired by glycosylases; the red arrows are for sites repaired by O6-alkylguanine-DNA alkyltransferases; the purple arrows ... The SN1 type methylating agents such as MNU and N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) are highly mutagenic because they attack the oxygen atoms on DNA bases to give a significant amount of O6-methylguanine (O6-meG) and a small amount of O4-methylthymine (Figure 1).13,14 O6-meG mispairs with thymine during DNA replication, which gives rise to a transition mutation of G:C to A:T.26–29 Thus, this lesion must be rapidly located and removed in order to maintain the integrity of the genome. The O6-alkylguanine-DNA alkyltransferase family of proteins performs this important task in almost all organisms.29–33 The SN2 type methylating agents such as MMS and methyl halides can react with single-stranded DNA (ssDNA) to generate large portions of N1-methyladenine and N3-methylcytosine (Figure 1).3,9,13,14 These two positions are protected by hydrogen bonding in dsDNA but are quite nucleophilic when exposed in ssDNA or replication forks. When these sites are exposed, they are vulnerable to nucleophilic attack; the pKa’s of these two nitrogen sites are 4.1 and 4.5 in ssDNA, which are higher than that of N7-guanine.34–38 The resulting lesions prevent formation of Watson–Crick base pairs which could be toxic for cells. The protein involved in the repair of these lesions has been revealed only very recently. A family of iron(II)-dependent dioxygenases was found to catalytically remove these alkylation lesions.9,39,40 The phosphodiester DNA backbone is also subject to alkylation damage. For instance, 17% of the total methylation occurs on the backbone to yield methylphosphotriesters when dsDNA is treated with MNU (Figure 1). The neutral phosphotriester can be hydrolyzed by water much faster than the diester, which leads to cleavage of the backbone. The Sp-methylphosphotriester is repaired by the N-terminal domain of the Ada protein (N-Ada) in E. coli.17,41 This repair serves mostly as a signaling pathway to induce expression of methylation resistance genes, as will be discussed below. The other diastereomer, Rp-methylphosphotriester, cannot be repaired by N-Ada. There is no homologue of N-Ada found in eukaryotes. It is unclear whether methylphosphotriester is repaired in eukaryotes.

Replication past a trans-4-Hydroxynonenal Minor-Groove Adduct by the Sequential Action of Human DNA Polymerases ι and κ

The X-ray crystal structure of human DNA polymerase iota (Poliota) has shown that it differs from all known Pols in its dependence upon Hoogsteen base pairing for synthesizing DNA. Hoogsteen base pairing provides an elegant mechanism for synthesizing DNA opposite minor-groove adducts that present a severe block to synthesis by replicative DNA polymerases. Germane to this problem, a variety of DNA adducts form at the N2 minor-groove position of guanine. Previously, we have shown that proficient and error-free replication through the gamma-HOPdG (gamma-hydroxy-1,N2-propano-2'-deoxyguanosine) adduct, which is formed from the reaction of acrolein with the N2 of guanine, is mediated by the sequential action of human Poliota and Polkappa, in which Poliota incorporates the nucleotide opposite the lesion site and Polkappa carries out the subsequent extension reaction. To test the general applicability of these observations to other adducts formed at the N2 position of guanine, here we examine the proficiency of human Poliota and Polkappa to synthesize past stereoisomers of trans-4-hydroxy-2-nonenal-deoxyguanosine (HNE-dG). Even though HNE- and acrolein-modified dGs share common structural features, due to their increased size and other structural differences, HNE adducts are potentially more blocking for replication than gamma-HOPdG. We show here that the sequential action of Poliota and Polkappa promotes efficient and error-free synthesis through the HNE-dG adducts, in which Poliota incorporates the nucleotide opposite the lesion site and Polkappa performs the extension reaction.

3-Nitrobenzanthrone, a potential human cancer hazard in diesel exhaust and urban air pollution: a review of the evidence

Epidemiological studies have shown that exposure to diesel exhaust and urban air pollution is associated with an increased risk of lung cancer. 3-Nitrobenzanthrone [3-nitro-7H-benz[de]anthracen-7-one (3-NBA)] is an extremely potent mutagen and suspected human carcinogen identified in diesel exhaust and ambient air particulate matter. The main metabolite of 3-NBA, 3-aminobenzanthrone (3-ABA), was found in the urine of salt mine workers occupationally exposed to diesel emissions, indicating that human exposure to 3-NBA due to diesel emissions can be significant and is detectable. There is clear evidence that 3-NBA is a genotoxic mutagen forming DNA adducts after metabolic activation through simple reduction of the nitro group. Several human enzymes have been shown to activate 3-NBA and its metabolites in vitro and in cells to form electrophilic arylnitrenium and rearranged carbenium ions, leading to the formation of purine adducts at the C8 and N2 position of guanine and at the C8 and N6 position of adenine. The predominant DNA adducts in vivo, 2-(2'-deoxyguanosin-N2-yl)-3-aminobenzanthrone and N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone are also the most persistent adducts in target tissue in rodents, and are most probably responsible for the induction of GC-->TA transversion mutations observed in vivo. It is concluded that these adducts not only represent premutagenic lesions in DNA but are of primary importance for the initiation of the carcinogenic process and subsequent tumour formation in target tissue. Indeed, 3-NBA is carcinogenic in rats after intratracheal instillation, inducing mainly squamous cell carcinoma in lung. The intention of this article is to provide a critical review on the potential genotoxic effects of 3-NBA on human health. However, in general, there is a need for more mechanistic studies that relate 3-NBA to all processes that are considered to orchestrate tumour development and of studies on the ability of particles to promote 3-NBA genotoxicity. Because of its widespread environmental presence, 3-NBA may represent not only an occupational health hazard but also a hazard for larger sections of the general population. For an accurate risk assessment more epidemiological studies on 3-NBA-exposed individuals and a broader monitoring of environmental levels of 3-NBA are required.

Adduct Size Limits Efficient and Error-free Bypass Across Bulky N2-Guanine DNA Lesions by Human DNA Polymerase η

The N2 position of guanine (G) is one of the major sites for DNA modification by various carcinogens. Eight oligonucleotides with varying adduct bulk at guanine N2 were analyzed for catalytic efficiency and fidelity with human DNA polymerase (pol) eta, which is involved in translesion synthesis (TLS). Pol eta effectively bypassed N2-methyl(Me)G, N2-ethyl(Et)G, N2-isobutyl(Ib)G, N2-benzyl(Bz)G, and N2-CH2(2-naphthyl)G but was severely blocked at N2-CH2(9-anthracenyl)G (N2-AnthG) and N2-CH2(6-benzo[a]pyrenyl)G (N2-BPG). Steady-state kinetic analysis showed proportional decreases of kcat/Km in dCTP insertion opposite N2-AnthG and N2-BPG (73 and 320-fold) and also kcat/Km in next-base extension from a C paired with each adduct (15 and 51-fold relative to G). Frequencies of dATP misinsertion and extension beyond mispairs were also proportionally increased (70 and 450-fold; 12 and 44-fold) with N2-AnthG and N2-BPG, indicating the effect of adduct bulk on blocking and misincorporation in TLS by pol eta. N2-AnthG and N2-BPG also greatly decreased the pre-steady-state kinetic burst rate (25 and 125-fold) compared to unmodified G. N2-AnthG decreased dCTP binding affinity (2.6-fold) and increased DNA substrate binding affinity. These results and the small kinetic thio effects (S(p)-dCTPalphaS) suggest that the early steps, possibly conformational change, are interfered with by the bulky adducts. In contrast, human pol delta bypassed adducts effectively up to N2-EtG but was strongly blocked by N2-IbG and larger adducts. We conclude that TLS DNA polymerases may be required for the efficient bypass of pol delta-blocking N2-G adducts bulkier than N2-EtG in human cells, and the bulk size can be a major factor for efficient and error-free bypass at these adducts by TLS DNA polymerases.

Comparison of structural effects in 1,4 DNA–DNA interstrand cross-links formed by dinuclear and trinuclear platinum complexes

The novel anticancer drug ([{ trans-PtCl(NH 3) 2} 2-μ-{ trans-Pt(NH 3) 2(NH 2(CH 2) 6NH 2) 2}](NO 3) 4) (BBR3464, 1,0,1/t,t,t, TPC) forms a 1,4-interstrand cross-linked adduct with the self-complementary DNA octamer 5′-d(ATG*TACAT) 2-3′, with the two platinum atoms coordinated in the major groove at N7 positions of guanines four base pairs apart on opposite DNA strands [Y. Qu, N.J. Scarsdale, M.-C. Tran, N. Farrell, J. Biol. Inorg. Chem. 8 (2003) 19–28]. The structure of the identical cross-link formed by the dinuclear [{ trans-PtCl(NH 3) 2} 2-μ-NH 2(CH 2) 6NH 2}](NO 3) 2 (BBR3005, 1,1/t,t, DPC) was examined for comparison. The adduct was characterized and analyzed by MS, UV and NMR spectroscopy. NMR analysis of the adduct shows platination of the unique guanine residues. The strong H8/H1′ intraresidue cross-peaks observed for all purine residues (A1, G3, A5 and A7) are consistent with a syn-conformation of the nucleoside unit in all cases. Thus, the structure resembles closely that formed by the trinuclear compound. Further confirmation of this similarity comes from the increase in melting temperature (66° for DPC, 60° for TPC, 22° for free oligonucleotide). Since DNA is the principal target in vivo for these Pt cross-linking agents, the unique structural perturbations induced by these cross-links may be related to the increased cytotoxicity and antitumor activity of polynuclear platinum compounds as compared to cisplatin ( cis-DDP). The similarity in the structures suggests opportunities to “deliver” the cross-link in a more efficient manner than the current clinically tested drug.

Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids

Binding modes of hydrated Zn2+ and Mg2+ cations to the N7 and O6 positions of guanine have been characterized by state-of-the-art ab initio model calculations. We show how differences in the electronic structure of the cationic complexes, as revealed by gas-phase computations, translate into differences in the biological function of the two studied metals. The thermodynamic driving force of the metal binding process is estimated on the basis of interaction energies and total electronic energies. The computed results unambiguously reveal that the N7 position of guanine exhibits a greater propensity to bind Zn2+ than Mg2+ while both cations have a similar affinity to bind to O6. Contrary to the intuitive expectations, however, the computed data do not suggest any superiority of the N7 inner shell binding mode for Zn2+ compared to the O6 binding. For Mg2+ the O6 inner shell binding mode is favored over the N7 one. The gas-phase data, when properly exrapolated, provide a relevant picture of many (though not all) fundamental aspects of the diversity of cation binding to nucleic acids.

Preclinical and clinical results with the natural marine product ET-743

ET-743 (Yondelis™, trabectedin) is a natural marine product with antitumour properties derived from the tunicate Ecteinascidia turbinata. ET-743 binds to the N2 position of guanine in the minor groove of DNA with some degree of sequence specificity, altering the transcription regulation of induced genes. Cells that are deficient in nucleotide excision repair, hypersensitive to UV rays, cisplatin and conventional alkylating agents, are resistant to ET-743. This is a unique property of ET-743 and is of potential importance for the drug activity when administered alone or in combination with other drugs. ET-743 showed striking antitumour activity against sensitive and resistant human xenografts. The dose-limiting toxicities in animal models, hepatobiliary events, were of concern, but the pattern of the reversibility noted in monkeys and the evidence of a positive therapeutic index in tumour-bearing nude mice prompted its clinical development. The Phase I programme investigated different schedules of administration, with the dose-limiting toxicities being neutropenia and fatigue. As anticipated in the preclinical models, reversible non-cumulative transaminitis was a prevalent finding from one-third of the maximum tolerated dose level; long-lasting objective responses in pretreated resistant patients were noted, including consistent efficacy data in mesenchymal tumours. The Phase II data for ET-743 administered as a single agent has established a clinical role for the compound in advanced pretreated soft tissue sarcoma and a promising potential in pretreated ovarian and breast cancer. ET-743 combined with other drugs (i.e., cisplatin, paclitaxel or doxorubicin) showed more than additive effects in several preclinical systems and initial clinical results (e.g., a combination of ET-743 with cisplatin) appear to confirm the preclinical findings. In summary, ET-743 is a new drug with a novel mode of action, which has demonstrated activity in human tumours resistant to the available anticancer drugs. Further comparative studies are needed to define the role of ET-743 alone or in combination in cancer chemotherapy.

Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine?

The thermodynamics and kinetics for the monofunctional binding of the antitumor drug cisplatin, cis-diamminedichloroplatinum(II), to a purine base site of DNA were studied computationally using guanine and adenine as model reactants. A dominating preference for initial attack at the N7-position of guanine is established experimentally, which is a crucial first step for the formation of a 1,2-intrastrand cross-link of adjacent guanine bases that leads to bending and unwinding of DNA. These structural distortions are proposed ultimately to be responsible for the anticancer activity of cisplatin. Utilizing density functional theory in combination with a continuum solvation model, we developed a concept for the initial Pt-N7 bond formation to atomic detail. In good agreement with experiments that suggested DeltaG++ = approximately 23 kcal/mol for the monofunctional platination of guanine, our model gives DeltaG++ = 24.6 kcal/mol for guanine, whereas 30.2 kcal/mol is computed when adenine is used. This result predicts that guanine is 3-4 orders of magnitude more reactive toward cisplatin than adenine. A detailed energy decomposition and molecular orbital analysis was conducted to explain the different barrier heights. Two effects are equally important to give the preference for guanine over adenine: First, the transition state is characterized by a strong hydrogen bond between the ammine-hydrogen of cisplatin and the O=C6 moiety of guanine in addition to a stronger electrostatic interaction between the two reacting fragments. When adenine binds, only a weak hydrogen bond forms between the chloride ligand of cisplatin and the H(2)N-C6 group of adenine. Second, a significantly stronger molecular orbital interaction is identified for guanine compared to adenine. A detailed MO analysis is presented to provide an intuitive view into the different electronic features governing the character of the Pt-N7 bond in platinated purine bases.

Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in the Presence and Absence of Nucleobase. The Role of Nonelectrostatic Effects

Inner-shell binding of selected hydrated metal ions (Mg2+, Cu2+, Zn2+, and Cd2+) to the guanine N7 position accompanied with outer- and inner-shell binding to an anionic phosphate group is investigated using quantum chemical approaches. The study is focused on the mutual interplay between the metal−phosphate and metal-nucleobase binding and the role of nonelectrostatic effects in the metal binding as these contributions are not included in conventional empirical force fields. The analysis of the equilibrium structures and the energy decompositions reveal that these effects substantially contribute to the differences in the coordination behavior of the studied metal ions. The Zn2+ and Cd2+ cations show a clear preference to bind to N7 of guanine compared to Mg2+. The selectivity is of ca. 3−4 kcal·mol-1 on the energy scale. This energy difference is sufficient to provide enough binding selectivity in the condensed phase where the dominant pair electrostatic terms (ion−ion, molecule−ion) are attenuated. Cu2...

Cooperative effects in long-range 1,4 DNA-DNA interstrand cross-links formed by polynuclear platinum complexes: an unexpected syn orientation of adenine bases outside the binding sites.

The novel phase II anticancer drug BBR3464 ([[ trans-PtCl(NH(3))(2)](2)- micro -[ trans-Pt(NH(3))(2)(NH(2)(CH(2))(6)NH(2))(2)]](NO(3))(4)) forms a 1,4-interstrand cross-link adduct with the self-complementary DNA octamer 5'-d(ATG*TACAT)(2)-3', with the two platinum atoms coordinated in the major groove at the N7 positions of guanines that are four base pairs apart on opposite DNA strands. The "central" tetraamine linker [ trans-H(2)N(CH(2))(6)NH(2)Pt(NH(3))(2)NH(2)(CH(2))(6)NH(2)] was located in or close to the minor groove. The adduct was characterized and analyzed by MS, UV and NMR spectroscopy. NMR analysis of the adduct shows strong H8/H1' intraresidue crosspeaks observed for the A1 and A7 resonances, consistent with a syn conformation for these bases which is usually not observed for adenine residues and bases not directly involved in the cross-link in oligonucleotides. The strong intraresidue H8/H1' crosspeak is also observed for G3. Examination of the structure thus reveals unusual cooperative effects unique to this class of anticancer drugs and is the first demonstration of cooperative effects in solution for an anticancer drug. The significant characteristic of the structure is the lack of severe DNA distortion such as a kink, directed bend or significant unwinding of the helices which are characteristic for DNA adducts of mononuclear complexes. This may contribute to the lack of protein recognition of the cross-link by HMG-domain proteins, a biological consequence significantly different from that of mononuclear complexes such as cisplatin. Since DNA is the principal target in vivo for these Pt cross-linking agents, the unique structural perturbations induced by BBR3464 cross-links are likely related to its increased cytotoxicity and antitumor activity as compared to cisplatin ( cis-DDP).

Smoking, lung cancers and their TP53 mutations.

The TP53 suppressor gene possesses several properties that have facilitated its use as a reporter of genotoxic exposure (Biggs et al., 1993). In particular, it is mutated in a high proportion of many types of human cancer and it sustains a broad spectrum of mutations that can vary in both their position and type. In lung tumours from smokers, the high frequency of G→T transversions (30% compared with 10% in cancers without tobacco aetiology) has been attributed to DNA adducts of polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene, that are present in tobacco smoke (Hainaut and Pfeifer, 2001). Benzo[a]pyrene is activated to form benzo[a]pyrene diol epoxide (BPDE), which reacts with DNA predominantly at the N2-position of guanine, and both in vitro and in vivo studies have demonstrated that BP and BPDE can, in common with other PAHs, induce G→T transversions (Wei et al., 1991; DeMarini et al., 1995; Schiltz et al., 1999; Wijnhoven et al., 2000). A single point mutation in the TP53 gene results in a base change in both DNA strands with, for example, a G→T mutation in one strand corresponding to a C→A change in the complementary strand (G:C→T:A). The question then arises whether such a change was induced by modification of G in one strand or of the C in the complementing strand. Recently, Rodin and Rodin (2000) examined the spectra of mutations that they believed were induced by damage of each of the two DNA strands of TP53 and concluded that when each strand was examined individually, there were no significant differences between the spectra in lung adenocarcinomas in smokers and non-smokers. The plot of mutations that represents the core of their argument and around which other arguments and conclusions in their paper are based is shown in Figure 1A, where all 12 possible base pair substitution mutations are grouped into six pairs, each consisting of two complementary substitutions. In this figure the mutations above the line represent the changes presumed to be induced by damage in the non-transcribed strand (NTS) of TP53 whereas those below the line represent the same changes induced in the transcribed strand (TS). For example, on the left-hand side, the G→T above the line represents a mutation induced in the NTS, whereas C→A below the line represents the G→T mutation induced in the TS. (Note that by convention all mutations are referred to by the mutation found in the NTS.) The data as presented show: (i) that above the central line the ratio of the mutation frequency in smokers to that of the same mutations in non-smokers remains approximately constant; (ii) that a similar relationship, albeit with a different value of the ratio,

Structural refinement of the 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct in a 5'-Cp(AFB)G-3' sequence.

The structure of the cationic 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct embedded in a 5'-CpG-3' sequence context and paired with deoxycytosine in the oligodeoxynucleotide d(ACATC(AFB)GATCT) x d(AGATCGATGT) was refined using molecular dynamics calculations restrained by NOE data and dihedral angle restraints obtained from NMR data. The aflatoxin moiety intercalated above the 5' face of the modified guanine. It stacked between C(5) x G(16) and (AFB)G(6) x C(15). The AFB(1) H5, OCH(3), and methylene protons faced into the minor groove, with the methylene protons oriented between the C(15) and G(16) nucleobases. The aflatoxin B(1) H6a, H8, H9, and H9a protons faced the major groove, with H6a and H9a pointing toward the 5' direction from the lesion site. The refined structure was compared to the structure of the aflatoxin B(1) adduct embedded in a 5'-ATGCAT-3' sequence in the oligodeoxynucleotide d(TAT(AFB)GCATA)(2) [Jones, W. R., Johnston, D. S., and Stone, M. P. (1998) Chem. Res. Toxicol.11, 873-881]. The structure of the intercalated aflatoxin B(1) lesion in the ATC(AFB)GAT sequence is similar to its structure in the d(AT(AFB)GCAT) sequence. This is consistent with a mechanism in which the precovalent intercalation of aflatoxin-8,9-exo-epoxide on the 5' face of guanine places the epoxide in close proximity and in the proper orientation to the N7 position of guanine, thus facilitating an S(N)2 reaction. The data provides additional insight into the nature of the disruption of the B-DNA duplex induced by aflatoxin B(1) intercalation. Overall, the results suggest that sequence contributes a minor role in modulating the structure of the cationic guanine N7 AFB(1) lesion in duplex DNA. On the other hand, structural differences are observed when the correctly paired structure is compared to the structure of the cationic AFB(1) adduct mispaired with dA [Giri, I., Johnston, D. S., and Stone, M. P. (2002) Biochemistry 41, 5462-5472].