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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications. Bioorg Chem 2019; 95:103518. [PMID: 31911308 DOI: 10.1016/j.bioorg.2019.103518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022]
Abstract
Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.
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Affiliation(s)
- Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Piotr Putaj
- FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland.
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2
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Ono A, Atsugi T, Goto M, Saneyoshi H, Tomori T, Seio K, Dairaku T, Kondo J. Crystal structure of a DNA duplex cross-linked by 6-thioguanine–6-thioguanine disulfides: reversible formation and cleavage catalyzed by Cu( ii) ions and glutathione. RSC Adv 2019; 9:22859-22862. [PMID: 35514505 PMCID: PMC9067110 DOI: 10.1039/c9ra03515j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/04/2019] [Indexed: 11/21/2022] Open
Abstract
Herein, we determined the crystal structure of a DNA duplex containing consecutive 6-thioguanine–6-thioguanine disulfides. The disulfide bonds were reversibly formed and cleaved in the presence of Cu(ii) ions and glutathione. To our knowledge, this is the first reaction in which metal ions efficiently accelerated disulfide bond formation between thio-bases in duplexes. The crystal structure of a DNA duplex cross-linked by 6-thioguanine–6-thioguanine disulfides has been solved.![]()
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Affiliation(s)
- Akira Ono
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Takahiro Atsugi
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Misato Goto
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Hisao Saneyoshi
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Takahito Tomori
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Kohji Seio
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | | | - Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Tokyo 102-8554
- Japan
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3
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Liczner C, Grenier V, Wilds CJ. Reversible diselenide cross-links are formed between oligonucleotides containing 2′-deoxy-6-selenoinosine. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.11.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Beuck C, Weinhold E. Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes. Beilstein J Org Chem 2014; 10:2293-306. [PMID: 25298797 PMCID: PMC4187101 DOI: 10.3762/bjoc.10.239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/28/2014] [Indexed: 12/16/2022] Open
Abstract
Covalently interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function. The ideal DNA cross-link to study protein–DNA interactions should be specific and easy to synthesize, be stable during protein binding experiments, have a short covalent linker to avoid steric hindrance of protein binding, and should be available as a mimic for both A/T and G/C base pairs to cover all possible binding specificities. Several covalent interstrand cross-links have been described in the literature, but most of them fall short of at least one of the above criteria. We developed an efficient method to site-specifically and reversibly cross-link thionucleoside base pairs in synthetic duplex oligodeoxynucleotides by bisalkylation with 1,2-diiodoethane resulting in an ethylene-bridged base pair. Both linked A/T and G/C base pair analogs can conveniently be prepared which allows studying any base pair-opening enzyme regardless of its sequence specificity. The cross-link is stable in the absence of reducing agents but the linker can be quickly and tracelessly removed by the addition of thiol reagents like dithiothreitol. This property makes the cross-linking reaction fully reversible and allows for a switching of the linked base pair from locked to unlocked during biochemical experiments. Using the DNA methyltransferase from Thermus aquaticus (M.TaqI) as example, we demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI.
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Affiliation(s)
- Christine Beuck
- Department of Structural & Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 2-5, D-45141 Essen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
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Hatano A, Okada M, Kawai G. Solution structure of S-DNA formed by covalent base pairing involving a disulfide bond. Org Biomol Chem 2013; 10:7327-33. [PMID: 22875009 DOI: 10.1039/c2ob25346a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Here, we present the solution structure of a DNA duplex containing a disulfide base pair (S-DNA). The unnatural nucleoside "S" possessing a thiophenyl group as base was incorporated into a self-complementary singled-stranded oligonucleotide. Crosslinking of the disulfide base pair was analyzed by non-denaturing polyacrylamide gel electrophoresis. Under oxidizing conditions a high molecular weight band as 18 mer, corresponding to the double-stranded molecule (5'-GCGASTCGC: 3'-CGCTSAGCG), was found, whereas single-stranded self-complementary 9 mer oligonucleotide GCGASTCGC was detected in the presence of a reducing agent. These results suggest that the oligonucleotide is covalently linked by disulfide bonding under oxidizing conditions, which can be reversibly reduced to two thiol groups under reducing conditions. CD spectrum of S-DNA (CGASTCG) under oxidizing conditions suggested that the duplex had a right-handed double-stranded structure similar to that of natural DNA (B-form, CGATCG). NMR studies confirmed that this CGASTCG resembled natural B-DNA and that the two phenyl rings derived from the disulfide base pairing intercalated into the duplex. However, these two phenyl rings were not positioned in the same plane as the other base pairs. Specifically, NOEs suggest that although CGASTCG adopts a structure similar to B-type DNA, the S-DNA duplex is bent at the point of disulfide base pairing to face the major groove.
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Affiliation(s)
- Akihiko Hatano
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Saitama, 337-8570, Japan.
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Beddows A, Patel N, Finger LD, Atack JM, Williams DM, Grasby JA. Interstrand disulfide crosslinking of DNA bases supports a double nucleotide unpairing mechanism for flap endonucleases. Chem Commun (Camb) 2012; 48:8895-7. [PMID: 22850542 DOI: 10.1039/c2cc33400c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Flap endonucleases (FENs) are proposed to select their target phosphate diester by unpairing the two terminal nucleotides of duplex. Interstrand disulfide crosslinks, introduced by oxidation of thiouracil and thioguanine bases, abolished the specificity of human FEN1 for hydrolysis one nucleotide into the 5'-duplex.
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Affiliation(s)
- Amanda Beddows
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, S3 7HF, UK
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Seela F, Ding P, Budow S. DNA Gold Nanoparticle Conjugates Incorporating Thiooxonucleosides: 7-Deaza-6-thio-2′-deoxyguanosine as Gold Surface Anchor. Bioconjug Chem 2011; 22:794-807. [DOI: 10.1021/bc200069j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| | - Ping Ding
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| | - Simone Budow
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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Bergstrom DE. Unnatural nucleosides with unusual base pairing properties. ACTA ACUST UNITED AC 2009; Chapter 1:1.4.1-1.4.32. [PMID: 19488968 DOI: 10.1002/0471142700.nc0104s37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.
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Wenska G, Filipiak P, Asmus KD, Bobrowski K, Koput J, Marciniak B. Formation of a Sandwich-Structure Assisted, Relatively Long-Lived Sulfur-Centered Three-Electron Bonded Radical Anion in the Reduction of a Bis(1-substituted-uracilyl) Disulfide in Aqueous Solution. J Phys Chem B 2008; 112:10045-53. [DOI: 10.1021/jp8041928] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Grazyna Wenska
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznan, Poland, and Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland
| | - Piotr Filipiak
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznan, Poland, and Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland
| | - Klaus-Dieter Asmus
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznan, Poland, and Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland
| | - Krzysztof Bobrowski
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznan, Poland, and Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland
| | - Jacek Koput
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznan, Poland, and Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland
| | - Bronislaw Marciniak
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznan, Poland, and Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland
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Hatano A, Makita S, Kirihara M. Synthesis and redox-active base-pairing properties of DNA incorporating mercapto C-nucleosides. Tetrahedron 2005. [DOI: 10.1016/j.tet.2004.12.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Wenska G, Taras-Goślińska K, Skalski B, Hug GL, Carmichael I, Marciniak B. Generation of Thiyl Radicals by the Photolysis of 5-Iodo-4-thiouridine. J Org Chem 2005; 70:982-8. [PMID: 15675858 DOI: 10.1021/jo048496g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photochemistry of 2',3',5'-tri-O-acetyl-5-iodo-4-thiouridine (3) in deoxygenated 1:1 CH(3)CN-H(2)O pH 5.8 (phosphate buffer) solution has been studied by means of steady-state and nanosecond laser flash photolysis methods. Under steady-state irradiation (lambda > or = 334 nm), the stable photoproducts were iodide ion, 2',3',5'-tri-O-acetyl-4-thiouridine (4), and two disulfides. The disulfides were the symmetrical bis-(2',3',5'-tri-O-acetyl-5-iodo-4-thiouridine) (5) and unsymmetrical 6, which contains both 4-thiouridine and 5-iodo-4-thiouridine residues. The formation of the dehalogenated photoproduct suggests that C(5)-I bond cleavage is a primary photochemical step. Attempts to scavenge the resulting C(5)-centered radical by suitable addends, bis-(N-alpha-acetyl)cystine-bis-N-ethylamide or benzene, were unsuccessful. Analysis of the photoproducts formed under these conditions showed that the S-atom is the reactive center. The photoproduct 4, obtained by irradiation of 3 in CD(3)CN-H(2)O, followed by reversed-phase HPLC isolation using nonlabeled eluents, did not contain deuterium. An analogous experiment performed in CH(3)CN-D(2)O gave deuterated product 4-d with 88% of the deuterium incorporated at C(5). Transient absorption observed upon laser excitation (lambda= 308 nm) of 3 was assigned to the 4-uridinylthiyl radical on the basis of the similarity of this spectrum with that obtained upon laser photolysis of the disulfide: bis-(2',3',5'-tri-O-acetyl-4-thiouridine) 14. On the basis of the results of steady-state and laser photolysis studies, a mechanism of the photochemical reaction of 3 is proposed. The key mechanistic step is a transformation of the C(5)-centered radical formed initially by C(5)-I bond cleavage into a long-lived S-centered radical via a 1,3-hydrogen shift. Theoretical calculations confirmed that the long-lived S-centered radical is the most stable radical derived from the 4-thiouracil residue.
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Affiliation(s)
- Grazyna Wenska
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland.
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Hatano A, Makita S, Kirihara M. Synthesis and characterization of a DNA analogue stabilized by mercapto C-nucleoside induced disulfide bonding. Bioorg Med Chem Lett 2004; 14:2459-62. [PMID: 15109632 DOI: 10.1016/j.bmcl.2004.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 03/04/2004] [Accepted: 03/04/2004] [Indexed: 11/27/2022]
Abstract
A redox-active nucleobase analogue of a nucleotide was synthesized and incorporated into DNA using phosphoramidite chemistry. An analogue-containing oligonucleotide in the absence of a reducing reagent formed a stable duplex with a substantially higher melting temperature compared to that of a standard DNA duplex of the same length.
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Affiliation(s)
- Akihiko Hatano
- Department of Materials Science, Shizuoka Institute of Science and Technology, 2200-2 Toyosawa, Fukuroi, Shizuoka 437-8555, Japan.
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Chambert S, Décout JL. RECENT DEVELOPMENTS IN THE SYNTHESIS, CHEMICAL MODIFICATIONS AND BIOLOGICAL APPLICATIONS OF SULFUR MODIFIED NUCLEOSIDES, NUCLEOTIDES AND OLIGONUCLEOTIDES. ORG PREP PROCED INT 2002. [DOI: 10.1080/00304940209355745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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