Synthesis and characterization of oligodeoxynucleotides containing N-(deoxyguanosin-8-yl)-1-aminopyrene

Establishing Linkages Among DNA Damage, Mutagenesis, and Genetic Diseases

DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.

Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution

Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.

Synthesis of oligonucleotides containing 2'-deoxyguanosine adducts of nitropyrenes

Two different approaches to synthesize oligonucleotides containing the 2 '-deoxyguanosine adducts formed by nitropyrenes are described. A direct reaction of an unmodified oligonucleotide with an activated nitropyrene derivative is a convenient biomimetic approach for generating the major adducts in DNA. A total synthetic approach, by contrast, involves several synthetic steps, including Buchwald-Hartwig Pd-catalyzed coupling, but can be used for incorporating both the major and minor adducts in DNA in high yield.

Biological properties of single chemical-DNA adducts: a twenty year perspective

The genome and its nucleotide precursor pool are under sustained attack by radiation, reactive oxygen and nitrogen species, chemical carcinogens, hydrolytic reactions, and certain drugs. As a result, a large and heterogeneous population of damaged nucleotides forms in all cells. Some of the lesions are repaired, but for those that remain, there can be serious biological consequences. For example, lesions that form in DNA can lead to altered gene expression, mutation, and death. This perspective examines systems developed over the past 20 years to study the biological properties of single DNA lesions.

Mutagenicity of the 1-nitropyrene-DNA adduct N-(deoxyguanosin-8-yl)-1-aminopyrene in mammalian cells

The mutagenesis of the major DNA adduct N-(deoxyguanosin-8-yl)-1-aminopyrene (C8-AP-dG) formed by 1-nitropyrene was compared with the analogous C8-dG adducts of 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF) in simian kidney (COS-7) cells. The DNA sequence chosen for this comparison contained 5'-CCATC GCTACC-3' that has been used for solution NMR investigations. The structural and conformational differences among these lesions are well-established [Patel, D. J., Mao, B., Gu, Z., Hingerty, B. E., Gorin, A., Basu, A. K., and Broyde,S. (1998) NMR solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance. Chem. Res. Toxicol. 11, 391- 407.]. Accordingly, we found a notable difference in the viability of the progeny, which showed that the AAF adduct was most toxic and that the AF adduct was least toxic, with the AP adduct exhibiting intermediate toxicity. However, analysis of the progeny showed that translesion synthesis was predominantly error-free. Only low-level mutations (<3%) were detected with G-->T as the dominant type of mutation by all three DNA adducts. When C8-AP-dG was evaluated in a repetitive 5'-CGC GCG-3' sequence, higher mutational frequency ( approximately 8%) was observed. Again, G-->T was the major type of mutations in simian kidney cells, even though in bacteria CpG deletions predominate in this sequence [Hilario, P., Yan, S., Hingerty, B. E., Broyde, S., and Basu, A. K. (2002) Comparative mutagenesis of the C8-guanine adducts of 1-nitropyrene,and 1,6- and 1,8-dinitropyrene in a CpG repeat sequence: A slipped frameshift intermediate model for dinucleotide deletion. J. Biol. Chem. 277, 45068- 45074.]. Mutagenesis of C8-AP-dG in a 12-mer containing the local DNA sequence around codon 273 of the p53 tumor suppressor gene, where the adduct was located at the second base of this codon, was also investigated. In this 5'-GTGC GTGTTTGT-3' site, the mutations were slightly lower but not very different from the progeny derived from the 5'-CGC GCG-3' sequence. However, the mutational frequency increased by more than 50% when the 5'-C to the adduct was replaced with a 5-methylcytosine (5-MeC). With a 5-MeC, the most notable change in mutation was the enhancement of G-->A, which occurred 2.5 times relative to a 5'-C. The C8-AP-dG adduct in codon 273 dodecamer sequence with a 5'-C or 5-MeC was also evaluated in human embryonic kidney (293T) cells. Similar to COS cells, targeted mutations doubled with a 5-MeC 5' to the adduct. Except for an increase in G-->C transversions, the results in 293T were similar to that in COS cells. We conclude that C8-AP-dG mutagenesis depends on the type of cell in which it is replicated, the neighboring DNA sequence, and the methylation status of the 5'-C.

Synthesis of N2 2'-deoxyguanosine adducts formed by 1-nitropyrene

[reaction: see text] Synthesis of N(2) 2'-deoxyguanosine adducts formed by the ubiquitous carcinogen, 1-nitropyrene, is reported. Various conditions of Buchwald-Hartwig palladium-catalyzed amination are examined. The most convenient synthetic approach involved a straightforward coupling between protected 2'-deoxyguanosine and bromonitropyrenes, which, upon reductive deprotection, provided excellent yield of the two 1-nitropyrene adducts.

Comparative mutagenesis of the C8-guanine adducts of 1-nitropyrene and 1,6- and 1,8-dinitropyrene in a CpG repeat sequence. A slipped frameshift intermediate model for dinucleotide deletion

In the Ames Salmonella typhimurium reversion assay 1,6- and 1,8-dinitropyrenes (1,6- and 1,8-DNPs) are much more potent mutagens than 1-nitropyrene (1-NP). Genetic experiments established that certain differences in the metabolism of the DNPs, which in turn result in increased DNA adduction, play a role. It remained unclear, however, if the DNP adducts, N-(guanin-8-yl)-1-amino-6 ()-nitropyrene (Gua-C8-1,6-ANP and Gua-C8-1,8-ANP), which contain a nitro group on the pyrene ring covalently linked to the guanine C8, are more mutagenic than the major 1-NP adduct, N-(guanin-8-yl)-1-aminopyrene (Gua-C8-AP). In order to address this, we have compared the mutation frequency of the three guanine C8 adducts, Gua-C8-AP, Gua-C8-1,6-ANP, and Gua-C8-1,8-ANP in a CGCG*CG sequence. Single-stranded M13mp7L2 vectors containing these adducts and a control were constructed and replicated in Escherichia coli. A remarkable difference in the induced CpG deletion frequency between these adducts was noted. In repair-competent cells the 1-NP adduct induced 1.7% CpG deletions without SOS, whereas the 1,6- and 1,8-DNP adducts induced 6.8 and 10.0% two-base deletions, respectively. With SOS, CpG deletions increased up to 1.9, 11.1, and 15.1% by 1-NP, 1,6-, and 1,8-DNP adducts, respectively. This result unequivocally established that DNP adducts are more mutagenic than the 1-NP adduct in the repetitive CpG sequence. In each case the mutation frequency was significantly increased in a mutS strain, which is impaired in methyl-directed mismatch repair, and a dnaQ strain, which carries a defect in proofreading activity of the DNA polymerase III. Modeling studies showed that the nitro group on the pyrene ring at the 8-position can provide additional stabilization to the two-nucleotide extrahelical loop in the promutagenic slipped frameshift intermediate through its added hydrogen-bonding capability. This could account for the increase in CpG deletions in the M13 vector with the nitro-containing adducts compared with the Gua-C8-AP adduct itself.

Synthesis and characterization of oligodeoxynucleotides containing the major DNA adducts formed by 1,6- and 1,8-dinitropyrene

[reaction: see text] An efficient method for the synthesis of oligonucleotides containing a site-specific DNA adduct formed by the carcinogens 1,6- and 1, 8-dinitropyrene has been developed. Palladium-catalyzed amination provided a straightforward route for the synthesis of aminonitropyrenes which, following separation, were reduced to the nitrosonitropyrenes. The N-hydroxyaminonitropyrene, generated in situ from each nitrosonitropyrene, was used successfully to introduce the dinitropyrene-derived DNA adduct at a defined site in an oligonucleotide.