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Hellendahl KF, Kaspar F, Zhou X, Yang Z, Huang Z, Neubauer P, Kurreck A. Optimized Biocatalytic Synthesis of 2-Selenopyrimidine Nucleosides by Transglycosylation*. Chembiochem 2021; 22:2002-2009. [PMID: 33594780 PMCID: PMC8251958 DOI: 10.1002/cbic.202100067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/16/2021] [Indexed: 01/09/2023]
Abstract
Selenium-modified nucleosides are powerful tools to study the structure and function of nucleic acids and their protein interactions. The widespread application of 2-selenopyrimidine nucleosides is currently limited by low yields in established synthetic routes. Herein, we describe the optimization of the synthesis of 2-Se-uridine and 2-Se-thymidine derivatives by thermostable nucleoside phosphorylases in transglycosylation reactions using natural uridine or thymidine as sugar donors. Reactions were performed at 60 or 80 °C and at pH 9 under hypoxic conditions to improve the solubility and stability of the 2-Se-nucleobases in aqueous media. To optimize the conversion, the reaction equilibria in analytical transglycosylation reactions were studied. The equilibrium constants of phosphorolysis of the 2-Se-pyrimidines were between 5 and 10, and therefore differ by an order of magnitude from the equilibrium constants of any other known case. Hence, the thermodynamic properties of the target nucleosides are inherently unfavorable, and this complicates their synthesis significantly. A tenfold excess of sugar donor was needed to achieve 40-48 % conversion to the target nucleoside. Scale-up of the optimized conditions provided four Se-containing nucleosides in 6-40 % isolated yield, which compares favorably to established chemical routes.
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Affiliation(s)
- Katja F. Hellendahl
- Technische Universität Berlin Faculty III Process Sciences, Institute of Biotechnology Chair of Bioprocess EngineeringAckerstraße 7613355BerlinGermany
| | - Felix Kaspar
- Technische Universität Berlin Faculty III Process Sciences, Institute of Biotechnology Chair of Bioprocess EngineeringAckerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Xinrui Zhou
- Sichuan University, College of Life Sciences Key Laboratory of Bio-Resource and Eco-Environment Ministry of EducationNo. 17 People's South Road Section 3610041ChengduP. R. China
| | - Zhaoyi Yang
- Sichuan University, College of Life Sciences Key Laboratory of Bio-Resource and Eco-Environment Ministry of EducationNo. 17 People's South Road Section 3610041ChengduP. R. China
| | - Zhen Huang
- Sichuan University, College of Life Sciences Key Laboratory of Bio-Resource and Eco-Environment Ministry of EducationNo. 17 People's South Road Section 3610041ChengduP. R. China
| | - Peter Neubauer
- Technische Universität Berlin Faculty III Process Sciences, Institute of Biotechnology Chair of Bioprocess EngineeringAckerstraße 7613355BerlinGermany
| | - Anke Kurreck
- Technische Universität Berlin Faculty III Process Sciences, Institute of Biotechnology Chair of Bioprocess EngineeringAckerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
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Sun Z, Wang X, Zhang JZH, He Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys Chem Chem Phys 2019; 21:14923-14940. [PMID: 31233058 DOI: 10.1039/c9cp01989h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Base flipping is widely observed in a number of important biological processes. The genetic codes deposited inside the DNA duplex become accessible to external agents upon base flipping. The sulfur substitution of guanine leads to thioguanine, which alters the thermodynamic stability of the GC base pairs and the GT mismatches. Experimental studies conclude that the sulfur substitution decreases the lifetime of the GC base pair. In this work, under three AMBER force fields for nucleotide systems, we firstly performed equilibrium and nonequilibrium free energy simulations to investigate the variation of the thermodynamic profiles in base flipping upon sulfur substitution. It is found that the bsc0 modification, the bsc1 modification and the OL15 modification of AMBER force fields are able to qualitatively describe the sulfur-substitution dependent behavior of the thermodynamics. However, only the two last-generation AMBER force fields are able to provide quantitatively correct predictions. The second computational study on the sulfur substitutions focused on the relative stability of the S6G-C base pair and the S6G-T mismatch. Two conflicting experimental observations were reported by the same authors. One suggested that the S6G-C base pair was more stable, while the other concludes that the S6G-T mismatch was more stable. We answered this question by constructing the free energy profiles along the base flipping pathway computationally.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich 52425, Germany.
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Institute of Computational Science, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China and Department of Chemistry, New York University, NY, NY 10003, USA
| | - Qiaole He
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Wilhelm-Johnen-Str. 1, 52425 Jülich, Germany. and State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
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Maddila S, Lavanya P, Jonnalagadda SB. Cesium loaded on silica as an efficient and recyclable catalyst for the novel synthesis of selenophenes. ARAB J CHEM 2016. [DOI: 10.1016/j.arabjc.2013.09.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Selenium-Functionalized Molecules (SeFMs) as Potential Drugs and Nutritional Supplements. TOPICS IN MEDICINAL CHEMISTRY 2015. [DOI: 10.1007/7355_2015_87] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Hansen DJ, Manuguerra I, Kjelstrup MB, Gothelf KV. Synthesis, Dynamic Combinatorial Chemistry, and PCR Amplification of 3′-5′ and 3′-6′ Disulfide-linked Oligonucleotides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hansen DJ, Manuguerra I, Kjelstrup MB, Gothelf KV. Synthesis, dynamic combinatorial chemistry, and PCR amplification of 3'-5' and 3'-6' disulfide-linked oligonucleotides. Angew Chem Int Ed Engl 2014; 53:14415-8. [PMID: 25413927 DOI: 10.1002/anie.201405761] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/22/2014] [Indexed: 11/11/2022]
Abstract
Disulfide dithymidines linked 3'-5' or 3'-6' were synthesized and incorporated into oligonucleotides through a combined phosphotriester and phosphoramidite solid-phase oligonucleotide synthesis approach. The disulfide links are cleaved and formed reversibly in the presence of thiols and oligonucleotides. This link was shown to be sequence-adaptive in response to given templates in the presence of mercaptoethanol. The artificial 3'-5' and 3'-6' disulfide link was tolerated by polymerases in the polymerase chain reaction (PCR). By using sequencing analysis, we show that single mutations frequently occurred randomly in the amplification products of the PCR.
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Affiliation(s)
- Dennis Jul Hansen
- Danish National Research Foundation: Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C (Denmark) http://www.cdna.dk
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Fernandes AP, Gandin V. Selenium compounds as therapeutic agents in cancer. Biochim Biophys Acta Gen Subj 2014; 1850:1642-60. [PMID: 25459512 DOI: 10.1016/j.bbagen.2014.10.008] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/06/2014] [Accepted: 10/08/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND With cancer cells encompassing consistently higher production of reactive oxygen species (ROS) and with an induced antioxidant defense to counteract the increased basal ROS production, tumors have a limited reserve capacity resulting in an increased vulnerability of some cancer cells to ROS. Based on this, oxidative stress has been recognized as a tumor-specific target for the rational design of new anticancer agents. Among redox modulating compounds, selenium compounds have gained substantial attention due to their promising chemotherapeutic potential. SCOPE OF REVIEW This review aims in summarizing and providing the recent developments of our understanding of the molecular mechanisms that underlie the potential anticancer effects of selenium compounds. MAJOR CONCLUSIONS It is well established that selenium at higher doses readily can turn into a prooxidant and thereby exert its potential anticancer properties. However, the biological activity of selenium compounds and the mechanism behind these effects are highly dependent on its speciation and the specific metabolic pathways of cells and tissues. Conversely, the chemical properties and the main molecular mechanisms of the most relevant inorganic and organic selenium compounds as well as selenium-based nanoparticles must be taken into account and are discussed herein. GENERAL SIGNIFICANCE Elucidating and deepening our mechanistic knowledge of selenium compounds will help in designing and optimizing compounds with more specific antitumor properties for possible future application of selenium compounds in the treatment of cancer. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Affiliation(s)
- Aristi P Fernandes
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden.
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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Abstract
We have developed a simple method to synthesize 6-seleno-2'-deoxyguanosine (SedG) by selectively replacing the 6-oxygen atom with selenium. This selenium-atom-specific modification (SAM) alters the optical properties of the naturally occurring 2'-deoxyguanosine (dG). Unlike the native dG, the UVabsorption of SedG is significantly influenced by the pH of the aqueous solution. Moreover, SedG is fluorescent at the physiological pH and exhibits pH-dependent fluorescence in aqueous solutions. Furthermore, SedG has noticeable fluorescence in non-aqueous solutions, indicating its sensitivity to environmental changes. This is the first time a fluorescent nucleoside by single-atom alteration has been observed. Fluorescent nucleosides modified by a single atom have great potential as molecular probes with minimal perturbations to investigate nucleoside interactions with proteins, such as membrane-transporter proteins.
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Affiliation(s)
- Kaur Manindar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Huang Zhen
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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Faustino I, Curutchet C, Luque FJ, Orozco M. The DNA-forming properties of 6-selenoguanine. Phys Chem Chem Phys 2013; 16:1101-10. [PMID: 24287926 DOI: 10.1039/c3cp53885k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We present here an exhaustive characterization of the structure and properties of 6-selenoguanine, an isoster of guanine, and the impact of its introduction in DNA. This study reports the results of state-of-the-art quantum mechanical calculations and atomistic molecular dynamics simulations carried out to shed light on the impact of the replacement of guanine (G) by 6-selenoguanine (SeG) in different forms of DNA. The results point out that the G → SeG substitution leads to stable DNA duplex, antiparallel triplex and G-quadruplex structures, though local distortions are also found. These structural changes affect the thermodynamic stability of the mutation leading to a clear destabilization for all studied systems. Interestingly, the lowest effect has been found when the mutation was placed in the triplex-forming oligonucleotide strand in a reverse Hoogsteen orientation, which favours the antiparallel triplex formation regarding the G-tetraplex formation. Detailed QM studies strongly suggest that SeG impacts the HOMO-LUMO gap and accordingly the transfer properties of DNA, opening the way to modulate the conductivity properties of non-natural DNAs.
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Affiliation(s)
- Ignacio Faustino
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain
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Caton-Williams J, Hoxhaj R, Fiaz B, Huang Z. Use of a novel 5'-regioselective phosphitylating reagent for one-pot synthesis of nucleoside 5'-triphosphates from unprotected nucleosides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 1:1.30.1-1.30.21. [PMID: 23512692 PMCID: PMC3655200 DOI: 10.1002/0471142700.nc0130s52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
5'-Triphosphates are building blocks for enzymatic synthesis of DNA and RNA. This unit presents a protocol for convenient synthesis of 2'-deoxyribo- and ribonucleoside 5'-triphosphates (dNTPs and NTPs) from any natural or modified base. This one-pot synthesis can also be employed to prepare triphosphate analogs with a sulfur or selenium atom in place of a non-bridging oxygen atom of the α-phosphate. These S- or Se-modified dNTPs and NTPs can be used to prepare diastereomerically pure phosphorothioate or phosphoroselenoate nucleic acids. Even without extensive purification, the dNTPs or NTPs synthesized by this method are of high quality and can be used directly in DNA polymerization or RNA transcription. Synthesis and purification of the 5'-triphosphates, as well as analysis and confirmation of natural and sulfur- or selenium-modified nucleic acids, are described in this protocol unit.
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Lin L, Sheng J, Huang Z. Nucleic acid X-ray crystallography via direct selenium derivatization. Chem Soc Rev 2011; 40:4591-602. [PMID: 21666919 DOI: 10.1039/c1cs15020k] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
X-ray crystallography has proven to be an essential tool for structural studies of bio-macromolecules at the atomic level. There are two major bottle-neck problems in the macromolecular crystal structure determination: phasing and crystallization. Although the selenium derivatization is routinely used for solving novel protein structures through the MAD phasing technique, the phase problem is still a critical issue in nucleic acid crystallography. The background and current progress of using direct selenium-derivatization of nucleic acids (SeNA) to solve the phase problem and to facilitate nucleic acid crystallization for X-ray crystallography are summarized in this tutorial review.
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Affiliation(s)
- Lina Lin
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
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Sheng J, Huang Z. Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies. Chem Biodivers 2010; 7:753-85. [PMID: 20397215 DOI: 10.1002/cbdv.200900200] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is estimated that over two thirds of all new crystal structures of proteins are determined via the protein selenium derivatization (selenomethionine (Se-Met) strategy). This selenium derivatization strategy via MAD (multi-wavelength anomalous dispersion) phasing has revolutionized protein X-ray crystallography. Through our pioneer research, similarly, Se has also been successfully incorporated into nucleic acids to facilitate the X-ray crystal-structure and function studies of nucleic acids. Currently, Se has been stably introduced into nucleic acids by replacing nucleotide O-atom at the positions 2', 4', 5', and in nucleobases and non-bridging phosphates. The Se derivatization of nucleic acids can be achieved through solid-phase chemical synthesis and enzymatic methods, and the Se-derivatized nucleic acids (SeNA) can be easily purified by HPLC, FPLC, and gel electrophoresis to obtain high purity. It has also been demonstrated that the Se derivatization of nucleic acids facilitates the phase determination via MAD phasing without significant perturbation. A growing number of structures of DNAs, RNAs, and protein-nucleic acid complexes have been determined by the Se derivatization and MAD phasing. Furthermore, it was observed that the Se derivatization can facilitate crystallization, especially when it is introduced to the 2'-position. In addition, this novel derivatization strategy has many advantages over the conventional halogen derivatization, such as more choices of the modification sites via the atom-specific substitution of the nucleotide O-atom, better stability under X-ray radiation, and structure isomorphism. Therefore, our Se-derivatization strategy has great potentials to provide rational solutions for both phase determination and high-quality crystal growth in nucleic-acid crystallography. Moreover, the Se derivatization generates the nucleic acids with many new properties and creates a new paradigm of nucleic acids. This review summarizes the recent developments of the atomic site-specific Se derivatization of nucleic acids for structure determination and function study. Several applications of this Se-derivatization strategy in nucleic acid and protein research are also described in this review.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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Egli M, Pallan PS. The many twists and turns of DNA: template, telomere, tool, and target. Curr Opin Struct Biol 2010; 20:262-75. [PMID: 20381338 DOI: 10.1016/j.sbi.2010.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 03/15/2010] [Indexed: 11/16/2022]
Abstract
If any proof were needed of DNA's versatile roles and use, it is certainly provided by the numerous depositions of new three-dimensional (3D) structures to the coordinate databanks (PDB, NDB) over the last two years. Quadruplex motifs involving G-repeats, adducted sequences and oligo-2'-deoxynucleotides (ODNs) with bound ligands are particularly well represented. In addition, structures of chemically modified DNAs (CNAs) and artificial analogs are yielding insight into stability, pairing properties, and dynamics, including those of the native nucleic acids. Besides being of significance for establishing diagnostic tools and in the analysis of protein-DNA interactions, chemical modification in conjunction with investigations of the structural consequences may yield novel nucleic acid-based therapeutics. DNA's predictable and highly specific pairing behavior makes it the material of choice for constructing 3D-nanostructures of defined architecture. Recently the first examples of DNA nanoparticle and self-assembled 3D-crystals were reported. Although the structures discussed in this review are all based either on X-ray crystallography or solution NMR, small angle X-ray scattering (SAXS), and cryoEM are proving to be useful approaches for the characterization of nanoscale DNA architecture.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA.
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Maza S, López Ó, Martos S, Maya I, Fernández-Bolaños JG. Synthesis of the First Selenium-Containing Acyclic Nucleosides and Anomeric Spironucleosides from Carbohydrate Precursors. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900793] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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