1
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Crisalli AM, Chen YT, Cai A, Li D, Cho BP. Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts. Nucleic Acids Res 2023; 51:12043-12053. [PMID: 37953358 PMCID: PMC10711442 DOI: 10.1093/nar/gkad1038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/27/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.
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Affiliation(s)
- Alicia M Crisalli
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Ang Cai
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Bongsup P Cho
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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2
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Jeong YER, Kung RW, Bykowski J, Deak TK, Wetmore SD. Effect of Guanine Adduct Size, Shape, and Linker Type on the Conformation of Adducted DNA: A DFT and Molecular Dynamics Study. J Phys Chem B 2023; 127:9035-9049. [PMID: 37831812 DOI: 10.1021/acs.jpcb.3c04864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
DNA is damaged through various exogenous sources (e.g., automobile exhaust, tobacco smoke, and processed foods), which can yield diverse C8-dG bulky aryl adducts. Adducts are known to induce structural changes to DNA that can lead to various biological outcomes, ranging from cell death to diseases such as cancer. Unfortunately, the relationship between the chemical composition of the damaged product, the adducted DNA structure, and the biological consequences is not well understood, which limits the development of disease detection and prevention strategies. The present study uses density functional theory (DFT) calculations and quintuplicate 1 μs molecular dynamics (MD) simulations to characterize the structure of DNA containing 21 model C8-dG adducts that systematically differ in size (phenyl to pyrenyl), shape (α (2,3), β (3,4) fusion, or ring substitution), and nucleobase-aryl group linkage (N, O, and C-linked). DFT calculations reveal that the inherent structural features of the G nucleobase adducts are impacted by linker type and bulky moiety shape, but not size, with the conformational flexibility reducing with α-ring fusion and linker composition as N > O > C. These structural properties are maintained in nucleoside models, which also reveal an increased propensity for anti-to-syn rotation about the glycosidic bond with N < O < C linker type. Although these diverse chemical features do not influence the global structure of adducted DNA, the adducts differentially impact the conformation local to the adducted site, including the relative populations of structures with the bulky moiety in the major groove (B conformer) and intercalated (stacked) into the helix (S conformer). Specifically, while the smallest phenyl adducts favor the B conformation and the largest pyrenyl-derived adducts stabilize the S conformation, the B/S ratio decreases with an increase in ring size and N > O > C linker composition. The shape and size (length) of the adduct can further finetune the B/S ratio, with β-fused naphthyl or α-fused phenanthryl N-linked adducts and O or C-linked adducts containing ring substitution increasing the prevalence of the S adducted DNA conformation. Overall, this work uncovers the significant effect of bulky moiety size and linker type, as well as the lesser impact of aryl group shape, on adducted DNA structure, which suggests differential replication and repair outcomes, and thereby represents an important step toward rationalizing connections between the structure and biological consequences of diverse DNA adducts.
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Affiliation(s)
- Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Janelle Bykowski
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Trinity K Deak
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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3
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Khoshbin Z, Zamanian J, Davoodian N, Mohammad Danesh N, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. A simple and ultrasensitive metal-organic framework-based aptasensor for fluorescence detection of ethanolamine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120488. [PMID: 34739893 DOI: 10.1016/j.saa.2021.120488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
In this research, a facile fluorescence aptasensor was designed for the ultrasensitive determination of ethanolamine (ETA) as an aliphatic amino alcohol molecule with harmful side effects for human health. Zeolitic imidazolate framework-8 (ZIF-8) as an efficient metal-organic framework was applied to quench the fluorescence emission of the FAM-labeled ETA aptamer. The presence of ETA could recover the fluorescence response under the optimal experimental conditions. ETA could be sensitively detected by the designed aptasensor in the linear concentration range of 0.1 nM-20 µM with the detection limit of 14.38 pM. The designed aptasensor was utilized to determine ETA in milk and serum samples with the detection limits of 17.86 and 15.21 pM, respectively. The aptasensor with the remarkable features of high sensitivity, simplicity and feasibility holds the supreme potential to construct a low-cost portable sensing method for food safety control, human diagnostics, and environmental monitoring with coupling to the microfluidic paper-based devices.
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Affiliation(s)
- Zahra Khoshbin
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Javad Zamanian
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negin Davoodian
- Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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4
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Kung RW, Takyi NA, Wetmore SD. Effects of a Second Local DNA Damage Event on the Toxicity of the Human Carcinogen 4-Aminobiphenyl: A Molecular Dynamics Study of a Damaged DNA Structure. Chem Res Toxicol 2022; 35:499-511. [PMID: 35147430 DOI: 10.1021/acs.chemrestox.1c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exposure of humans to carcinogenic aromatic amines (AAs) occurs daily. AAs are bioactivated in cells into products that attack DNA, primarily leading to N-linked C8-dG adducts. Previous work on DNA containing a single AA-derived adduct (monoadducted DNA) has shown a structure-function relationship between the damaged DNA conformation and cellular outcomes. However, relatively little is known about the conformation and biological outcomes of DNA containing two bulky adducts (diadducted DNA) in close proximity. To fill this current void in the literature, the present work uses quintuplet 0.5 μs MD simulations to understand the structural impact of DNA exposure to the potent bladder carcinogen 4-aminobiphenyl (ABP), which is found in cigarette smoke and select dyes, and results in the widely studied N-linked ABPdG adduct. Specifically, 18 unique DNA duplexes were investigated that contain one or two ABPdG adducts in the anti and/or syn glycosidic orientation(s) in all combinations of three G positions in the NarI mutation hotspot for AAs (5'-G1G2CG3CC). Monoadducted DNA displays sequence-dependent conformational heterogeneity, with the G1 site having the greatest anti preference, and highlights the range of helical structures associated with the syn lesion orientation [i.e., stacked (S), intercalated (I), and wedge (W) conformations]. Diadducted DNA results in interesting lesion separation effects on the conformational heterogeneity, including a greater anti preference for neighboring adducts (G1G2) and a greater syn preference for next-nearest neighbor damaged sites (G2G3) compared to monoadducted DNA. As a result, an increase in the number of ABPdG adducts changes the conformational heterogeneity of ABP-exposed DNA depending on the relative positions of the lesions and thereby could result in increased or decreased toxicity upon human exposure to elevated levels of ABP.
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Affiliation(s)
- Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Kung RW, Deak TK, Griffith-Salik CA, Takyi NA, Wetmore SD. Impact of DNA Adduct Size, Number, and Relative Position on the Toxicity of Aromatic Amines: A Molecular Dynamics Case Study of ANdG- and APdG-Containing DNA Duplexes. J Chem Inf Model 2021; 61:2313-2327. [PMID: 33977716 DOI: 10.1021/acs.jcim.1c00202] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human exposure to aromatic amines (AAs) can result in carcinogenic DNA adducts. To complement previous work geared toward understanding the mutagenicity of AA-derived adducts, which has almost exclusively studied (monoadducted) DNA containing a single lesion, the present work provides the first in-depth comparison of the structure of monoadducted and diadducted DNA duplexes. Specifically, molecular dynamics (MD) simulations were initially performed on DNA containing the nonmutagenic single-ringed N-(deoxyguanosin-8-yl)-aniline (ANdG) or the mutagenic four-ringed N-(deoxyguanosin-8-yl)-1-aminopyrene (APdG) lesion at G1, G2, or G3 in the AA deletion hotspot (5'-G1G2CG3CC) in the anti or syn glycosidic orientation (B/S duplex conformation). Subsequently, diadducted strands were assessed that span each combination of damaged sites (G1G2 (nearest neighbors), G2G3 (next-nearest neighbors), and G1G3 (two intervening nucleotides)) and anti/syn lesion glycosidic orientations. Despite other N-linked C8-dG adducts exhibiting sequence dependence conformational heterogeneity, a single ANdG or APdG lesion induces helical conformational homogeneity that is exclusively controlled by aryl moiety size. However, the preferred damaged DNA conformation can change upon the addition of a second adduct depending on lesion separation, with neighboring lesions stabilizing a nonmutagenic conformation and next-nearest damaged sites stabilizing a promutagenic conformation regardless of adduct size. As a result, diadducted DNA is found to adopt conformations that are unfavored for the corresponding monoadducted system, pointing to differential replication and repair outcomes for diadducted DNA compared to those for monoadducted DNA. Thus, although the toxicity of monoadducted DNA is most significantly dictated by lesion size, the toxicity can increase or decrease upon a second damaging event depending on lesion size and relative position. Overall, our work adds the number of lesions and their spatial separation to the growing list of factors that determine the structure and biological outcomes of adducted DNA.
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Affiliation(s)
- Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Trinity K Deak
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Cassidy A Griffith-Salik
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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Cai A, Wilson KA, Patnaik S, Wetmore SD, Cho BP. DNA base sequence effects on bulky lesion-induced conformational heterogeneity during DNA replication. Nucleic Acids Res 2019; 46:6356-6370. [PMID: 29800374 PMCID: PMC6158707 DOI: 10.1093/nar/gky409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/03/2018] [Indexed: 12/11/2022] Open
Abstract
4-Aminobiphenyl (ABP) and its structure analog 2-aminofluorene (AF) are well-known carcinogens. In the present work, an unusual sequence effect in the 5′-CTTCTG1G2TCCTCATTC-3′ DNA duplex is reported for ABP- and AF-modified G. Specifically, the ABP modification at G1 resulted in a mixture of 67% major groove B-type (B) and 33% stacked (S) conformers, while at the ABP modification at G2 exclusively resulted in the B-conformer. The AF modification at G1 and G2 lead to 25%:75% and 83%:17% B:S population ratios, respectively. These differences in preferred conformation are due to an interplay between stabilizing (hydrogen bonding and stacking that is enhanced by lesion planarity) and destabilizing (solvent exposure) forces at the lesion site. Furthermore, while the B-conformer is a thermodynamic stabilizer and the S-conformer is a destabilizer in duplex settings, the situation is reversed at the single strands/double strands (ss/ds) junction. Specifically, the twisted biphenyl is a better stacker at the ss/ds junction than the coplanar AF. Therefore, the ABP modification leads to a stronger strand binding affinity of the ss/ds junction than the AF modification. Overall, the current work provides conformational insights into the role of sequence and lesion effects in modulating DNA replication.
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Affiliation(s)
- Ang Cai
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Satyakam Patnaik
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Bongsup P Cho
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
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7
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Cai A, Bian K, Chen F, Tang Q, Carley R, Li D, Cho BP. Probing the Effect of Bulky Lesion-Induced Replication Fork Conformational Heterogeneity Using 4-Aminobiphenyl-Modified DNA. Molecules 2019; 24:molecules24081566. [PMID: 31009995 PMCID: PMC6514942 DOI: 10.3390/molecules24081566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/14/2019] [Accepted: 04/17/2019] [Indexed: 11/16/2022] Open
Abstract
Bulky organic carcinogens are activated in vivo and subsequently react with nucleobases of cellular DNA to produce adducts. Some of these DNA adducts exist in multiple conformations that are slowly interconverted to one another. Different conformations have been implicated in different mutagenic and repair outcomes. However, studies on the conformation-specific inhibition of replication, which is more relevant to cell survival, are scarce, presumably due to the structural dynamics of DNA lesions at the replication fork. It is difficult to capture the exact nature of replication inhibition by existing end-point assays, which usually detect either the ensemble of consequences of all the conformers or the culmination of all cellular behaviors, such as mutagenicity or survival rate. We previously reported very unusual sequence-dependent conformational heterogeneities involving FABP-modified DNA under different sequence contexts (TG1*G2T [67%B:33%S] and TG1G2*T [100%B], G*, N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl) (Cai et al. Nucleic Acids Research, 46, 6356–6370 (2018)). In the present study, we attempted to correlate the in vitro inhibition of polymerase activity to different conformations from a single FABP-modified DNA lesion. We utilized a combination of surface plasmon resonance (SPR) and HPLC-based steady-state kinetics to reveal the differences in terms of binding affinity and inhibition with polymerase between these two conformers (67%B:33%S and 100%B).
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Affiliation(s)
- Ang Cai
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Rachel Carley
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Bongsup P Cho
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
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8
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Nandhini T, Vaidyanathan V, Nair B. Effect of conformation of the arylamine-DNA adduct on the sensitivity of [Ru(phen)2(dppz)]2+ complex. INORG CHEM COMMUN 2016. [DOI: 10.1016/j.inoche.2016.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Aptamer-based biosensor for label-free detection of ethanolamine by electrochemical impedance spectroscopy. Anal Chim Acta 2016; 936:222-8. [PMID: 27566359 DOI: 10.1016/j.aca.2016.06.056] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/22/2022]
Abstract
A label-free sensing assay for ethanolamine (EA) detection based on G-quadruplex-EA binding interaction is presented by using G-rich aptamer DNA (Ap-DNA) and electrochemical impedance spectroscopy (EIS). The presence of K(+) induces the Ap-DNA to form a K(+)-stabilized G-quadruplex structure which provides binding sites for EA. The sensing mechanism was further confirmed by circular dichroism (CD) spectroscopy and EIS measurement. As a result, the charge transfer resistance (RCT) is strongly increased as demonstrated by using the ferro/ferricyanide ([Fe(CN)6](3-/4-)) as a redox probe. Under the optimized conditions, a linear relationship between ΔRCT and EA concentration was obtained over the range of 0.16 nM and 16 nM EA, with a detection limit of 0.08 nM. Interference by other selected chemicals with similar structure was negligible. Analytical results of EA spiked into tap water and serum by the sensor suggested the assay could be successfully applied to real sample analysis. With the advantages of high sensitivity, selectivity and simple sensor construction, this method is potentially suitable for the on-site monitoring of EA contamination.
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Kathuria P, Sharma P, Wetmore SD. Effect of base sequence context on the conformational heterogeneity of aristolactam-I adducted DNA: structural and energetic insights into sequence-dependent repair and mutagenicity. Toxicol Res (Camb) 2016; 5:197-209. [PMID: 30090337 PMCID: PMC6061885 DOI: 10.1039/c5tx00302d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Aristolochic acids (AAs) are nephrotoxic and potentially carcinogenic plant mutagens that form bulky DNA adducts at the exocyclic amino groups of the purines. The present work utilizes classical molecular dynamics simulations and free energy calculations to investigate the role of lesion site sequence context in dictating the conformational outcomes of DNA containing ALI-N6-dA, the most persistent and mutagenic adduct arising from the AAs. Our calculations reveal that the anti base-displaced intercalated conformer is the lowest energy conformer of damaged DNA in all sequence contexts considered (CXC, CXG, GXC and GXG). However, the experimentally-observed greater mutagenicity of the adduct in the CXG sequence context does not correlate with the relative thermodynamic stability of the adduct in different sequences. Instead, AL-N6-dA adducted DNA is least distorted in the CXG sequence context, which points toward a possible differential repair propensity of the lesion in different sequences. Nevertheless, the structural deviations between adducted DNA with different lesion site sequences are small, and therefore other factors (such as interactions between the adducted DNA and lesion-bypass polymerases during replication) are likely more important for dictating the observed sequence-dependent mutagenicity of ALI-N6-dA.
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Affiliation(s)
- Preetleen Kathuria
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
| | - Purshotam Sharma
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
- Centre for Computational Sciences , Central University of Punjab , Bathinda , Punjab , India 151001
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
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11
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Xu L, Vaidyanathan VG, Cho BP. Real-time surface plasmon resonance study of biomolecular interactions between polymerase and bulky mutagenic DNA lesions. Chem Res Toxicol 2014; 27:1796-807. [PMID: 25195494 PMCID: PMC4203393 DOI: 10.1021/tx500252z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Surface plasmon resonance (SPR) was
used to measure polymerase-binding
interactions of the bulky mutagenic DNA lesions N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl
(FABP) or N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene
(FAAF) in the context of two unique 5′-flanking bases (CG*A and TG*A). The enzymes used
were exo-nuclease-deficient Klenow fragment (Kf-exo–) or polymerase β (pol β). Specific binary and ternary
DNA binding affinities of the enzymes were characterized at subnanomolar
concentrations. The SPR results showed that Kf-exo– binds strongly to a double strand/single strand template/primer
junction, whereas pol β binds preferentially to double-stranded
DNA having a one-nucleotide gap. Both enzymes exhibited tight binding
to native DNA, with high nucleotide selectivity, where the KD values for each base pair increased in the
order dCTP ≪ dTTP ∼ dATP ≪ dGTP. In contrast
to that for pol β, Kf-exo– binds tightly to
lesion-modified templates; however, both polymerases exhibited minimal
nucleotide selectivity toward adducted DNA. Primer steady-state kinetics
and 19F NMR results support the SPR data. The relative
insertion efficiency fins of dCTP opposite
FABP was significantly higher in the TG*A sequence
compared to that in CG*A. Although Kf-exo– was not sensitive to the presence of a DNA lesion,
FAAF-induced conformational heterogeneity perturbed the active site
of pol β, weakening the enzyme’s ability to bind to FAAF
adducts compared to FABP adducts. The present study demonstrates the
effectiveness of SPR for elucidating how lesion-induced conformational
heterogeneity affects the binding capability of polymerases and ultimately
the nucleotide insertion efficiency.
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Affiliation(s)
- Lifang Xu
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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12
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Frequencies of mutagenic translesion DNA synthesis over cisplatin-guanine intra-strand crosslinks in lacZ plasmids propagated in human cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 770:23-8. [DOI: 10.1016/j.mrgentox.2014.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022]
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13
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Jain V, Vaidyanathan VG, Patnaik S, Gopal S, Cho BP. Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: 19F NMR, surface plasmon resonance, and primer kinetic studies. Biochemistry 2014; 53:4059-71. [PMID: 24915610 PMCID: PMC4075988 DOI: 10.1021/bi5003212] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Adduct-induced DNA damage can affect
transcription efficiency and
DNA replication and repair. We previously investigated the effects
of the 3′-next flanking base (G*CT vs G*CA; G*, FABP, N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl;
FAF, N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene)
on the conformation of arylamine-DNA lesions in relation to E. coli nucleotide excision repair (JainV., HiltonB., LinB., PatnaikS., LiangF., DarianE., ZouY., MackerellA. D.Jr., and ChoB. P. (2013) , 41, 869−88023180767). Here,
we report the differential effects of the same pair of sequences on
DNA replication in vitro by the polymerases exofree
Klenow fragment (Kf-exo–) and Dpo4. We obtained
dynamic 19F NMR spectra for two 19-mer modified templates
during primer elongation: G*CA [d(5′-CTTACCATCG*CAACCATTC-3′)]
and G*CT [d(5′-CTTACCATCG*CTACCATTC-3′)].
We found that lesion stacking is favored in the G*CT sequence compared to the G*CA counterpart. Surface
plasmon resonance binding results showed consistently weaker affinities
for the modified DNA with the binding strength in the order of FABP
> FAF and G*CA > G*CT. Primer extension was stalled at
(n) and near (n – 1 and n + 1) the lesion site, and the extent of blockage and the extension
rates across the lesion were influenced by not only the DNA sequences
but also the nature of the adduct’s chemical structure (FAF
vs FABP) and the polymerase employed (Kf-exo– vs
Dpo4). Steady-state kinetics analysis with Kf-exo– revealed the most dramatic sequence and lesion effects at the lesion
(n) and postinsertion (n + 1) sites,
respectively. Taken together, these results provide insights into
the important role of lesion-induced conformational heterogeneity
in modulating translesion DNA synthesis.
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Affiliation(s)
- Vipin Jain
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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14
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Vrtis KB, Markiewicz RP, Romano LJ, Rueda D. Carcinogenic adducts induce distinct DNA polymerase binding orientations. Nucleic Acids Res 2013; 41:7843-53. [PMID: 23814187 PMCID: PMC3763543 DOI: 10.1093/nar/gkt554] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/15/2013] [Accepted: 05/24/2013] [Indexed: 12/18/2022] Open
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.
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Affiliation(s)
- Kyle B. Vrtis
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
| | - Radoslaw P. Markiewicz
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
| | - Louis J. Romano
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
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15
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Vaidyanathan VG, Liang F, Beard WA, Shock DD, Wilson SH, Cho BP. Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site. J Biol Chem 2013; 288:23573-85. [PMID: 23798703 DOI: 10.1074/jbc.m113.476150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo(-)) and DNA polymerase β (pol β) using (19)F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2'-deoxycytosine-5'-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with (19)F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential.
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Affiliation(s)
- Vaidyanathan G Vaidyanathan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, USA
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16
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Belov OV, Chuluunbaatar O, Kapralov MI, Sweilam NH. The role of the bacterial mismatch repair system in SOS-induced mutagenesis: a theoretical background. J Theor Biol 2013; 332:30-41. [PMID: 23643530 DOI: 10.1016/j.jtbi.2013.04.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 04/20/2013] [Accepted: 04/22/2013] [Indexed: 10/26/2022]
Abstract
A theoretical study is performed of the possible role of the methyl-directed mismatch repair system in the ultraviolet-induced mutagenesis of Escherichia coli bacterial cells. For this purpose, mathematical models of the SOS network, translesion synthesis and mismatch repair are developed. Within the proposed models, the key pathways of these repair systems were simulated on the basis of modern experimental data related to their mechanisms. Our model approach shows a possible mechanistic explanation of the hypothesis that the bacterial mismatch repair system is responsible for attenuation of mutation frequency during ultraviolet-induced SOS response via removal of the nucleotides misincorporated by DNA polymerase V (the UmuD'2C complex).
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Affiliation(s)
- Oleg V Belov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, 6 Joliot-Curie Street, 141980 Dubna, Moscow Region, Russia.
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17
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Liang G, Li T, Li X, Liu X. Electrochemical detection of the amino-substituted naphthalene compounds based on intercalative interaction with hairpin DNA by electrochemical impedance spectroscopy. Biosens Bioelectron 2013; 48:238-43. [PMID: 23693094 DOI: 10.1016/j.bios.2013.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/27/2013] [Accepted: 04/03/2013] [Indexed: 02/01/2023]
Abstract
The amino-substituted naphthalene compounds, such as 1,8-diaminonaphthalene (1,8-DANAP), 2,3-diaminonaphthalene (2,3-DANAP), 1,5-diaminonaphthalene (1,5-DANAP), 1-naphthylamine (1-NAP) and 2-naphthylamine (2-NAP), were investigated by electrochemical impedance spectroscopy (EIS), which was based on the interaction with hairpin DNA immobilized on the gold electrodes. Upon hairpin DNA interacting with the target chemicals, the charge transfer resistance (RCT) of the hairpin DNA films was significantly decreased and the charge transfer resistance change (ΔR(CT)) decreased in a sequence of ΔR(CT) (1,8-DANAP)>ΔR(CT) (2,3-DANAP)>ΔR(CT) (1,5-DANAP)>ΔR(CT) (1-NAP)>ΔR(CT) (2-NAP). The ΔR(CT) changes were due to the difference in the binding constant (K(SV)) of the target chemicals to DNA. In addition, the interaction mechanism was further explored using 1,8-DANAP as a model analyte by fluorescence spectra, Raman spectroscopy, differential pulse voltammetry (DPV) and EIS, correspondingly. The results demonstrated that the amino-substituted naphthalene compounds intercalated into "stem" appearing in the hairpin DNA. Moreover, the hairpin DNA sensor exhibited high sensitivity to the amino-substituted naphthalene compounds with the detection limit of nano-mole, and maintained high selectivity over other selected environmental pollutants. Finally, the DNA sensor was challenged in natural water sample with a recovery of 96-102%, which offered a platform for prospective future development of a simple, rapid, sensitive and low-cost assay for the detection of target aromatic amine pollutants.
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Affiliation(s)
- Gang Liang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
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18
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Kawanishi M, Kanno T, Nishida H, Takamura-Enya T, Yagi T. Translesion DNA synthesis across various DNA adducts produced by 3-nitrobenzanthrone in Escherichia coli. Mutat Res 2013; 754:32-8. [PMID: 23583687 DOI: 10.1016/j.mrgentox.2013.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/23/2013] [Accepted: 04/02/2013] [Indexed: 11/19/2022]
Abstract
To analyze translesion DNA synthesis (TLS) across lesions derived from the air pollutant 3-nitrobenzanthrone in Escherichia coli, we constructed site-specifically modified plasmids containing single molecule adducts derived from 3-nitrobenzanthrone. For this experiment, we adopted a modified version of the method developed by Fuchs et al. [29]. Each plasmid contained one of the following lesions in its LacZ' gene: N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG-C8-N-ABA); 2-(2'-deoxyguanosin-N(2)-yl)-3-aminobenzanthrone (dG-N(2)-C2-ABA); 2-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG-C8-C2-ABA); 2-(2'-deoxyadenosin-N(6)-yl)-3-aminobenzanthrone (dA-N(6)-C2-ABA); N-(2'-deoxyguanosin-8-yl)-3-acetylaminobenzanthrone (dG-C8-N-AcABA); or 2-(2'-deoxyguanosin-8-yl)-3-acetylaminobenzanthrone (dG-C8-C2-AcABA). All of the adducts inhibited DNA synthesis by replicative DNA polymerases in E. coli; however, the extent of the inhibition varied among the adducts. All five dG-adducts strongly blocked replication by replicative DNA polymerases; however, the dA-adduct only weakly blocked DNA replication. The induction of the SOS response increased the frequency of TLS, which was higher for the dG-C8-C2-ABA, dG-C8-N-AcABA and dG-C8-C2-AcABA adducts than for the other adducts. In our previous study, dG-C8-N-ABA blocked DNA replication more strongly and induced mutations more frequently than dG-N(2)-C2-ABA in human cells. In contrast, in E. coli the frequency of TLS over dG-N(2)-C2-ABA was markedly reduced, even under the SOS(+) conditions, and dG-N(2)-C2-ABA induced G to T mutations. All of the other adducts were bypassed in a less mutagenic manner. In addition, using E. coli strains that lacked particular DNA polymerases we found that DNA polymerase V was responsible for TLS over dG-C8-N-AcABA and dG-C8-C2-AcABA adducts.
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Affiliation(s)
- Masanobu Kawanishi
- Graduate School of Science and Radiation Research Center, Osaka Prefecture University, 1-2 Gakuen-cho, Sakai, Osaka 599-8570, Japan
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19
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C8-linked bulky guanosine DNA adducts: experimental and computational insights into adduct conformational preferences and resulting mutagenicity. Future Med Chem 2012; 4:1981-2007. [PMID: 23088278 DOI: 10.4155/fmc.12.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bulky DNA adducts are formed through the covalent attachment of aryl groups to the DNA nucleobases. Many of these adducts are known to possess conformational heterogeneity, which is responsible for the variety of mutagenic outcomes associated with these lesions. The present contribution reviews several conformational and mutagenic themes that are prevalent among the DNA adducts formed at the C8-site of the guanine nucleobase. The most important conclusions obtained (to date) from experiments are summarized including the anti/syn conformational preference of the adducts, their potential to inflict DNA mutations and mismatch stabilization, and their interactions with DNA polymerases and repair enzymes. Additionally, the unique role that computer calculations can play in understanding the structural properties of these adducts are highlighted.
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20
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Vaidyanathan VG, Xu L, Cho BP. Binary and ternary binding affinities between exonuclease-deficient Klenow fragment (Kf-exo(-)) and various arylamine DNA lesions characterized by surface plasmon resonance. Chem Res Toxicol 2012; 25:1568-70. [PMID: 22804627 DOI: 10.1021/tx300289d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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)).
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Affiliation(s)
- V G Vaidyanathan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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