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1.
J Biol Inorg Chem ; 27(1): 189-199, 2022 02.
Article in English | MEDLINE | ID: mdl-34843001

ABSTRACT

Mutagenic agents such as aromatic amines undergo metabolic activation and produce DNA adducts at C8 position of guanine bases. N-2-acetylaminofluorene (AAF) generates different mutational outcomes when placed at G1, G2, and G3 of a NarI sequence (-G1G2CG3CC/T-). These outcomes are dictated by the conformations adopted by these adducts. Detection of such lesions is of considerable interest owing to their hazardous effects. Here, we report the synthesis of three cyclometalated [Ir(L)2dppz]+ complexes (L = 2-phenylpyridine (ppy) 1; benzo[h]quinoline (bhq) 2; 2-phenylquinoline (pq) 3; dppz = dipyrido[3,2-a:2',3'-c]phenazine) and their interaction with AAF adducted NarI DNA. Remarkably, complexes 1 and 2 displayed dominant 3LC transition characteristic of polar environment despite binding to the adducted sites. On the other hand, complex 3 binds to NarI sequences and behaves as a luminescent reporter for AAF-modified DNA. The results reported here emphasize that molecular light switching phenomenon can be stimulated by switching ancillary ligands and might act as potential probes for covalent-DNA defects.


Subject(s)
2-Acetylaminofluorene , DNA Adducts , 2-Acetylaminofluorene/chemistry , DNA , Ligands , Molecular Conformation
2.
Chem Res Toxicol ; 29(2): 213-26, 2016 Feb 15.
Article in English | MEDLINE | ID: mdl-26733364

ABSTRACT

Frameshift mutagenesis encompasses the gain or loss of DNA base pairs, resulting in altered genetic outcomes. The NarI restriction site sequence 5'-G1G2CG3CX-3' in Escherichia coli is a well-known mutational hotspot, in which lesioning of acetylaminofluorene (AAF) at G3* induces a greater -2 deletion frequency than that at other guanine sites. Its mutational efficiency is modulated by the nature of the nucleotide in the X position (C ∼ A > G ≫ T). Here, we conducted a series of polymerase-free solution experiments that examine the conformational and thermodynamic basis underlying the propensity of adducted G3 to form a slipped mutagenic intermediate (SMI) and its sequence dependence during translesion synthesis (TLS). Instability of the AAF-dG3:dC pair at the replication fork promoted slippage to form a G*C bulge-out SMI structure, consisting of S- ("lesion stacked") and B-SMI ("lesion exposed") conformations, with conformational rigidity increasing as a function of primer elongation. We found greater stability of the S- compared to the B-SMI conformer throughout TLS. The dependence of their population ratios was determined by the 3'-next flanking base X at fully elongated bulge structures, with 59% B/41% S and 86% B/14% S for the dC and dT series, respectively. These results indicate the importance of direct interactions of the hydrophobic AAF lesion with the 3'-next flanking base pair and its stacking fit within the -2 bulge structure. A detailed conformational understanding of the SMI structures and their sequence dependence may provide a useful model for DNA polymerase complexes.


Subject(s)
2-Acetylaminofluorene/chemistry , DNA Adducts/chemistry , Deoxyribonucleases, Type II Site-Specific/metabolism , Guanine/chemistry , Calorimetry, Differential Scanning , Chromatography, High Pressure Liquid , Circular Dichroism , DNA/chemistry , DNA/metabolism , DNA Adducts/analysis , DNA Adducts/metabolism , DNA Repair , Escherichia coli/genetics , Escherichia coli/metabolism , Frameshift Mutation , Nucleic Acid Conformation , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Thermodynamics
3.
Nucleic Acids Res ; 43(20): 9918-27, 2015 Nov 16.
Article in English | MEDLINE | ID: mdl-26481355

ABSTRACT

Bulky DNA damage inhibits DNA synthesis by replicative polymerases and often requires the action of error prone bypass polymerases. The exact mechanism governing adduct-induced mutagenesis and its dependence on the DNA sequence context remains unclear. In this work, we characterize Dpo4 binding conformations and activity with DNA templates modified with the carcinogenic DNA adducts, 2-aminofluoene (AF) or N-acetyl-2-aminofluorene (AAF), using single-molecule FRET (smFRET) analysis and DNA synthesis extension assays. We find that in the absence of dNTPs, both adducts alter polymerase binding as measured by smFRET, but the addition of dNTPs induces the formation of a ternary complex having what appears to be a conformation similar to the one observed with an unmodified DNA template. We also observe that the misincorporation pathways for each adduct present significant differences: while an AF adduct induces a structure consistent with the previously observed primer-template looped structure, its acetylated counterpart uses a different mechanism, one consistent with a dNTP-stabilized misalignment mechanism.


Subject(s)
2-Acetylaminofluorene/chemistry , Carcinogens/chemistry , DNA Adducts/chemistry , DNA Polymerase beta/metabolism , Fluorenes/chemistry , DNA/biosynthesis , DNA/chemistry , DNA/metabolism , DNA Primers , Guanine/chemistry , Nucleotides/metabolism , Protein Binding , Templates, Genetic
4.
Proc Natl Acad Sci U S A ; 112(27): 8272-7, 2015 Jul 07.
Article in English | MEDLINE | ID: mdl-26100901

ABSTRACT

Nucleotide excision repair (NER) is responsible for the removal of a large variety of structurally diverse DNA lesions. Mutations of the involved proteins cause the xeroderma pigmentosum (XP) cancer predisposition syndrome. Although the general mechanism of the NER process is well studied, the function of the XPA protein, which is of central importance for successful NER, has remained enigmatic. It is known, that XPA binds kinked DNA structures and that it interacts also with DNA duplexes containing certain lesions, but the mechanism of interactions is unknown. Here we present two crystal structures of the DNA binding domain (DBD) of the yeast XPA homolog Rad14 bound to DNA with either a cisplatin lesion (1,2-GG) or an acetylaminofluorene adduct (AAF-dG). In the structures, we see that two Rad14 molecules bind to the duplex, which induces DNA melting of the duplex remote from the lesion. Each monomer interrogates the duplex with a ß-hairpin, which creates a 13mer duplex recognition motif additionally characterized by a sharp 70° DNA kink at the position of the lesion. Although the 1,2-GG lesion stabilizes the kink due to the covalent fixation of the crosslinked dG bases at a 90° angle, the AAF-dG fully intercalates into the duplex to stabilize the kinked structure.


Subject(s)
DNA Damage , DNA Repair Enzymes/chemistry , DNA Repair , Saccharomyces cerevisiae Proteins/chemistry , 2-Acetylaminofluorene/chemistry , 2-Acetylaminofluorene/metabolism , Amino Acid Sequence , Cisplatin/chemistry , Cisplatin/metabolism , Crystallography, X-Ray , DNA Repair Enzymes/genetics , DNA Repair Enzymes/metabolism , DNA, Fungal/chemistry , DNA, Fungal/genetics , DNA, Fungal/metabolism , Models, Molecular , Molecular Sequence Data , Nucleic Acid Conformation , Nucleic Acid Denaturation , Protein Binding , Protein Structure, Tertiary , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Sequence Homology, Amino Acid , Thermodynamics , Transition Temperature
5.
Biochemistry ; 53(35): 5683-91, 2014 Sep 09.
Article in English | MEDLINE | ID: mdl-25148552

ABSTRACT

DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase κ (Polκ), a member of the Y family of lesion bypass polymerases, is specialized to bypass bulky DNA minor groove lesions in a predominantly error-free manner, by housing them in its unique gap. We have investigated the role of the unique Polκ gap and N-clasp structural features in the fidelity of minor groove lesion processing with extensive molecular modeling and molecular dynamics simulations to pinpoint their functioning in lesion bypass. Here we consider the N(2)-dG covalent adduct derived from the carcinogenic aromatic amine, 2-acetylaminofluorene (dG-N(2)-AAF), that is produced via the combustion of kerosene and diesel fuel. Our simulations reveal how the spacious gap directionally accommodates the lesion aromatic ring system as it transits through the stages of incorporation of the predominant correct partner dCTP opposite the damaged guanine, with preservation of local active site organization for nucleotidyl transfer. Furthermore, flexibility in Polκ's N-clasp facilitates the significant misincorporation of dTTP opposite dG-N(2)-AAF via wobble pairing. Notably, we show that N-clasp flexibility depends on lesion topology, being markedly reduced in the case of the benzo[a]pyrene-derived major adduct to N(2)-dG, whose bypass by Polκ is nearly error-free. Thus, our studies reveal how Polκ's unique structural and dynamic properties can regulate its bypass fidelity of polycyclic aromatic lesions and how the fidelity is impacted by lesion structures.


Subject(s)
DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/metabolism , 2-Acetylaminofluorene/analogs & derivatives , 2-Acetylaminofluorene/chemistry , 2-Acetylaminofluorene/metabolism , Base Pair Mismatch , Catalytic Domain , DNA Adducts/chemistry , DNA Adducts/metabolism , Deoxyguanosine/analogs & derivatives , Deoxyguanosine/chemistry , Deoxyguanosine/metabolism , Humans , Models, Molecular , Molecular Dynamics Simulation , Protein Conformation , Substrate Specificity
6.
Nucleic Acids Res ; 41(16): 7843-53, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23814187

ABSTRACT

DNA polymerases must accurately replicate DNA to maintain genome integrity. Carcinogenic adducts, such as 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF), covalently bind DNA bases and promote mutagenesis near the adduct site. The mechanism by which carcinogenic adducts inhibit DNA synthesis and cause mutagenesis remains unclear. Here, we measure interactions between a DNA polymerase and carcinogenic DNA adducts in real-time by single-molecule fluorescence. We find the degree to which an adduct affects polymerase binding to the DNA depends on the adduct location with respect to the primer terminus, the adduct structure and the nucleotides present in the solution. Not only do the adducts influence the polymerase dwell time on the DNA but also its binding position and orientation. Finally, we have directly observed an adduct- and mismatch-induced intermediate state, which may be an obligatory step in the DNA polymerase proofreading mechanism.


Subject(s)
2-Acetylaminofluorene/analogs & derivatives , Carcinogens/chemistry , DNA Adducts/chemistry , DNA Polymerase I/metabolism , Deoxyguanosine/analogs & derivatives , Fluorenes/chemistry , 2-Acetylaminofluorene/chemistry , DNA/biosynthesis , DNA/chemistry , DNA Polymerase I/chemistry , Deoxyguanosine/chemistry , Fluorometry/methods , Protein Binding
7.
Chem Res Toxicol ; 26(8): 1251-62, 2013 Aug 19.
Article in English | MEDLINE | ID: mdl-23841451

ABSTRACT

Cluster DNA damage refers to two or more lesions in a single turn of the DNA helix. Such clustering may occur with bulky DNA lesions, which may be responsible for their sequence-dependent repair and mutational outcomes. Here we prepared three 16-mer cluster duplexes in which two fluoroacetylaminofluorene adducts (dG-FAAF) are separated by zero, one, and two nucleotides in the Escherichia coli NarI mutational hot spot (5'-CTCTCG1G2CG3CCATCAC-3'): 5'-CG1*G2*CG3CC-3', 5'-CG1G2*CG3*CC-3', and 5'-CG1*G2CG3*CC-3' (G* = dG-FAAF), respectively. We conducted spectroscopic, thermodynamic, and molecular dynamics studies of these di-FAAF duplexes, and the results were compared with those of the corresponding mono-FAAF adducts in the same NarI sequence [Jain, V., et al. (2012) Nucleic Acids Res. 40, 3939-3951]. Our nucleotide excision repair results showed the diadducts were more reparable than the corresponding monoadducts. Moreover, we observed dramatic flanking base sequence effects on their repair efficiency in the following order: NarI-G2G3 > NarI-G1G3 > NarI-G1G2. The nuclear magnetic resonance, circular dichroism, ultraviolet melting, and molecular dynamics simulation results revealed that in contrast to the monoadducts, diadducts produced a synergistic effect on duplex destabilization. In addition, dG-FAAF at G2G3 and G1G3 destacks the neighboring bases, with greater destabilization occurring with the former. Overall, the results indicate the importance of base stacking and related thermal and thermodynamic destabilization in the repair of bulky cluster arylamine DNA adducts.


Subject(s)
2-Acetylaminofluorene/chemistry , DNA Adducts/metabolism , Deoxyribonucleases, Type II Site-Specific/metabolism , Endodeoxyribonucleases/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Base Pairing , Base Sequence , Cluster Analysis , DNA Adducts/chemistry , DNA Repair , Deoxyribonucleases, Type II Site-Specific/chemistry , Deoxyribonucleases, Type II Site-Specific/genetics , Molecular Dynamics Simulation , Mutation , Oligodeoxyribonucleotides/chemical synthesis , Oligodeoxyribonucleotides/chemistry , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Thermodynamics
8.
Chem Res Toxicol ; 26(6): 937-51, 2013 Jun 17.
Article in English | MEDLINE | ID: mdl-23688347

ABSTRACT

2-Acetylaminofluorene (AAF) is a prototype arylamine carcinogen that forms C8-substituted dG-AAF and dG-AF as the major DNA lesions. The bulky N-acetylated dG-AAF lesion can induce various frameshift mutations depending on the base sequence around the lesion. We hypothesized that the thermodynamic stability of bulged-out slipped mutagenic intermediates (SMIs) is directly related to deletion mutations. The objective of the present study was to probe the structural/conformational basis of various dG-AAF-induced SMIs formed during translesion synthesis. We performed spectroscopic, thermodynamic, and molecular dynamics studies of several AAF-modified 16-mer model DNA duplexes, including fully paired and -1, -2, and -3 deletion duplexes of the 5'-CTCTCGATG[FAAF]CCATCAC-3' sequence and an additional -1 deletion duplex of the 5'-CTCTCGGCG[FAAF]CCATCAC-3' NarI sequence. Modified deletion duplexes existed in a mixture of external B and stacked S conformers, with the population of the S conformer being 'GC'-1 (73%) > 'AT'-1 (72%) > full (60%) > -2 (55%) > -3 (37%). Thermodynamic stability was in the order of -1 deletion > -2 deletion > fully paired > -3 deletion duplexes. These results indicate that the stacked S-type conformer of SMIs is thermodynamically more stable than the conformationally flexible external B conformer. Results from the molecular dynamics simulations indicate that perturbation of base stacking dominates the relative stability along with contributions from bending, duplex dynamics, and solvation effects that are important in specific cases. Taken together, these results support a hypothesis that the conformational and thermodynamic stabilities of the SMIs are critical determinants for the induction of frameshift mutations.


Subject(s)
2-Acetylaminofluorene/pharmacology , DNA/drug effects , Frameshift Mutation/genetics , Frameshifting, Ribosomal/drug effects , Mutagenesis/drug effects , Thermodynamics , 2-Acetylaminofluorene/chemistry , DNA/genetics , Models, Chemical , Molecular Dynamics Simulation , Molecular Structure
9.
Nucleic Acids Res ; 41(2): 869-80, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23180767

ABSTRACT

The environmental arylamine mutagens are implicated in the etiology of various sporadic human cancers. Arylamine-modified dG lesions were studied in two fully paired 11-mer duplexes with a -G*CN- sequence context, in which G* is a C8-substituted dG adduct derived from fluorinated analogs of 4-aminobiphenyl (FABP), 2-aminofluorene (FAF) or 2-acetylaminofluorene (FAAF), and N is either dA or dT. The FABP and FAF lesions exist in a simple mixture of 'stacked' (S) and 'B-type' (B) conformers, whereas the N-acetylated FAAF also samples a 'wedge' (W) conformer. FAAF is repaired three to four times more efficiently than FABP and FAF. A simple A- to -T polarity swap in the G*CA/G*CT transition produced a dramatic increase in syn-conformation and resulted in 2- to 3-fold lower nucleotide excision repair (NER) efficiencies in Escherichia coli. These results indicate that lesion-induced DNA bending/thermodynamic destabilization is an important DNA damage recognition factor, more so than the local S/B-conformational heterogeneity that was observed previously for FAF and FAAF in certain sequence contexts. This work represents a novel 3'-next flanking sequence effect as a unique NER factor for bulky arylamine lesions in E. coli.


Subject(s)
2-Acetylaminofluorene/chemistry , Aminobiphenyl Compounds/chemistry , DNA Adducts/chemistry , DNA Damage , DNA Repair , Deoxyguanosine/analogs & derivatives , Fluorenes/chemistry , Base Sequence , Circular Dichroism , DNA Adducts/metabolism , Deoxyguanosine/chemistry , Electrophoretic Mobility Shift Assay , Endodeoxyribonucleases/metabolism , Escherichia coli/genetics , Escherichia coli Proteins/metabolism , Models, Molecular , Molecular Dynamics Simulation , Nuclear Magnetic Resonance, Biomolecular , Nucleic Acid Conformation , Thermodynamics
10.
Chem Res Toxicol ; 25(11): 2462-8, 2012 Nov 19.
Article in English | MEDLINE | ID: mdl-23088760

ABSTRACT

Nucleotide excision repair (NER) removes lesions caused by environmental mutagens or UV light from DNA. A hallmark of NER is the extraordinarily wide substrate specificity, raising the question of how one set of proteins is able to recognize structurally diverse lesions. Two key features of good NER substrates are that they are bulky and thermodynamically destabilize DNA duplexes. To understand what the limiting step in damage recognition in NER is, we set out to test the hypothesis that there is a correlation of the degree of thermodynamic destabilization induced by a lesion, binding affinity to the damage recognition protein XPC-RAD23B, and overall NER efficiency. We chose to use acetylaminofluorene (AAF) and aminofluorene (AF) adducts at the C8 position of guanine in different positions within the NarI (GGCGCC) sequence, as it is known that the structures of the duplexes depend on the position of the lesion in this context. We found that the efficiency of NER and the binding affinity of the damage recognition factor XPC-RAD23B correlated with the thermodynamic destabilization induced by the lesion. Our study is the first systematic analysis correlating these three parameters and supports the idea that initial damage recognition by XPC-RAD23B is a key rate-limiting step in NER.


Subject(s)
2-Acetylaminofluorene/pharmacology , DNA Adducts/pharmacology , DNA Repair/drug effects , 2-Acetylaminofluorene/chemical synthesis , 2-Acetylaminofluorene/chemistry , DNA Adducts/chemical synthesis , DNA Adducts/chemistry , Humans , Models, Molecular , Molecular Structure , Oligodeoxyribonucleotides/chemistry , Thermodynamics
11.
Nucleic Acids Res ; 40(19): 9675-90, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22904073

ABSTRACT

Nucleotide excision repair (NER) efficiencies of DNA lesions can vary by orders of magnitude, for reasons that remain unclear. An example is the pair of N-(2'-deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF) and N-(2'-deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) adducts that differ by a single acetyl group. The NER efficiencies in human HeLa cell extracts of these lesions are significantly different when placed at G(1), G(2) or G(3) in the duplex sequence (5'-CTCG(1)G(2)CG(3)CCATC-3') containing the NarI mutational hot spot. Furthermore, the dG-C8-AAF adduct is a better substrate of NER than dG-C8-AF in all three NarI sequence contexts. The conformations of each of these adducts were investigated by Molecular dynamics (MD) simulation methods. In the base-displaced conformational family, the greater repair susceptibility of dG-C8-AAF in all sequences stems from steric hindrance effects of the acetyl group which significantly diminish the adduct-base stabilizing van der Waals stacking interactions relative to the dG-C8-AF case. Base sequence context effects for each adduct are caused by differences in helix untwisting and minor groove opening that are derived from the differences in stacking patterns. Overall, the greater NER efficiencies are correlated with greater extents of base sequence-dependent local untwisting and minor groove opening together with weaker stacking interactions.


Subject(s)
2-Acetylaminofluorene/analogs & derivatives , DNA Adducts/chemistry , DNA Repair , Deoxyguanosine/analogs & derivatives , Fluorenes/chemistry , 2-Acetylaminofluorene/chemistry , 2-Acetylaminofluorene/metabolism , Base Sequence , DNA Adducts/metabolism , Deoxyguanosine/chemistry , Deoxyguanosine/metabolism , Fluorenes/metabolism , HeLa Cells , Humans , Molecular Dynamics Simulation , Nucleic Acid Conformation
12.
Chem Res Toxicol ; 25(8): 1568-70, 2012 Aug 20.
Article in English | MEDLINE | ID: mdl-22804627

ABSTRACT

We used surface plasmon resonance (SPR) to characterize the binding interactions between the exonulease-free Klenow fragment (Kf-exo(-)) and unmodified and modified dG adducts derived from arylamine carcinogens: fluorinated 2-aminofluorene (FAF), 2-acetylaminofluorene (FAAF), and 4-aminobiphenyl (FABP). Tight polymerase binding was detected with unmodified dG and the correct dCTP. The discrimination of correct versus incorrect nucleotides was pronounced with K(D) values in the order of dCTP ≪ dTTP < dATP < dGTP. In contrast, minimal selectivity was observed for the modified templates with Kf-exo(-) binding tighter to the FAAF (k(off): 0.02 s(-1)) and FABP (k(off): 0.01 s(-1)) lesions than to FAF (k(off): 0.04 s(-1)).


Subject(s)
2-Acetylaminofluorene/chemistry , Aminobiphenyl Compounds/chemistry , DNA Polymerase I/metabolism , DNA/chemistry , Fluorenes/chemistry , DNA/metabolism , DNA Adducts/chemistry , Deoxyadenine Nucleotides/chemistry , Deoxycytosine Nucleotides/chemistry , Deoxyguanine Nucleotides/chemistry , Kinetics , Surface Plasmon Resonance , Thymine Nucleotides/chemistry
13.
Nucleic Acids Res ; 40(9): 3939-51, 2012 May.
Article in English | MEDLINE | ID: mdl-22241773

ABSTRACT

Nucleotide excision repair (NER) is a major repair pathway that recognizes and corrects various lesions in cellular DNA. We hypothesize that damage recognition is an initial step in NER that senses conformational anomalies in the DNA caused by lesions. We prepared three DNA duplexes containing the carcinogen adduct N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene (FAAF) at G(1), G(2) or G(3) of NarI sequence (5'-CCG(1)G(2)CG(3)CC-3'). Our (19)F-NMR/ICD results showed that FAAF at G(1) and G(3) prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G(2). We found that the repair of FAAF occurs in a conformation-specific manner, i.e. the highly S/W-conformeric G(3) and -G(1) duplexes incised more efficiently than the B-type G(2) duplex (G(3)∼G(1)> G(2)). The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization. The N-deacetylated N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (FAF) adducts in the same NarI sequence are repaired 2- to 3-fold less than FAAF: however, the incision efficiency was in order of G(2)∼G(1)> G(3), a reverse trend of the FAAF case. We have envisioned the so-called N-acetyl factor as it could raise conformational barriers of FAAF versus FAF. The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts.


Subject(s)
2-Acetylaminofluorene/chemistry , DNA Adducts/chemistry , DNA Repair , Deoxyguanosine/chemistry , Fluorenes/chemistry , Thermodynamics , Adenosine Triphosphatases/metabolism , Base Sequence , Calorimetry , Circular Dichroism , DNA-Binding Proteins/metabolism , Deoxyribonucleases, Type II Site-Specific , Escherichia coli Proteins/metabolism , Nuclear Magnetic Resonance, Biomolecular , Nucleic Acid Conformation , Nucleic Acid Denaturation , Spectrometry, Mass, Electrospray Ionization
15.
J Am Chem Soc ; 133(32): 12600-7, 2011 Aug 17.
Article in English | MEDLINE | ID: mdl-21751809

ABSTRACT

Water-soluble conjugated polymers with controlled molecular weight characteristics, absence of ionic groups, high emission quantum yields, and end groups capable of selective reactions of wide scope are desirable for improving their performance in various applications and, in particular, fluorescent biosensor schemes. The synthesis of such a structure is described herein. 2-Bromo-7-iodofluorene with octakis(ethylene glycol) monomethyl ether chains at the 9,9'-positions, i.e., compound 4, was prepared as the reactive premonomer. A high-yielding synthesis of the organometallic initiator (dppe)Ni(Ph)Br (dppe = 1,2-bis(diphenylphosphino)ethane) was designed and implemented, and the resulting product was characterized by single-crystal X-ray diffraction techniques. Polymerization of 4 by (dppe)Ni(Ph)Br can be carried out in less than 30 s, affording excellent control over the average molecular weight and polydispersity of the product. Quenching of the polymerization with [2-(trimethylsilyl)ethynyl]magnesium bromide yields silylacetylene-terminated water-soluble poly(fluorene) with a photoluminescence quantum efficiency of 80%. Desilylation, followed by copper-catalyzed azide-alkyne cycloaddition reaction, yields a straightforward route to introduce a wide range of specific end group functionalities. Biotin was used as an example. The resulting biotinylated conjugated polymer binds to streptavidin and acts as a light-harvesting chromophore to optically amplify the emission of Alexa Fluor-488 chromophores bound onto the streptavidin. Furthermore, the biotin end group makes it possible to bind the polymer onto streptavidin-functionalized cross-linked agarose beads and thereby incorporate a large number of optically active segments.


Subject(s)
2-Acetylaminofluorene/analogs & derivatives , Biosensing Techniques/methods , Fluorescent Dyes/chemistry , Polymers/chemistry , 2-Acetylaminofluorene/chemical synthesis , 2-Acetylaminofluorene/chemistry , 2-Acetylaminofluorene/metabolism , Biotinylation , Click Chemistry , Ethylene Glycol/chemical synthesis , Ethylene Glycol/chemistry , Ethylene Glycol/metabolism , Fluorescent Dyes/chemical synthesis , Fluorescent Dyes/metabolism , Luminescence , Models, Molecular , Polymerization , Polymers/chemical synthesis , Polymers/metabolism , Solubility , Streptavidin/metabolism , Water/chemistry
16.
Proc Natl Acad Sci U S A ; 107(48): 20720-5, 2010 Nov 30.
Article in English | MEDLINE | ID: mdl-21076032

ABSTRACT

Heterocyclic aromatic amines produce bulky C8 guanine lesions in vivo, which interfere and disrupt DNA and RNA synthesis. These lesions are consequently strong replication blocks. In addition bulky adducts give rise to point and frameshift mutations. The translesion synthesis (TLS) DNA polymerase η is able to bypass slowly C8 bulky adduct lesions such as the widely studied 2-aminofluorene-dG and its acetylated analogue mainly in an error-free manner. Replicative polymerases are in contrast fully blocked by the acetylated lesion. Here, we show that TLS efficiency of Pol η depends critically on the size of the bulky adduct forming the lesion. Based on the crystal structure, we show why the bypass reaction is so difficult and we provide a model for the bypass reaction. In our model, TLS is accomplished without rotation of the lesion into the anti conformation as previously thought.


Subject(s)
2-Acetylaminofluorene/metabolism , DNA Adducts/metabolism , DNA Replication , DNA-Directed DNA Polymerase/metabolism , Saccharomyces cerevisiae/enzymology , 2-Acetylaminofluorene/chemistry , Crystallography, X-Ray , DNA Adducts/chemistry , DNA Damage , DNA-Directed DNA Polymerase/chemistry , Models, Molecular , Molecular Conformation , Protein Binding
17.
Chem Res Toxicol ; 23(11): 1650-2, 2010 Nov 15.
Article in English | MEDLINE | ID: mdl-20954689

ABSTRACT

Despite the extensive data on dG-AAF, the major DNA adduct derived from the model carcinogen 2-acetylaminofluorene, little is known with respect to its solution structures. Here, we provide NMR/CD evidence for three conformers of dG-AAF in duplex DNA: major groove B-type (B), base-displaced stacked (S), and minor groove wedge (W). The S/B/W-conformational heterogeneities were found to be sensitive to the nature of the flanking DNA sequence contexts and pH.


Subject(s)
2-Acetylaminofluorene/chemistry , DNA/chemistry , Carcinogens/chemistry , Circular Dichroism , DNA Adducts/chemistry , Hydrogen-Ion Concentration , Magnetic Resonance Spectroscopy , Molecular Conformation , Temperature
18.
Biochemistry ; 48(19): 4209-16, 2009 May 19.
Article in English | MEDLINE | ID: mdl-19354292

ABSTRACT

The well-studied aromatic amine carcinogen, N-2-acetylaminofluorene (AAF), forms adducts at the C8 position of guanine in DNA. Unlike replicative polymerases, Y-family polymerases have been shown to have the ability to bypass such bulky DNA lesions. To better understand the mechanism of translesion synthesis by the yeast DNA polymerase eta (yPoleta), a gel retardation technique was used to measure equilibrium dissociation constants of this polymerase for unmodified DNA or DNA containing dG-C8-AAF or the related deacylated dG-C8-AF adduct. These results show that the binding of yPoleta to the unmodified primer-template is substantially stronger in the presence of the next correct nucleotide than when no or an incorrect nucleotide is present. In addition, binding of yPoleta to either dG-C8-AAF or AF-modified templates is also stronger in the presence of dCTP. Finally, the yPoleta complex is destabilized if the primer extends to a position across from the adduct, and stronger binding is not observed in the presence of the next correct nucleotide. Taken together, these data are consistent with the ability of yPoleta to undergo a conformational change to a closed ternary complex in the presence of the next correct nucleotide and on templates containing an AAF or AF adduct but do not rule out other possible explanations.


Subject(s)
2-Acetylaminofluorene/chemistry , DNA Adducts/chemistry , DNA, Fungal/metabolism , DNA-Directed DNA Polymerase/metabolism , Fluorenes/chemistry , Saccharomyces cerevisiae/enzymology , Carcinogens/chemistry , Molecular Conformation , Molecular Structure
19.
Biochemistry ; 48(1): 7-18, 2009 Jan 13.
Article in English | MEDLINE | ID: mdl-19072536

ABSTRACT

Bypass across DNA lesions by specialized polymerases is essential for maintenance of genomic stability. Human DNA polymerase iota (poliota) is a bypass polymerase of the Y family. Crystal structures of poliota suggest that Hoogsteen base pairing is employed to bypass minor groove DNA lesions, placing them on the spacious major groove side of the enzyme. Primer extension studies have shown that poliota is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF). We present molecular dynamics simulations and free energy calculations suggesting that Watson-Crick base pairing could be employed in poliota for bypass of dG-AAF. In poliota with Hoogsteen-paired dG-AAF the bulky AAF moiety would reside on the cramped minor groove side of the template. The Hoogsteen-capable conformation distorts the active site, disrupting interactions necessary for error-free incorporation of dC opposite the lesion. Watson-Crick pairing places the AAF rings on the spacious major groove side, similar to the position of minor groove adducts observed with Hoogsteen pairing. Watson-Crick-paired structures show a well-ordered active site, with a near reaction-ready ternary complex. Thus our results suggest that poliota would utilize the same spacious region for lesion bypass of both major and minor groove adducts. Therefore, purine adducts with bulk on the minor groove side would use Hoogsteen pairing, while adducts with the bulky lesion on the major groove side would utilize Watson-Crick base pairing as indicated by our MD simulations for dG-AAF. This suggests the possibility of an expanded role for poliota in lesion bypass.


Subject(s)
2-Acetylaminofluorene/analogs & derivatives , Base Pairing , DNA Adducts/chemistry , DNA-Directed DNA Polymerase/chemistry , Deoxyguanosine/analogs & derivatives , 2-Acetylaminofluorene/chemistry , Catalytic Domain , Deoxyguanosine/chemistry , Humans , Models, Molecular , Molecular Structure , Thermodynamics , DNA Polymerase iota
20.
Bioorg Med Chem ; 16(14): 7070-7, 2008 Jul 15.
Article in English | MEDLINE | ID: mdl-18586499

ABSTRACT

Oxidation of 2-acetylaminofluorene (AAF), a carcinogen, by a chemical model for cytochrome P450 was investigated to identify an active mutagen and elucidate the oxidation pathway. The oxidation system consisted of a water-insoluble tetrakis(pentafluorophenyl)porphyrinatoiron(III) chloride and tert-butyl hydroperoxide. The mutagen derived from AAF by the chemical model was 2-nitro-9-fluorenone (NO(2)=FO), which was mutagenic in Salmonella typhimurium TA1538. AAF was oxidized initially at position 9 of the fluorene carbon by the chemical model forming 2-acetylamino-9-fluorenol (AAF-OH), and then oxidized further to 2-acetylamino-9-fluorenone (AAF=O) as a major product. Initial oxidation of the nitrogen formed 2-nitrofluorene (NO(2)F), and further oxidation yielded 2-nitro-9-fluorenol (NO(2)F-OH) as a minor product. These products, AAF-OH, AAF=O, NO(2)F, and NO(2)F-OH, and their presumable common intermediate, N-hydroxy-2-acetylaminofluorene, were oxidized by the chemical model, and the formation of NO(2)F=O was determined. These results showed that NO(2)F=O was the mutagen derived from AAF in the presence of the chemical model and was formed via oxidation of N-OH-AAF, NO(2)F, and NO(2)F-OH. These results may lead to a new metabolic pathway of AAF.


Subject(s)
2-Acetylaminofluorene/chemistry , Carcinogens/chemistry , Cytochrome P-450 Enzyme System , Models, Chemical , Porphyrins/chemistry , tert-Butylhydroperoxide/chemistry , Mutagenicity Tests , Oxidation-Reduction , Salmonella typhimurium/drug effects , Water
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