1
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Berdis A. Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery. Front Chem 2022; 10:1051525. [PMID: 36531317 PMCID: PMC9748101 DOI: 10.3389/fchem.2022.1051525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
. DNA is often referred to as the "molecule of life" since it contains the genetic blueprint for all forms of life on this planet. The core building blocks composing DNA are deoxynucleotides. While the deoxyribose sugar and phosphate group are ubiquitous, it is the composition and spatial arrangement of the four natural nucleobases, adenine (A), cytosine (C), guanine (G), and thymine (T), that provide diversity in the coding information present in DNA. The ability of DNA to function as the genetic blueprint has historically been attributed to the formation of proper hydrogen bonding interactions made between complementary nucleobases. However, recent chemical and biochemical studies using nucleobase-modified nucleotides that contain "non-hydrogen bonding" functional groups have challenged many of the dogmatic views for the necessity of hydrogen-bonding interactions for DNA stability and function. Based on years of exciting research, this area has expanded tremendously and is thus too expansive to provide a comprehensive review on the topic. As such, this review article provides an opinion highlighting how nucleobase-modified nucleotides are being applied in diverse biomedical fields, focusing on three exciting areas of research. The first section addresses how these analogs are used as mechanistic probes for DNA polymerase activity and fidelity during replication. This section outlines the synthetic logic and medicinal chemistry approaches used to replace hydrogen-bonding functional groups to examine the contributions of shape/size, nucleobase hydrophobicity, and pi-electron interactions. The second section extends these mechanistic studies to provide insight into how nucleobase-modified nucleosides are used in synthetic biology. One example is through expansion of the genetic code in which changing the composition of DNA makes it possible to site-specifically incorporate unnatural amino acids bearing unique functional groups into enzymes and receptors. The final section describes results of pre-clinical studies using nucleobase-modified nucleosides as potential therapeutic agents against diseases such as cancer.
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Affiliation(s)
- Anthony Berdis
- Department of Chemistry, Cleveland State University, Cleveland, OH, United States
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2
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Miyahara R, Taniguchi Y. Selective Unnatural Base Pairing and Recognition of 2-Hydroxy-2'-deoxyadenosine in DNA Using Pseudo-dC Derivatives. J Am Chem Soc 2022; 144:16150-16156. [PMID: 36001794 DOI: 10.1021/jacs.2c07000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The formation of unnatural base pairs within duplex DNA would facilitate DNA nanotechnology and biotechnology. Iso-2'-deoxyguanosine (iso-dG) forms base pairs with iso-2'-deoxycytidine, and its use as an unnatural base pair was investigated. Iso-dG is one of the tautomers of 2-hydroxy-2'-deoxyadenosine (2-OH-dA), known as an oxidatively damaged nucleobase, and its selective recognition in DNA plays an important role in the diagnosis and pathogenesis of disease. Therefore, we focused on pseudo-dC (ψdC) as a suitable molecule that recognizes 2-OH-dA in DNA. Since 2-OH-dA shows tautomeric structures in DNA, we designed and used ψdC, which also has a tautomeric structure. We successfully synthesized a ψdC phosphoramidite compound for the synthesis of oligonucleotides (ODNs) as well as its triphosphate derivative (ψdCTP). Tm measurements revealed that ODNs including ψdC showed stable base pair formation with ODNs having 2-OH-dA. In contrast, low Tm values were observed for other bases (dG, dA, dC, and T). The results obtained for the single-nucleotide primer extension reaction revealed that ψdCTP was incorporated into the complementary position of 2-OH-dA in template DNA with high selectivity. In addition, the primer elongation reaction was confirmed to proceed in the presence of dNTPs. The present study reports an artificial nucleic acid that selectively and stably forms unnatural base pairs with 2-OH-dA in DNA.
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Affiliation(s)
- Ryo Miyahara
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
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3
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Zhang J, Wang Y, Wang Y, Zhang P, Chen HY, Huang S. Discrimination between Different DNA Lesions by Monitoring Single-Molecule Polymerase Stalling Kinetics during Nanopore Sequencing. NANO LETTERS 2022; 22:5561-5569. [PMID: 35713465 DOI: 10.1021/acs.nanolett.2c01833] [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] [Indexed: 06/15/2023]
Abstract
O6-Carboxymethylguanosine (O6-CMG), O6-methylguanosine (O6-MeG), and abasic site (AP site) are DNA lesions induced by alkylating agents. Identification of these lesions in DNA may aid in understanding their relevance to carcinogenesis and may be used for diagnosis. Nanopore sequencing (NPS) may directly report nucleotide modifications solely from the nanopore readout. However, the conventional NPS strategy still suffers from interferences from neighboring sequences. Instead, by observation of the enzymatic stalling kinetics caused by the O6-CMG, O6-MeG, or AP site, discrimination between different DNA lesions is directly achieved. This strategy is not interfered with by the sequence context around the lesion. The lesion, which retards the movement of the DNA through the pore, efficiently prohibits misreading of the DNA lesion. These results suggest a new strategy in the identification of DNA lesions or DNA modifications. It also provides a high-resolution biophysical tool to investigate enzymatic kinetics caused by DNA lesions and the corresponding enzymes.
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Affiliation(s)
- Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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4
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Aloisi CMN, Sandell ES, Sturla SJ. A Chemical Link between Meat Consumption and Colorectal Cancer Development? Chem Res Toxicol 2021; 34:12-23. [PMID: 33417435 DOI: 10.1021/acs.chemrestox.0c00395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
O6-carboxymethylguanine (O6-CMG) is a mutagenic DNA adduct that forms at increased levels when people eat meat. It has been studied as a potential initiating event in colorectal carcinogenesis. It can arise from alkylation of guanine in DNA by electrophilic degradation products of N-nitroso compounds. There is significant data regarding biochemical and cellular process, including DNA repair and translesion DNA synthesis that control O6-CMG accumulation, persistence, and mutagenicity. Mutation spectra arising from the adduct closely resemble common mutations in colorectal cancer; however, gaps remain in understanding the biochemical processes that regulate how and where the damage persists in the genome. Addressing such questions relies on advances in chemistry such as synthesis approaches and bioanalytical methods. Results of research in this area help advance our understanding of the toxicological relevance of O6-CMG-modified DNA. Further attention should focus on understanding how a combination of genetic and environmental factors control its biological persistence and how this information can be used as a basis of biomoniotoring and prevention efforts to help mitigate colon cancer risk.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Emma S Sandell
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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5
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Abstract
Cellular DNA is constantly chemically altered by exogenous and endogenous agents. As all processes of life depend on the transmission of the genetic information, multiple biological processes exist to ensure genome integrity. Chemically damaged DNA has been linked to cancer and aging, therefore it is of great interest to map DNA damage formation and repair to elucidate the distribution of damage on a genome-wide scale. While the low abundance and inability to enzymatically amplify DNA damage are obstacles to genome-wide sequencing, new developments in the last few years have enabled high-resolution mapping of damaged bases. Recently, a number of DNA damage sequencing library construction strategies coupled to new data analysis pipelines allowed the mapping of specific DNA damage formation and repair at high and single nucleotide resolution. Strikingly, these advancements revealed that the distribution of DNA damage is heavily influenced by chromatin states and the binding of transcription factors. In the last seven years, these novel approaches have revealed new genomic maps of DNA damage distribution in a variety of organisms as generated by diverse chemical and physical DNA insults; oxidative stress, chemotherapeutic drugs, environmental pollutants, and sun exposure. Preferred sequences for damage formation and repair have been elucidated, thus making it possible to identify persistent weak spots in the genome as locations predicted to be vulnerable for mutation. As such, sequencing DNA damage will have an immense impact on our ability to elucidate mechanisms of disease initiation, and to evaluate and predict the efficacy of chemotherapeutic drugs.
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Affiliation(s)
- Cécile Mingard
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
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6
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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7
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Aloisi CMN, Nilforoushan A, Ziegler N, Sturla SJ. Sequence-Specific Quantitation of Mutagenic DNA Damage via Polymerase Amplification with an Artificial Nucleotide. J Am Chem Soc 2020; 142:6962-6969. [PMID: 32196326 PMCID: PMC7192524 DOI: 10.1021/jacs.9b11746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
DNA mutations can result from replication
errors due to different
forms of DNA damage, including low-abundance DNA adducts induced by
reactions with electrophiles. The lack of strategies to measure DNA
adducts within genomic loci, however, limits our understanding of
chemical mutagenesis. The use of artificial nucleotides incorporated
opposite DNA adducts by engineered DNA polymerases offers a potential
basis for site-specific detection of DNA adducts, but the availability
of effective artificial nucleotides that insert opposite DNA adducts
is extremely limited, and furthermore, there has been no report of
a quantitative strategy for determining how much DNA alkylation occurs
in a sequence of interest. In this work, we synthesized an artificial
nucleotide triphosphate that is selectively inserted opposite O6-carboxymethyl-guanine DNA by an engineered
polymerase and is required for DNA synthesis past the adduct. We characterized
the mechanism of this enzymatic process and demonstrated that the
artificial nucleotide is a marker for the presence and location in
the genome of O6-carboxymethyl-guanine.
Finally, we established a mass spectrometric method for quantifying
the incorporated artificial nucleotide and obtained a linear relationship
with the amount of O6-carboxymethyl-guanine
in the target sequence. In this work, we present a strategy to identify,
locate, and quantify a mutagenic DNA adduct, advancing tools for linking
DNA alkylation to mutagenesis and for detecting DNA adducts in genes
as potential diagnostic biomarkers for cancer prevention.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Nathalie Ziegler
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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8
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Wang Y, Patil KM, Yan S, Zhang P, Guo W, Wang Y, Chen H, Gillingham D, Huang S. Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion O
6
‐Carboxymethyl Guanine and Reveals Its Behavior in Replication. Angew Chem Int Ed Engl 2019; 58:8432-8436. [DOI: 10.1002/anie.201902521] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Yu Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Kiran M. Patil
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuanghong Yan
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Panke Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Weiming Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Yuqin Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Hong‐Yuan Chen
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Dennis Gillingham
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuo Huang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
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9
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Abstract
Chemical damage to DNA is a key initiator of adverse biological consequences due to disruption of the faithful reading of the genetic code. For example, O6-alkylguanine ( O6-alkylG) DNA adducts are strongly miscoding during DNA replication when the damaged nucleobase is a template for polymerase-mediated translesion DNA synthesis. Thus, mutations derived from O6-alkylG adducts can have severe adverse effects on protein translation and function and are an early event in the initiation of carcinogenesis. However, the low abundance of these adducts places significant limitations on our ability to relate their presence and biological influences with resultant mutations or disease risk. As a consequence, there is a critical need for novel tools to detect and study the biological role of alkylation adducts. Incorporating DNA bases with altered structures that are derived synthetically is a strategy that has been used widely to interrogate biological processes involving DNA. Such synthetic nucleosides have contributed to our understanding of DNA structure, DNA polymerase (Pol) and repair enzyme function, and to the expansion of the genetic alphabet. This Account describes our efforts toward creating and applying synthetic nucleosides directed at DNA adducts. We synthesized a variety of nucleosides with altered base structures that complement the altered hydrogen bonding capacity and hydrophilicity of O6-alkylG adducts. The heterocyclic perimidinone-derived nucleoside Per was the first of such adduct-directed synthetic nucleosides; it specifically stabilized O6-benzylguanine ( O6-BnG) in a DNA duplex. Structural variants of Per were used to determine hydrogen bonding and base-stacking contributions to DNA duplex stability in templates containing O6-BnG as well as O6-methylguanine ( O6-MeG) adducts. We created synthetic probes able to stabilize damaged over undamaged templates and established how altered hydrogen bonding or base-stacking properties impact DNA duplex stability as a function of adduct structures. This knowledge was then applied to devise a hybridization-based detection strategy involving gold nanoparticles that distinguish damaged from undamaged DNA by colorimetric changes. Furthermore, synthetic nucleosides were used as mechanistic tools to understand chemical determinants such as hydrogen bonding, π-stacking, and size and shape deviations that impact the efficiency and fidelity of DNA adduct bypass by DNA Pols. Finally, we reported the first example of amplifying alkylated DNA, accomplished by combining an engineered polymerase and synthetic triphosphate for which incorporation is templated by a DNA adduct. The presence of the synthetic nucleoside in amplicons could serve as a marker for the presence and location of DNA damage at low levels in DNA strands. Adduct-directed synthetic nucleosides have opened new concepts to interrogate the levels, locations, and biological influences of DNA alkylation.
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Affiliation(s)
- Michael H. Räz
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Claudia M. N. Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Hailey L. Gahlon
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
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10
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Wang Y, Patil KM, Yan S, Zhang P, Guo W, Wang Y, Chen H, Gillingham D, Huang S. Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion O
6
‐Carboxymethyl Guanine and Reveals Its Behavior in Replication. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yu Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Kiran M. Patil
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuanghong Yan
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Panke Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Weiming Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Yuqin Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Hong‐Yuan Chen
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Dennis Gillingham
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuo Huang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
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11
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Aloisi CMN, Sturla SJ, Gahlon HL. A gene-targeted polymerase-mediated strategy to identify O 6-methylguanine damage. Chem Commun (Camb) 2019; 55:3895-3898. [PMID: 30860216 DOI: 10.1039/c9cc00278b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Detecting DNA adducts in cancer genes is important for understanding cancer etiology. This study reports a strategy to identify the mutagenic DNA adduct O6-methylguanine in K-Ras. The strategy involves selective replication past a synthetic primer when placed opposite O6-methylguanine. Future work can apply this approach to other cancer-relevant genes.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
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12
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Kraus A, McKeague M, Seiwert N, Nagel G, Geisen SM, Ziegler N, Trantakis IA, Kaina B, Thomas AD, Sturla SJ, Fahrer J. Immunological and mass spectrometry-based approaches to determine thresholds of the mutagenic DNA adduct O6-methylguanine in vivo. Arch Toxicol 2018; 93:559-572. [DOI: 10.1007/s00204-018-2355-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
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13
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McKeague M, Otto C, Räz MH, Angelov T, Sturla SJ. The Base Pairing Partner Modulates Alkylguanine Alkyltransferase. ACS Chem Biol 2018; 13:2534-2541. [PMID: 30040894 DOI: 10.1021/acschembio.8b00446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
O6-Alkylguanine DNA adducts are repaired by the suicide enzyme alkylguanine alkyltransferase (AGT). AGT facilitates repair by binding DNA in the minor groove, flipping out the damaged base, and transferring the O6-alkyl group to a cysteine residue in the enzyme's active site. Despite there being significant knowledge concerning the mechanism of AGT repair, there is limited insight regarding how altered interactions of the adduct with its complementary base in the DNA duplex influence its recognition and repair. In this study, the relationship of base pairing interactions and repair by human AGT (hAGT) was tested in the frequently mutated codon 12 of the KRAS gene with complementary sequences containing each canonical DNA base. The rate of O6-MeG repair decreased 2-fold when O6-MeG was paired with G, whereas all other canonical bases had no impact on the repair rate. We used a combination of biochemical studies, molecular modeling, and artificial nucleobases to elucidate the mechanism accounting for the 2-fold decrease. Our results suggest that the reduced rate of repair is due to O6-MeG adopting a syn conformation about the glycosidic bond precluding the formation of a repair-active complex. These data provide a novel chemical basis for how direct reversion repair may be impeded through modification of the base pair partner and support the use of artificial nucleobases as tools to probe the biochemistry of damage repair processes.
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Affiliation(s)
- Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Claudia Otto
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Michael H. Räz
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Todor Angelov
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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14
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Kung RW, Sharma P, Wetmore SD. Effect of Size and Shape of Nitrogen-Containing Aromatics on Conformational Preferences of DNA Containing Damaged Guanine. J Chem Inf Model 2018; 58:1415-1425. [PMID: 29923712 DOI: 10.1021/acs.jcim.8b00238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ryan W. Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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15
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Betz K, Nilforoushan A, Wyss LA, Diederichs K, Sturla SJ, Marx A. Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase. Chem Commun (Camb) 2018; 53:12704-12707. [PMID: 29136072 DOI: 10.1039/c7cc07173f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The possibility to sequence cytotoxic O6-alkylG DNA adducts would greatly benefit research. Recently we reported a benzimidazole-derived nucleotide that is selectively incorporated opposite the damaged site by a mutated DNA polymerase. Here we provide the structural basis for this reaction which may spur future developments in DNA damage sequencing.
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Affiliation(s)
- K Betz
- Department of Chemistry & Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany.
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16
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Salam T, Premila Devi S, Duncan Lyngdoh RH. Molecular criteria for mutagenesis by DNA methylation: Some computational elucidations. Mutat Res 2018; 807:10-20. [PMID: 29220701 DOI: 10.1016/j.mrfmmm.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/05/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Alkylating agents and N-nitroso compounds are well-known mutagens and carcinogens which act by alkylating DNA at the nucleobase moieties. Criteria for mutagenicity through DNA alkylation include (a) absence of the Watson-Crick (N1-guanine and N3-thymine) protons, (b) rotation of the alkyl group away from the H-bonding zone, (c) configuration of the alkylated base pair close to the Watson-Crick type. This computational study brings together these three molecular criteria for the first time. Three methylated DNA bases-N7-methylguanine, O6-methylguanine and O4-methylthymine-are studied using computational chemical methods. Watson-Crick proton loss is predicted more feasible for the mutagenic O6-methylguanine and O4-methylthymine than for the non-mutagenic N7-methylguanine in agreement with the observed trend for pKa values. Attainment of a conformer conducive to mutagenesis is more feasible for O6-methylguanine than for O4-methylthymine, though the latter is more mutagenic. These methylated bases yield 9 H-bonded pairs with normal DNA bases. At biological pH, O6-methylguanine and O4-methylthymine would yield stable mutagenic pairs having Watson-Crick type configuration by H-bonded pairing with thymine and guanine respectively, while N7-methylguanine would yield a non-mutagenic pair with cytosine. The three criteria thus well differentiate the non-mutagenic N7-methylguanine from the mutagenic O6-methylguanine and O4-methylthymine in good accord with experimental observations.
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Affiliation(s)
- Tejeshwori Salam
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - S Premila Devi
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R H Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India.
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17
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McKeague M. Aptamers for DNA Damage and Repair. Int J Mol Sci 2017; 18:ijms18102212. [PMID: 29065503 PMCID: PMC5666892 DOI: 10.3390/ijms18102212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
DNA is damaged on a daily basis, which can lead to heritable mutations and the activation of proto-oncogenes. Therefore, DNA damage and repair are critical risk factors in cancer, aging and disease, and are the underlying bases of most frontline cancer therapies. Much of our current understanding of the mechanisms that maintain DNA integrity has been obtained using antibody-based assays. The oligonucleotide equivalents of antibodies, known as aptamers, have emerged as potential molecular recognition rivals. Aptamers possess several ideal properties including chemical stability, in vitro selection and lack of batch-to-batch variability. These properties have motivated the incorporation of aptamers into a wide variety of analytical, diagnostic, research and therapeutic applications. However, their use in DNA repair studies and DNA damage therapies is surprisingly un-tapped. This review presents an overview of the progress in selecting and applying aptamers for DNA damage and repair research.
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Affiliation(s)
- Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland.
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18
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Gowda ASP, Lee M, Spratt TE. N 2
-Substituted 2′-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- A. S. Prakasha Gowda
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla NY 10595 USA
| | - Thomas E. Spratt
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
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19
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Gowda ASP, Lee M, Spratt TE. N 2 -Substituted 2'-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017; 56:2628-2631. [PMID: 28140505 DOI: 10.1002/anie.201611607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Indexed: 11/09/2022]
Abstract
N2 -Alkyl-2'-deoxyguanosine triphosphate (N2 -alkyl-dGTP) derivatives with methyl, butyl, benzyl, or 4-ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N2 -Benzyl-dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N2 -4-ethynylbenzyl-dG with wild-type and pol κ deficient mouse embryonic fibroblasts. CuAAC reaction with 5(6)-FAM-azide demonstrated that only cells containing pol κ were able to incorporate N2 -4-ethynylbenzyl-dG into the nucleus. This is the first instance of a Y-family-polymerase-specific dNTP, and this method could be used to probe the activity of pol κ in vivo.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
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20
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Trantakis IA, Nilforoushan A, Dahlmann HA, Stäuble CK, Sturla SJ. In-Gene Quantification of O(6)-Methylguanine with Elongated Nucleoside Analogues on Gold Nanoprobes. J Am Chem Soc 2016; 138:8497-504. [PMID: 27314828 PMCID: PMC5726487 DOI: 10.1021/jacs.6b03599] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exposure of DNA to chemicals can result in the formation of DNA adducts, a molecular initiating event in genotoxin-induced carcinogenesis. O(6)-Methylguanine (O(6)-MeG) is a highly mutagenic DNA adduct that forms in human genomic DNA upon reaction with methylating agents of dietary, environmental, or endogenous origin. In this work, we report the design and synthesis of novel non-natural nucleoside analogues 1'-β-[1-naphtho[2,3-d]imidazol-2(3H)-one)]-2'-deoxy-d-ribofuranose and 1'-β-[1-naphtho[2,3-d]imidazole]-2'-deoxy-d-ribofuranose and their use for quantifying O(6)-MeG within mutational hotspots of the human KRAS gene. The novel nucleoside analogues were incorporated into oligonucleotides conjugated to gold nanoparticles to comprise a DNA hybridization probe system for detecting O(6)-MeG in a sequence-specific manner on the basis of colorimetric readout of the nanoparticles. The concept described herein is unique in utilizing new nucleoside analogues with elongated hydrophobic surfaces to successfully measure in-gene abundance of O(6)-MeG in mixtures with competing unmodified DNA.
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Affiliation(s)
- Ioannis A. Trantakis
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Heidi A. Dahlmann
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Celine K. Stäuble
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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