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Eyberg J, Ringenberg M, Richert C. Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles. Chemistry 2023; 29:e202203289. [PMID: 36395348 PMCID: PMC10107337 DOI: 10.1002/chem.202203289] [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: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.
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Affiliation(s)
- Juri Eyberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Mark Ringenberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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2
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Pajoudoro DN, Djacktayang I, Toze FAA, Lissouck D, Mama DB. Investigation of the influence of Z/E configuration on the antioxidant and antiradical activities of lapachol and its derivatives: DFT assessment. Struct Chem 2022. [DOI: 10.1007/s11224-022-02061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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3
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Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD. Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J Am Chem Soc 2022; 144:8054-8065. [PMID: 35499923 PMCID: PMC9097547 DOI: 10.1021/jacs.2c00193] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
N6-(2-Deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido pyrimidine (Fapy•dG) is a prevalent form of genomic DNA damage. Fapy•dG is formed in greater amounts under anoxic conditions than the well-studied, chemically related 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodGuo). Fapy•dG is more mutagenic in mammalian cells than 8-oxodGuo. A distinctive property of Fapy•dG is facile epimerization, but prior works with Fapy•dG analogues have precluded determining its effect on chemistry. We present crystallographic characterization of natural Fapy•dG in duplex DNA and as the template base for DNA polymerase β (Pol β). Fapy•dG adopts the β-anomer when base paired with cytosine but exists as a mixture of α- and β-anomers when promutagenically base paired with adenine. Rotation about the bond between the glycosidic nitrogen atom and the pyrimidine ring is also affected by the opposing nucleotide. Sodium cyanoborohydride soaking experiments trap the ring-opened Fapy•dG, demonstrating that ring opening and epimerization occur in the crystalline state. Ring opening and epimerization are facilitated by propitious water molecules that are observed in the structures. Determination of Fapy•dG mutagenicity in wild type and Pol β knockdown HEK 293T cells indicates that Pol β contributes to G → T transversions but also suppresses G → A transitions. Complementary kinetic studies have determined that Fapy•dG promotes mutagenesis by decreasing the catalytic efficiency of dCMP insertion opposite Fapy•dG, thus reducing polymerase fidelity. Kinetic studies have determined that dCMP incorporation opposite the β-anomer is ∼90 times faster than the α-anomer. This research identifies the importance of anomer dynamics, a feature unique to formamidopyrimidines, when considering the incorporation of nucleotides opposite Fapy•dG and potentially the repair of this structurally unusual lesion.
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Affiliation(s)
- Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jan Henric T Bacurio
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
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4
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Kielar C, Xin Y, Xu X, Zhu S, Gorin N, Grundmeier G, Möser C, Smith DM, Keller A. Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability. Molecules 2019; 24:E2577. [PMID: 31315177 PMCID: PMC6680526 DOI: 10.3390/molecules24142577] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023] Open
Abstract
DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Nelli Gorin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Christin Möser
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
- Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476 Potsdam, Germany
| | - David M Smith
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103 Leipzig, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
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5
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Dryden I, Hill B, Wang H, Laughton C. Covariance analysis for temporal data, with applications to DNA modelling. Stat (Int Stat Inst) 2017. [DOI: 10.1002/sta4.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ian Dryden
- School of Mathematical Sciences; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Blake Hill
- Department of Statistics; University of South Carolina; Columbia 29208 SC USA
| | - Hao Wang
- Prime Quantitative Research LLC; East Lansing 48824 MI USA
| | - Charles Laughton
- School of Mathematical Sciences; University of Nottingham; University Park Nottingham NG7 2RD UK
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6
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Zobo Mfomo J, Bikele Mama D, Lissouck D, Younang E, N’sikabaka S, Mbouombouo Ndassa I, Mbaze Meva’à L. Thermodynamics-antioxidant activity relationships of some 4-benzylidenamino-4, 5-dihydro-1h-1,2,4-triazol-5-one derivatives: Theoretical evaluation. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2017. [DOI: 10.1080/10942912.2016.1225307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Joseph Zobo Mfomo
- Department of Forestry and Wood Engineering, University of Douala, Advances Teachers Training College for Technical Education, Douala, Cameroon
- Department of Inorganic Chemistry, University of Yaoundé I, Faculty of Science, Yaounde, Cameroon
| | - Désiré Bikele Mama
- Department of Chemistry, University of Douala, Faculty of Science, Douala, Cameroon
| | - Daniel Lissouck
- Department of Physics, Faculty of Science, University of Douala, Douala, Cameroon
| | - Elie Younang
- Department of Inorganic Chemistry, University of Yaoundé I, Faculty of Science, Yaounde, Cameroon
| | - Samuel N’sikabaka
- Département de Chimie-Physique, Université Marien Ngouabi, Brazzaville Congo, Faculté des Sciences et Techniques, Brazzaville, Congo
| | | | - Luc Mbaze Meva’à
- Department of Chemistry, University of Douala, Faculty of Science, Douala, Cameroon
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Jena NR, Mishra PC. Is FapyG Mutagenic?: Evidence from the DFT Study. Chemphyschem 2013; 14:3263-70. [DOI: 10.1002/cphc.201300535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/10/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Nihar Ranjan Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Khamaria, Jabalpur‐482005 (India)
- Current address School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072 (Australia)
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Jena NR, Mishra PC. Formation of ring-opened and rearranged products of guanine: mechanisms and biological significance. Free Radic Biol Med 2012; 53:81-94. [PMID: 22583701 DOI: 10.1016/j.freeradbiomed.2012.04.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 03/30/2012] [Accepted: 04/06/2012] [Indexed: 11/16/2022]
Abstract
DNA damage by endogenous and exogenous agents is a serious concern, as the damaged products can affect genome integrity severely. Damage to DNA may arise from various factors such as DNA base modifications, strand break, inter- and intrastrand crosslinks, and DNA-protein crosslinks. Among these factors, DNA base modification is a common and important form of DNA damage that has been implicated in mutagenesis, carcinogenesis, and many other pathological conditions. Among the four DNA bases, guanine (G) has the smallest oxidation potential, because of which it is frequently modified by reactive species, giving rise to a plethora of lethal lesions. Similarly, 8-oxo-7,8-dihydroguanine (8-oxoG), an oxidatively damaged guanine lesion, also undergoes various degradation reactions giving rise to several mutagenic species. The various products formed from reactions of G or 8-oxoG with different reactive species are mainly 2,6-diamino-4-oxo-5-formamidopyrimidine, 2,5-diamino-4H-imidazolone, 2,2,4-triamino-5-(2H)-oxazolone, 5-guanidino-4-nitroimidazole, guanidinohydantoin, spiroiminodihydantoin, cyanuric acid, parabanic acid, oxaluric acid, and urea, among others. These products are formed from either ring opening or ring opening and subsequent rearrangement. The main aim of this review is to provide a comprehensive overview of various possible reactions and the mechanisms involved, after which these ring-opened and rearranged products of guanine would be formed in DNA. The biological significance of oxidatively damaged products of G is also discussed.
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Affiliation(s)
- N R Jena
- Department of Physics, Indian Institute of Information Technology, Design and Manufacturing, Khamaria, Jabalpur 482005, India.
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Kryston TB, Georgiev AB, Pissis P, Georgakilas AG. Role of oxidative stress and DNA damage in human carcinogenesis. Mutat Res 2011; 711:193-201. [DOI: 10.1016/j.mrfmmm.2010.12.016] [Citation(s) in RCA: 644] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/22/2010] [Accepted: 12/31/2010] [Indexed: 04/08/2023]
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Preston SP, Wood ATA. Bootstrap inference for mean reflection shape and size-and-shape with three-dimensional landmark data. Biometrika 2011. [DOI: 10.1093/biomet/asq065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Khandelwal G, Bhyravabhotla J. A phenomenological model for predicting melting temperatures of DNA sequences. PLoS One 2010; 5:e12433. [PMID: 20865157 PMCID: PMC2928768 DOI: 10.1371/journal.pone.0012433] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 08/02/2010] [Indexed: 11/29/2022] Open
Abstract
We report here a novel method for predicting melting temperatures of DNA sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of DNA. The model presented here attempts to quantify the energetic components stabilizing the structure of DNA such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. The model gives a Pearson product-moment correlation coefficient (r) of approximately 0.98 between experimental and predicted melting temperatures for over 300 sequences of varying lengths ranging from 15-mers to genomic level and at different salt concentrations. The approach is implemented as a web tool (www.scfbio-iitd.res.in/chemgenome/Tm_predictor.jsp) for the prediction of melting temperatures of DNA sequences.
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Affiliation(s)
- Garima Khandelwal
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, India
| | - Jayaram Bhyravabhotla
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, India
- School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
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Lenglet G, David-Cordonnier MH. DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences. J Nucleic Acids 2010; 2010. [PMID: 20725618 PMCID: PMC2915751 DOI: 10.4061/2010/290935] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 05/27/2010] [Accepted: 06/03/2010] [Indexed: 01/06/2023] Open
Abstract
DNA targeting drugs represent a large proportion of the actual anticancer drug pharmacopeia, both in terms of drug brands and prescription volumes. Small DNA-interacting molecules share the ability of certain proteins to change the DNA helix's overall organization and geometrical orientation via tilt, roll, twist, slip, and flip effects. In this ocean of DNA-interacting compounds, most stabilize both DNA strands and very few display helix-destabilizing properties. These types of DNA-destabilizing effect are observed with certain mono- or bis-intercalators and DNA alkylating agents (some of which have been or are being developed as cancer drugs). The formation of locally destabilized DNA portions could interfere with protein/DNA recognition and potentially affect several crucial cellular processes, such as DNA repair, replication, and transcription. The present paper describes the molecular basis of DNA destabilization, the cellular impact on protein recognition, and DNA repair processes and the latter's relationships with antitumour efficacy.
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Affiliation(s)
- Gaëlle Lenglet
- INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Team 4 Molecular and Cellular Targeting for Cancer Treatment, Institute for Research on Cancer of Lille (IRCL), Lille F-59045, France
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Sakkhachornphop S, Jiranusornkul S, Kodchakorn K, Nangola S, Sirisanthana T, Tayapiwatana C. Designed zinc finger protein interacting with the HIV-1 integrase recognition sequence at 2-LTR-circle junctions. Protein Sci 2009; 18:2219-30. [PMID: 19701937 PMCID: PMC2788277 DOI: 10.1002/pro.233] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 08/13/2009] [Indexed: 12/16/2022]
Abstract
Integration of HIV-1 cDNA into the host genome is a crucial step for viral propagation. Two nucleotides, cytosine and adenine (CA), conserved at the 3' end of the viral cDNA genome, are cleaved by the viral integrase (IN) enzyme. As IN plays a crucial role in the early stages of the HIV-1 life cycle, substrate blockage of IN is an attractive strategy for therapeutic interference. In this study, we used the 2-LTR-circle junctions of HIV-1 DNA as a model to design zinc finger protein (ZFP) targeting at the end terminal portion of HIV-1 LTR. A six-contiguous ZFP, namely 2LTRZFP was designed using zinc finger tools. The designed motif was expressed and purified from E. coli to determine its binding properties. Surface plasmon resonance (SPR) was used to determine the binding affinity of 2LTRZFP to its target DNA. The level of dissociation constant (K(d)) was 12.0 nM. The competitive SPR confirmed that 2LTRZFP specifically interacted with its target DNA. The qualitative binding activity was subsequently determined by EMSA and demonstrated the aforementioned correlation. In addition, molecular modeling and binding energy analyses were carried out to provide structural insight into the binding of 2LTRZFP to the specific and nonspecific DNA target. It is suggested that hydrogen-bonding interactions play a key role in the DNA recognition mechanisms of the designed ZFP. Our study suggested an alternative HIV therapeutic strategy using ZFP interference of the HIV integration process.
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Affiliation(s)
- Supachai Sakkhachornphop
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
- Research Institute for Health Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Supat Jiranusornkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering, Department of Biochemistry, Faculty of Medicine, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Sawitree Nangola
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
- Biomedical Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
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14
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Abstract
'Everything that living things do can be understood in terms of the jigglings and wigglings of atoms' as Richard Feynman provocatively stated nearly 50 years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge.
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Affiliation(s)
- Adrian J Mulholland
- School of Chemistry, Centre for Computational Chemistry, University of Bristol, Bristol, UK.
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