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Yang X, Dinuka Abeydeera N, Liu FW, Egli M. Origins of the enhanced affinity of RNA-protein interactions triggered by RNA phosphorodithioate backbone modification. Chem Commun (Camb) 2017; 53:10508-10511. [PMID: 28868553 PMCID: PMC5608642 DOI: 10.1039/c7cc05722a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The well-characterized interaction between the MS2 coat protein and its cognate RNA hairpin was used to evaluate changes in affinity as a result of phosphorodithioate (PS2) replacing phosphate by biolayer interferometry (BLI). A structure-based analysis of the data provides insights into the origins of the enhanced affinity of RNA-protein interactions triggered by the PS2 moiety.
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Affiliation(s)
- Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA.
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Yang X. Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages. ACTA ACUST UNITED AC 2017; 70:4.77.1-4.77.13. [PMID: 28921494 DOI: 10.1002/cpnc.40] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc.
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Yang X, Sierant M, Janicka M, Peczek L, Martinez C, Hassell T, Li N, Li X, Wang T, Nawrot B. Gene silencing activity of siRNA molecules containing phosphorodithioate substitutions. ACS Chem Biol 2012; 7:1214-20. [PMID: 22512638 DOI: 10.1021/cb300078e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Chemically synthesized small interfering RNAs (siRNAs) have been widely used to identify gene function and hold great potential in providing a new class of therapeutics. Chemical modifications are desired for therapeutic applications to improve siRNA efficacy. Appropriately protected ribonucleoside-3'-yl S-[β-(benzoylmercapto)ethyl]pyrrolidino-thiophosphoramidite monomers were prepared for the synthesis of siRNA containing phosphorodithioate (PS2) substitutions in which the two non-bridging oxygen atoms are replaced by sulfur atoms. A series of siRNAs containing PS2 substitutions have been strategically designed, synthesized, and evaluated for their gene silencing activities. These PS2-siRNA duplexes exhibit an A-form helical structure similar to unmodified siRNA. The effect of PS2 substitutions on gene silencing activity is position-dependent, with certain PS2-siRNAs showing activity significantly higher than that of unmodified siRNA. The relative gene silencing activities of siRNAs containing either PS2 or phosphoromonothioate (PS) linkages at identical positions are variable and depend on the sites of modification. 5'-Phosphorylation of PS2-siRNAs has little or no effect on gene silencing activity. Incorporation of PS2 substitutions into siRNA duplexes increases their serum stability. These results offer preliminary evidence of the potential value of PS2-modified siRNAs.
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Affiliation(s)
- Xianbin Yang
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, United
States
| | - Malgorzata Sierant
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Magdalena Janicka
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Lukasz Peczek
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Carlos Martinez
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, United States
| | - Tom Hassell
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, United States
| | - Na Li
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, United
States
| | - Xin Li
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, United
States
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Barbara Nawrot
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
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Sobkowski M, Stawinski J, Kraszewski A. Stereochemistry of internucleotide bond formation by the H-phosphonate method. Part 6: Optimization of the reaction conditions towards highest stereoselectivity. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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