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Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238379. [PMID: 36500495 PMCID: PMC9737395 DOI: 10.3390/molecules27238379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2'-MeTe, and 2'-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.
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Zhang W, Szostak JW, Huang Z. Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom. Front Chem Sci Eng 2016. [DOI: 10.1007/s11705-016-1565-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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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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Affeldt RF, Braga HC, Baldassari LL, Lüdtke DS. Synthesis of selenium-linked neoglycoconjugates and pseudodisaccharides. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Braga HC, Wouters AD, Zerillo FB, Lüdtke DS. Synthesis of seleno-carbohydrates derived from d-galactose. Carbohydr Res 2010; 345:2328-33. [DOI: 10.1016/j.carres.2010.08.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/26/2010] [Accepted: 08/29/2010] [Indexed: 12/11/2022]
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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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Braga AL, Severo Filho WA, Schwab RS, Rodrigues OE, Dornelles L, Braga HC, Lüdtke DS. Synthesis of selenium- and tellurium-containing nucleosides derived from uridine. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.164] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sheng J, Huang Z. Synthesis of a 4-selenothymidine phosphoramidite and incorporation into oligonucleotides. ACTA ACUST UNITED AC 2008; Chapter 1:Unit 1.19. [PMID: 18428801 DOI: 10.1002/0471142700.nc0119s32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The detailed synthetic protocol for a 4-selenothymidine phosphoramidite and its use to prepare modified oligonucleotides is described here. The Se-phosphoramidite synthesis was achieved by developing a useful protection and deprotection system for the selenium functionality. The coupling reaction of the Se-phosphoramidite during solid-phase oligonucleotide synthesis is quantitative, and the oligonucleotides containing the Se-modification are stable. Based on crystal structure analysis, the selenium-modified oligonucleotides retain base-pairing like their native counterparts, and the derivatized DNA structure is virtually identical to the native structure. This achievement will present a novel opportunity for structural studies of nucleic acids and their protein complexes, because selenium can resolve the phase problem in macromolecular X-ray crystallography. In addition, this atom-specific replacement of oxygen with selenium will provide a useful tool for investigating biochemical and biophysical properties of nucleic acids and their protein complexes.
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Affiliation(s)
- Jia Sheng
- Georgia State University, Atlanta, Georgia, USA
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Caton-Williams J, Huang Z. Biochemistry of selenium-derivatized naturally occurring and unnatural nucleic acids. Chem Biodivers 2008; 5:396-407. [PMID: 18357549 DOI: 10.1002/cbdv.200890040] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Selenium (Se) can provide unique biochemical and biological functions, and properties to macromolecules, including protein and RNA. Although Se has not yet been found in DNA, identification of the presence of Se in natural tRNAs has led to discovery of the naturally occurring 2-selenouridine and 5-[(methylamino)methyl]-2-selenouridine (mnm(5)se(2)U). The Se-atoms at C(2) of the modified uridines are introduced by 2-selenouridine synthase via displacement of the S-atoms in the corresponding 2-thiouridine nucleotides of the tRNAs, and selenophosphate is used as the Se donor. The research indicated that mnm(5)se(2)U is located at the first or wobble position of the anticodons in several bacterial tRNAs, including tRNA(Lys), tRNA(Glu), and tRNA(Gln). The 2-seleno functionality on this modified nucleotide probably improves the translation accuracy and/or efficiency. These observations in vivo suggest that the presence of Se can provide natural RNAs with useful properties to better function and survival. To further investigate the biochemical and structural properties of Se-derivatized nucleic acids (SeNA), we have pioneered chemical and enzymatic synthesis of Se-derivatized nucleic acids, and introduced Se into both RNA and DNA at a variety of positions by atom-specific replacement of oxygen. This review outlines the recent advancements in chemical and biochemical syntheses, and studies of SeNAs, and their potential applications in structural and functional investigation of nucleic acids and their protein complexes.
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Sheng J, Hassan AEA, Huang Z. New Telluride-Mediated Elimination for Novel Synthesis of 2′,3′-Didehydro-2′,3′-dideoxynucleosides. J Org Chem 2008; 73:3725-9. [DOI: 10.1021/jo7025806] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | | | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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Sheng J, Huang Z. Selenium derivatization of nucleic acids for phase and structure determination in nucleic acid X-ray crystallography. Int J Mol Sci 2008; 9:258-271. [PMID: 19325748 PMCID: PMC2635675 DOI: 10.3390/ijms9030258] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 02/18/2008] [Accepted: 02/25/2008] [Indexed: 11/16/2022] Open
Abstract
Selenium derivatization (via selenomethionine) of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2'-position of the ribose). All the synthesis of 2'-SeMe modified phosphoramidite building blocks (U, C, T, A, G) and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.
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Affiliation(s)
| | - Zhen Huang
- Author to whom correspondence should be addressed. E-mail:
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Puffer B, Moroder H, Aigner M, Micura R. 2'-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach. Nucleic Acids Res 2008; 36:970-83. [PMID: 18096613 PMCID: PMC2241898 DOI: 10.1093/nar/gkm880] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 10/01/2007] [Accepted: 10/01/2007] [Indexed: 11/15/2022] Open
Abstract
Site-specifically modified 2'-methylseleno RNA represents a valuable derivative for phasing of X-ray crystallographic data. Several successful applications in three-dimensional structure determination of nucleic acids, such as the Diels-Alder ribozyme, have relied on this modification. Here, we introduce synthetic routes to 2'-methylseleno phosphoramidite building blocks of all four standard nucleosides, adenosine, cytidine, guanosine and uridine, that are tailored for 2'-O-bis(acetoxyethoxy)methyl (ACE) RNA solid-phase synthesis. We additionally report on their incorporation into oligoribonucleotides including deprotection and purification. The methodological expansion of 2'-methylseleno labeling via ACE RNA chemistry is a major step to make Se-RNA generally accessible and to receive broad dissemination of the Se-approach for crystallographic studies on RNA. Thus far, preparation of 2'-methylseleno-modified oligoribonucleotides has been restricted to the 2'-O-[(triisopropylsilyl)oxy]methyl (TOM) and 2'-O-tert-butyldimethylsilyl (TBDMS) RNA synthesis methods.
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Affiliation(s)
| | | | | | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens University, Innrain 52a, 6020 Innsbruck, Austria
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Sheng J, Jiang J, Salon J, Huang Z. Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study. Org Lett 2007; 9:749-52. [PMID: 17263541 PMCID: PMC2532523 DOI: 10.1021/ol062937w] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] To investigate nucleic acids with selenium derivatization for crystallography, we report the first synthesis of 2'-methylseleno-thymidine phosphoramidite and its incorporation into DNAs and RNAs by solid-phase synthesis with over 99% coupling yield. The d(GT(Se)GTACAC)2 crystal structure was also determined at 1.40 A resolution using Se phasing, revealing that this Se derivatization did not cause significant structure perturbation, consistent with our UV melting study. In addition, we observed that the Se modification largely facilitated the crystallization.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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Jiang J, Sheng J, Carrasco N, Huang Z. Selenium derivatization of nucleic acids for crystallography. Nucleic Acids Res 2006; 35:477-85. [PMID: 17169989 PMCID: PMC1802610 DOI: 10.1093/nar/gkl1070] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 11/08/2006] [Accepted: 11/09/2006] [Indexed: 11/14/2022] Open
Abstract
The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 A resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 A). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 A resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native and Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.
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Affiliation(s)
- Jiansheng Jiang
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30302, USA
- Department of Biology, Brookhaven National LaboratoryUpton, NY 11973, USA
| | - Jia Sheng
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30302, USA
| | - Nicolas Carrasco
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30302, USA
| | - Zhen Huang
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30302, USA
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