1
|
Liu Q, Zhang Q, Zhang Y, Tian F, Long K, Yang Y, Wang W, Peng C, Wang H. A recognition-induced three-dimensional bipedal DNA walker for highly sensitive detection of APE1. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39193784 DOI: 10.1039/d4ay01353k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
In contrast to the unipedal DNA walker, a bipedal DNA walker features a broader walking area and exhibits faster walking kinetics, leading to enhanced amplification efficiency. In this study, we designed a stochastic three-dimensional (3D) bipedal DNA walker, capable of navigating AuNP-based 3D tracks, driven by exonuclease III (Exo III). This detection system enables the linear detection of the non-invasive biomarker apurinic/apyrimidinic endonuclease 1 (APE1) activity across a range of 0 to 120 U per mL, with a detection limit of 0.03 U per mL. The platform not only offers a novel DNA walker for sensitive APE1 detection in cell lysate but also facilitates the precise assessment of NCA's inhibitory effect on APE1. This research holds promise for future screening of other potential APE1 inhibitors.
Collapse
Affiliation(s)
- Qingyi Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Qiongdan Zhang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Yuting Zhang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Fanghong Tian
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Kang Long
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| | - Caiyun Peng
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
- Science & Technology Innovation Center, Hunan University of Chinese Medicine, 410208, Changsha, China
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, 410208, Changsha, China.
| |
Collapse
|
2
|
Bryan C, Le J, Wei X, Yang K. Saccharomyces cerevisiae apurinic/apyrimidinic endonuclease 1 repairs abasic site-mediated DNA-peptide/protein cross-links. DNA Repair (Amst) 2023; 126:103501. [PMID: 37075541 DOI: 10.1016/j.dnarep.2023.103501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023]
Abstract
Saccharomyces cerevisiae apurinic/apyrimidinic (AP) endonuclease 1 (yApn1) is a key player of the base excision repair pathway. This multifunctional enzyme is an AP endonuclease, 3'-5' exonuclease, 3'-phosphodiesterase, and participates in nucleotide incision repair. To the best of our knowledge, the known substrates of yApn1 are small DNA lesions such as AP sites and 3'-phospho-α,β-unsaturated aldehyde (3'-PUA). Here, we wish to report in vitro findings that yApn1 repairs bulky DNA-peptide cross-links (DpCs) and DNA-protein cross-links (DPCs) arising from AP sites and 3'-PUA. We chemically synthesized stable and linkage-defined DpCs and DPCs by oxime ligation and reductive amination, respectively. Our steady-state kinetic data showed that yApn1 repairs a 10-mer peptide-conjugated AP site and 3'-PUA with comparable efficiencies to that of processing the unconjugated lesions. We demonstrated that yApn1 is the predominant enzyme that incises AP-DpC in yeast cell extracts. We also demonstrated that yApn1 incises AP-DPCs in a DPC size-dependent manner, and prior DPC proteolysis by trypsin facilitates the repair. We further found that yApn1 removes 3'-PUA-histone DPCs with moderate efficiencies. Together, our results uncovered a novel role of yApn1 in DPC repair, and support the emerging model that proteolysis is required for efficient DPC repair.
Collapse
Affiliation(s)
- Cameron Bryan
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Jennifer Le
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Xiaoying Wei
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States.
| |
Collapse
|
3
|
Nagatsugi F, Onizuka K. Selective Chemical Modification to the Higher-Order Structures of Nucleic Acids. CHEM REC 2023; 23:e202200194. [PMID: 36111635 DOI: 10.1002/tcr.202200194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Indexed: 11/06/2022]
Abstract
DNA and RNA can adopt a variety of stable higher-order structural motifs, including G-quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher-order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher-order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher-order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher-order structures of nucleic acids is also underway. In this personal account, we focus on the following higher-order structures of nucleic acids, double-stranded DNA containing the abasic site, T-T/U-U mismatch structure, and G-quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.
Collapse
Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| |
Collapse
|
4
|
Onizuka K, Hazemi ME, Sato N, Tsuji GI, Ishikawa S, Ozawa M, Tanno K, Yamada K, Nagatsugi F. Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids. Nucleic Acids Res 2020; 47:6578-6589. [PMID: 31188442 PMCID: PMC6649768 DOI: 10.1093/nar/gkz512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/15/2019] [Accepted: 05/30/2019] [Indexed: 01/02/2023] Open
Abstract
Higher-ordered structure motifs of nucleic acids, such as the G-quadruplex (G-4), mismatched and bulge structures, are significant research targets because these structures are involved in genetic control and diseases. Selective alkylation of these higher-order structures is challenging due to the chemical instability of the alkylating agent and side-reactions with the single- or double-strand DNA and RNA. We now report the reactive OFF-ON type alkylating agents, vinyl-quinazolinone (VQ) precursors with a sulfoxide, thiophenyl or thiomethyl group for the OFF-ON control of the vinyl reactivity. The stable VQ precursors conjugated with aminoacridine, which bind to the G-4 DNA, selectively reacted with a T base on the G-4 DNA in contrast to the single- and double-strand DNA. Additionally, the VQ precursor reacted with the T or U base in the AP-site, G-4 RNA and T-T mismatch structures. These VQ precursors would be a new candidate for the T or U specific alkylation in the higher-ordered structures of nucleic acids.
Collapse
Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Madoka E Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Gen-Ichiro Tsuji
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Shunya Ishikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kousuke Tanno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| |
Collapse
|
5
|
Abe YS, Sasaki S. The adduct formation between the thioguanine-polyamine ligands and DNA with the AP site under UVA irradiated and non-irradiated conditions. Bioorg Med Chem 2019; 27:115160. [PMID: 31706680 DOI: 10.1016/j.bmc.2019.115160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022]
Abstract
The AP sites are representative of DNA damage and known as an intermediate in the base excision repair (BER) pathway which is involved in the repair of damaged nucleobases by reactive oxygen species, UVA irradiation, and DNA alkylating agents. Therefore, it is expected that the inhibition or modulation of the AP site repair pathway may be a new type of anticancer drug. In this study, we investigated the effects of the thioguanine-polyamine ligands (SG-ligands) on the affinity and the reactivity for the AP site under UVA irradiated and non-irradiated conditions. The SG-ligands have a photo-reactivity with the A-F-C sequence where F represents a tetrahydrofuran AP site analogue. Interestingly, the SG-ligands promoted the β-elimination of the AP site followed by the formation of a covalent bond with the β-eliminated fragment without UVA irradiation.
Collapse
Affiliation(s)
- Yukiko S Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| |
Collapse
|
6
|
Caron C, Duong XNT, Guillot R, Bombard S, Granzhan A. Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts. Chemistry 2019; 25:1949-1962. [DOI: 10.1002/chem.201805555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Coralie Caron
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Xuan N. T. Duong
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Régis Guillot
- CNRS UMR8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO)Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| |
Collapse
|
7
|
Saftić D, Ban Ž, Matić J, Tumirv LM, Piantanida I. Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications. Curr Med Chem 2018; 26:5609-5624. [PMID: 29737251 DOI: 10.2174/0929867325666180508090640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/27/2018] [Accepted: 04/10/2018] [Indexed: 11/22/2022]
Abstract
Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder - nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.
Collapse
Affiliation(s)
- Dijana Saftić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Željka Ban
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Josipa Matić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Lidija-Marija Tumirv
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| |
Collapse
|
8
|
Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
Collapse
Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| |
Collapse
|
9
|
Rideout MC, Liet B, Gasparutto D, Berthet N. A high-throughput screen for detection of compound-dependent phosphodiester bond cleavage at abasic sites. Anal Biochem 2016; 513:93-97. [PMID: 27594348 DOI: 10.1016/j.ab.2016.08.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/28/2016] [Accepted: 08/30/2016] [Indexed: 11/20/2022]
Abstract
We have employed a DNA molecular beacon with a real abasic site, namely a 2-deoxyribose, in a fluorescent high-throughput assay to identify artificial nucleases that cleave at abasic sites. We screened a 1280 compound chemical library and identified a compound that functions as an artificial nuclease. We validated a key structure-activity relationship necessary for abasic site cleavage using available analogs of the identified artificial nuclease. We also addressed the activity of the identified compound with dose titrations in the absence and presence of a source of non-specific DNA. Finally, we characterized the phosphodiester backbone cleavage at the abasic site using denaturing gel electrophoresis. This study provides a useful template for researchers seeking to rapidly identify new artificial nucleases.
Collapse
Affiliation(s)
- Marc C Rideout
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France.
| | - Benjamin Liet
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France
| | - Didier Gasparutto
- Institut des Nanosciences & Cryogénie (INAC), SPrAM - UMR 5819 CEA/CNRS/Université Grenoble Alpes, Commissariat à l'Energie Atomique, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Nathalie Berthet
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France.
| |
Collapse
|
10
|
Kotera N, Granzhan A, Teulade-Fichou MP. Comparative study of affinity and selectivity of ligands targeting abasic and mismatch sites in DNA using a fluorescence-melting assay. Biochimie 2016; 128-129:133-7. [PMID: 27523781 DOI: 10.1016/j.biochi.2016.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/08/2016] [Indexed: 11/29/2022]
Abstract
Recently, several families of small-molecule ligands have been developed to selectively target DNA pairing defects, such as abasic sites and mismatched base pairs, with the aim to interfere with the DNA repair and the template function of the DNA. However, the affinity and selectivity (with respect to well-matched DNA) of these ligands has barely been evaluated in a systematic way. Herein, we report a comparative study of binding affinity and selectivity of a representative panel of 16 ligands targeting abasic sites and a T-T mismatch in DNA, using a fluorescence-monitored melting assay. We demonstrate that bisintercalator-type macrocyclic ligands are characterized by moderate affinity but exceptionally high selectivity with respect to well-matched DNA, whereas other reported ligands show either modest selectivity or rather low affinity in identical conditions.
Collapse
Affiliation(s)
- Naoko Kotera
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
| |
Collapse
|
11
|
Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites. Sci Rep 2016; 6:28894. [PMID: 27363485 PMCID: PMC4929455 DOI: 10.1038/srep28894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/08/2016] [Indexed: 01/02/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites are constantly formed in cellular DNA due to instability of the glycosidic bond, particularly at purines and various oxidized, alkylated, or otherwise damaged nucleobases. AP sites are also generated by DNA glycosylases that initiate DNA base excision repair. These lesions represent a significant block to DNA replication and are extremely mutagenic. Some DNA glycosylases possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a β- or β,δ-elimination reaction. Various amines can incise AP sites via a similar mechanism, but this non-enzymatic cleavage typically requires high reagent concentrations. Herein, we describe a new class of small molecules that function at low micromolar concentrations as both β- and β,δ-elimination catalysts at AP sites. Structure-activity relationships have established several characteristics that appear to be necessary for the formation of an iminium ion intermediate that self-catalyzes the elimination at the deoxyribose ring.
Collapse
|