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Chen X, Xie L, Zhang C, Tian S, Tang Z, Xiang M, Tian W, Lu P, Yang X. Synthesis of Nucleotides Bearing the 2'-O-Trifluoromethyl Group and Their Application in RNA Analogs Preparation. Curr Protoc 2024; 4:e956. [PMID: 38230581 DOI: 10.1002/cpz1.956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The integration of fluorine atoms into biologically active organic compounds has proved to be a vital technique in small molecule drugs. This technique can substantially enhance crucial properties, including metabolic stability, lipophilicity, and bioavailability, often with a mere addition of a single fluorine atom or a trifluoromethyl group. Over the past few decades, this concept has also been applied in nucleic acid chemistry. A commonly employed 2'-OH substitution is the introduction of a 2'-deoxy-2'-fluoro (2'-F) group. The strong electronegativity of fluorine prompts the modified siRNA to readily adopt a C3'-endo conformation, resulting in significant advantages in terms of binding affinity. To enrich the toolbox of chemical modification of oligonucleotides, the replacement of the 2'-OH with the 2'-O-trifluoromethyl group has been developed in RNA analog synthesis. Oligodeoxynucleotides containing the 2'-O-trifluoromethyl group can greatly increase the thermal stability of DNA/RNA duplexes depending on the position and amount of the modification. Moreover, 2'-O-trifluoromethylated oligodeoxynucleotide also exhibited a slightly higher resistance to snake venom phosphodiesterase than the unmodified oligodeoxynucleotide. The 2'-O-trifluoromethylated oligonucleotides can emerge as a label to study RNA structure and function as well, or to develop DNA/RNA-based diagnostics. Hence, it is necessary to report an effective method for the synthesis, deprotection, purification, and characterization of oligonucleotides bearing a 2'-O-trifluoromethyl group. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-benzoyl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-isobutyryl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-trifluoromethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl) phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-trifluoromethylated RNA analogs Basic Protocol 6: Deprotection and purification of 2'-O-trifluoromethyl-RNAs.
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Chen X, Xie L, Zhang C, Tian S, Tang Z, Tian W, Lu P, Yang X. A Convenient Method for the Synthesis of 2'-O-Cyanoethylated Nucleotides and Their Application in the Solid-Phase Synthesis of Related RNA Analogs. Curr Protoc 2023; 3:e923. [PMID: 37962485 DOI: 10.1002/cpz1.923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Although small interfering RNA (siRNA) is a key player among gene inhibition therapeutics, there are many obstacles to the development of siRNA drugs due to inherent properties of oligonucleotides, including the unsatisfactory stability of unmodified siRNA, poor pharmacokinetic distribution, and the toxicity induced by off-target effects. To maximize treatment potency, chemical modification of siRNA has undoubtedly been the most successful strategy by far. Widely applied modifications include phosphorothioate linkages, 2'-O-methyl modifications, and 2'-fluoro modifications, among others. To extend the family of chemical modifications for oligonucleotides, 2'-O-cyanoethylated RNA analogs were developed through the replacement of the 2'-hydroxyl group with a 2'-O-cyanoethyl group (-OCH2 CH2 CN). This modification can provide several advantages over unmodified RNA, such as increased stability, improved binding affinity to complementary DNA or RNA strands, and resistance to degradation by cellular nucleases. The 2'-O-cyanoethyl-modified RNAs not only are applied in RNA silencing machinery but also act as research tools for studying RNA structure and function or for developing RNA-based diagnostics. Therefore, the efficient synthesis, deprotection, purification, and characterization of 2'-O-cyanoethylated RNAs deserves more attention. This protocol describes the chemical synthesis of 2'-O-cyanoethylated nucleotides and the solid-phase synthesis, deprotection, and purification of 2'-O-cyanoethylated RNAs. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-cyanoethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-cyanoethylated RNA analogs Basic Protocol 6: Deprotection and purification of synthesized 2'-O-cyanoethyl-RNAs.
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Affiliation(s)
- Xuan Chen
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Long Xie
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | | | - Shen Tian
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Zeyu Tang
- Sirnaomics Ltd. Suzhou, Suzhou, China
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Hydrolytic (in)stability of phosphate isosteres. Eur J Med Chem 2022; 244:114836. [DOI: 10.1016/j.ejmech.2022.114836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022]
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Rastogi R, Krishna G, Tarannum N, Mishra S, Rastogi A, Butcher RJ. Study based on docking of antimicrobial activity and fluorescence behavior of ammonium salt of diisopropyl dithiophosphate, O, O′- diisopropanediyl S-( N-phthalimido methyl) and zinc diisopropyl dithiophosphates. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2020.1860983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Rupali Rastogi
- Department of Chemistry, ITM University, Gwalior, Madhya Pradesh, India
| | - Gokul Krishna
- Department of Chemistry, ITM University, Gwalior, Madhya Pradesh, India
| | - Nazia Tarannum
- Department of Chemistry, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, India
| | - Swapnil Mishra
- Center of Bioinformatics, University of Allahabad, Allahabad, Uttar Pradesh, India
| | - Anugya Rastogi
- Department of Physics, Jiwaji University, Gwalior, Madhya Pradesh, India
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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Nizamov IS, Shumatbaev GG, Nizamov ID, Nikitin YN, Belov TG, Shulaeva MP, Pozdeev OK, Batyeva ES, Cherkasov RA. Chiral methylbenzylammonium salts of aryldithiophosphonic acids containing glucofuranose, allofuranose, and galactopyranose diacetonide scaffolds. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2020.1818242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ilyas S. Nizamov
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | | | - Ilnar D. Nizamov
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
| | - Yevgeniy N. Nikitin
- Federal State Budgetary Institution of Science Federal Research Center, Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | - Timur G. Belov
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
| | | | - Oscar K. Pozdeev
- Department of Microbiology, Kazan State Medical Academy, Kazan, Russia
| | - Elvira S. Batyeva
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
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Kour M, Kumar S, Andotra S, Lata S, Kaur R, Singh G, Vikas, Katoch M, Pandey SK. O,O′-Dimethyl diphenyldithiophosphates of titanium(IV): synthesis, spectroscopic, DFT and biological studies. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1685692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Mandeep Kour
- Department of Chemistry, University of Jammu, Jammu, India
| | - Sandeep Kumar
- Department of Chemistry, University of Jammu, Jammu, India
| | - Savit Andotra
- Department of Chemistry, University of Jammu, Jammu, India
| | - Suman Lata
- Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Punjab University, Chandigarh, India
| | - Ramanpreet Kaur
- Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Punjab University, Chandigarh, India
| | - Gurpreet Singh
- Microbial Biotechnology Department, Indian Institute of Integrative Medicine, Jammu, India
| | - Vikas
- Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Punjab University, Chandigarh, India
| | - Meenu Katoch
- Microbial Biotechnology Department, Indian Institute of Integrative Medicine, Jammu, India
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Kumar S, Radha A, Kour M, Kumar R, Chouaih A, Pandey SK. DFT studies of disubstituted diphenyldithiophosphates of nickel(II): Structural and some spectral parameters. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Rodriguez-Aguayo C, Bayraktar E, Ivan C, Aslan B, Mai J, He G, Mangala LS, Jiang D, Nagaraja AS, Ozpolat B, Chavez-Reyes A, Ferrari M, Mitra R, Siddik ZH, Shen H, Yang X, Sood AK, Lopez-Berestein G. PTGER3 induces ovary tumorigenesis and confers resistance to cisplatin therapy through up-regulation Ras-MAPK/Erk-ETS1-ELK1/CFTR1 axis. EBioMedicine 2019; 40:290-304. [PMID: 30655206 PMCID: PMC6411965 DOI: 10.1016/j.ebiom.2018.11.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/07/2018] [Accepted: 11/21/2018] [Indexed: 02/04/2023] Open
Abstract
Background Inflammatory mediator prostaglandin E2–prostaglandin E2 receptor EP3 (PTGER3) signaling is critical for tumor-associated angiogenesis, tumor growth, and chemoresistance. However, the mechanism underlying these effects in ovarian cancer is not known. Methods An association between higher tumoral expression of PTGER3 and shorter patient survival in the ovarian cancer dataset of The Cancer Genome Atlas prompted investigation of the antitumor effects of PTGER3 downmodulation. PTGER3 mRNA and protein levels were higher in cisplatin-resistant ovarian cancer cells than in their cisplatin-sensitive counterparts. Findings Silencing of PTGER3 via siRNA in cancer cells was associated with decreased cell growth and less invasiveness, as well as cell-cycle arrest and increased apoptosis, mediated through the Ras-MAPK/Erk-ETS1-ELK1/CFTR1 axis. Furthermore, sustained PTGER3 silencing with multistage vector and liposomal 2’-F-phosphorodithioate-siRNA–mediated silencing of PTGER3 combined with cisplatin resulted in robust antitumor effects in cisplatin-resistant ovarian cancer models. Interpretation These findings identify PTGER3 as a potential therapeutic target in chemoresistant ovarian cancers expressing high levels of this oncogenic protein. Fund National Institutes of Health/National Cancer Institute, USA.
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Affiliation(s)
- Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emine Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medical Biology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Burcu Aslan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junhua Mai
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Guangan He
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lingegowda S Mangala
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dahai Jiang
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Archana S Nagaraja
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Arturo Chavez-Reyes
- Centro de Investigación y Estudios Avanzados del IPN, Unidad Monterrey, Apodaca, NL, CP. 66600, Mexico
| | - Mauro Ferrari
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Rahul Mitra
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zahid H Siddik
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haifa Shen
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xianbin Yang
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
| | - Anil K Sood
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 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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Kour M, Kumar S, Andotra S, Kour G, Singh G, Gupta VK, Kant R, Katoch M, Pandey SK. Chromium(III) complexes of dimethyl diphenyldithiophosphates: Synthesis, characterization, and antibacterial studies. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2017.1333506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mandeep Kour
- Department of Chemistry, University of Jammu, Jammu, India
| | - Sandeep Kumar
- Department of Chemistry, University of Jammu, Jammu, India
| | - Savit Andotra
- Department of Chemistry, University of Jammu, Jammu, India
| | - Gurvinder Kour
- X-ray Crystallographic Laboratory, Department of Physics and Electronics, University of Jammu, Jammu, India
| | - Gurpreet Singh
- Microbial Biotechnology Department, Indian Institute of Integrative Medicine, Canal Road, Jammu, India
| | - Vivek K. Gupta
- X-ray Crystallographic Laboratory, Department of Physics and Electronics, University of Jammu, Jammu, India
| | - Rajni Kant
- X-ray Crystallographic Laboratory, Department of Physics and Electronics, University of Jammu, Jammu, India
| | - Meenu Katoch
- Microbial Biotechnology Department, Indian Institute of Integrative Medicine, Canal Road, Jammu, India
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Dutta AK, Captain I, Jessen HJ. New Synthetic Methods for Phosphate Labeling. Top Curr Chem (Cham) 2017; 375:51. [DOI: 10.1007/s41061-017-0135-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/27/2017] [Indexed: 12/12/2022]
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Lou X, Egli M, Yang X. Determining Functional Aptamer-Protein Interaction by Biolayer Interferometry. ACTA ACUST UNITED AC 2016; 67:7.25.1-7.25.15. [PMID: 27911494 DOI: 10.1002/cpnc.18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol). We also report on the protocol for the affinity screening of a panel of anti-thrombin RNA aptamers with a single phosphorodithioate (PS2) modification, whereby the position of the modification along the RNA backbone is varied systematically (Support Protocol). The PS2 modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphodiester backbone linkage. The PS2-modified RNAs are nuclease resistant and several in vitro and in vivo assays have demonstrated their biological activity. For example, combining the PS2 with the 2'-OMe modification affords increased loading of modified small interfering RNA (siRNA) duplexes into the RNA-induced silencing complex (RISC) as well as enhanced gene-silencing antitumor activity. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
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14
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Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, Lybrand TP, Frydman C, Monteiro RQ, Gomer RH, Nawrot B, Yang X. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res 2016; 44:8052-64. [PMID: 27566147 PMCID: PMC5041495 DOI: 10.1093/nar/gkw725] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/12/2022] Open
Abstract
RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.
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Affiliation(s)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Karen Mercier
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Jonas Nascimento Conde
- Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Daniella M Mizurini
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Fatima-Ezzahra Hibti
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Tom Hassell
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Feng-Wu Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Carlos Martinez
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Anil K Sood
- Departments of Gynecologic Oncology and Cancer Biology, and Center for RNAi and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Terry P Lybrand
- Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Chiraz Frydman
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Robson Q Monteiro
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
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Nizamov IS, Nikitin YN, Nizamov ID, Belov TG, Voloshina AD, Batyeva ES, Cherkasov RA. α-d-Glucofuranose and α-d-allofuranose diacetonides and silyl ether of α-d-glucofuranose diacetonide in dithiophosphorylation reactions. HETEROATOM CHEMISTRY 2016. [DOI: 10.1002/hc.21344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ilyas S. Nizamov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Kazan Russia
| | - Yevgeniy N. Nikitin
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
| | - Ilnar D. Nizamov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
| | - Timur G. Belov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
| | - Alexandra D. Voloshina
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Kazan Russia
| | - Elvira S. Batyeva
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Kazan Russia
| | - Rafael A. Cherkasov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
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16
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Yang X. Solid-Phase Synthesis of Oligodeoxynucleotide Analogs Containing Phosphorodithioate Linkages. ACTA ACUST UNITED AC 2016; 66:4.71.1-4.71.14. [PMID: 27584703 DOI: 10.1002/cpnc.13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The oligodeoxynucleotide phosphorodithioate modification (PS2-ODN) uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphordiester backbone linkage. Like a natural phosphodiester ODN backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-ODNs are highly stable to nucleases and numerous in vitro assays have demonstrated their biological activity. For example, PS2-ODNs activated RNase H in vitro, strongly inhibited human immunodeficiency virus (HIV) reverse transcriptase, induced B-cell proliferation and differentiation, and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-ODNs has spawned a variety of strategies for synthesizing, isolating, and characterizing this compounds. ODN-thiophosphoramidite monomers are commercially available from either AM Biotechnologies or Glen Research and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of ODNs having PS2 internucleotide linkages. © 2016 by John Wiley & Sons, Inc.
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17
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Nguyen D, Zandarashvili L, White MA, Iwahara J. Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity. Chembiochem 2016; 17:1636-42. [PMID: 27271797 DOI: 10.1002/cbic.201600265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 02/05/2023]
Abstract
Oxygen-to-sulfur substitutions in DNA phosphate often enhance affinity for DNA-binding proteins. Our previous studies have suggested that this effect of sulfur substitution of both OP1 and OP2 atoms is due to an entropic gain associated with enhanced ion pair dynamics. In this work, we studied stereospecific effects of single sulfur substitution of either the OP1 or OP2 atom in DNA phosphate at the Lys57 interaction site of the Antennapedia homeodomain-DNA complex. Using crystallography, we obtained structural information on the RP and SP diastereomers of the phosphoromonothioate and their interaction with Lys57. Using fluorescence-based assays, we found significant affinity enhancement upon sulfur substitution of the OP2 atom. Using NMR spectroscopy, we found significant mobilization of the Lys57 side-chain NH3 (+) group upon sulfur substitution of the OP2 atom. These data provide further mechanistic insights into the affinity enhancement by oxygen-to-sulfur substitution in DNA phosphate.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA.
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18
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Nizamov IS, Nikitin YN, Belov TG, Nizamov ID, Voloshina AD, Cherkasov RA. 1,2:5,6-Di-O-Cyclohexylidene-d-Mannitol and Its Bis(Trimethylsilyl) Ether in the Dithiophosphorylation Reactions. HETEROATOM CHEMISTRY 2016. [DOI: 10.1002/hc.21307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ilyas S. Nizamov
- Kazan Federal University; Kremlievskaya Str., 18; Kazan 420008 Russia
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Arbuzov Str. 8; 420088 Kazan Russia
| | | | - Timur G. Belov
- Kazan Federal University; Kremlievskaya Str., 18; Kazan 420008 Russia
| | - Ilnar D. Nizamov
- Kazan Federal University; Kremlievskaya Str., 18; Kazan 420008 Russia
| | - Alexandra D. Voloshina
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Arbuzov Str. 8; 420088 Kazan Russia
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19
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Sajgotra M, Khajuria R, Kumar S, Syed A, Andotra S, Kour G, Gupta VK, Kant R, Pandey SK. First Donor-Stabilized Complexes of Manganese(II) with Disubstituted diphenyldithiophosphates: synthesis, characterization, biological, and X-ray Analysis. PHOSPHORUS SULFUR 2015. [DOI: 10.1080/10426507.2015.1012668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Mehak Sajgotra
- Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Ruchi Khajuria
- Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Sandeep Kumar
- Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Atiya Syed
- Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Savit Andotra
- Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Gurvinder Kour
- Department of Physics & Electronics, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Vivek K. Gupta
- Department of Physics & Electronics, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Rajni Kant
- Department of Physics & Electronics, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
| | - Sushil K. Pandey
- Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu, Jammu and Kashmir, 180006, India
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20
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Nizamov IS, Gabdullina GT, Terenzhev DA, Nurmukhametov AR, Nizamov ID, Cherkasov RA. Optically active dithiophosphoric acid, its ammonium salt, and S-esters on the basis of (1R)-endo-(+)-fenchyl alcohol. PHOSPHORUS SULFUR 2014. [DOI: 10.1080/10426507.2013.860531] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ilyas S. Nizamov
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
- State Budgetary-Funded Institution of Science, A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | | | | | | | - Ilnar D. Nizamov
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
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21
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Nizamov IS, Gabdullina GT, Nurmukhametov AR, Nizamov ID, Cherkasov RA. Optically Active S-Esters of Dithiophosphoric Acid on the Basis of (1S)-endo-(-)-Borneol. HETEROATOM CHEMISTRY 2013. [DOI: 10.1002/hc.21122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ilyas S. Nizamov
- Kazan Federal University; Kremlievskaya 18; Kazan 420008 Russia
- State Budgetary-Funded Institution of Science; A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Arbuzov 8; Kazan 420088 Russia
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22
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Nizamov IS, Al’metkina LA, Gabdullina GT, Shamilov RR, Sofronov AV, Nikitina LE, Lisovskaya SA, Glushko NI, Cherkasov RA. Chiral phosphorus dithio acids derived from (1S,2S,3S,5R)-(+)-isopinocampheol. Synthesis and fungicidal activity. Russ Chem Bull 2013. [DOI: 10.1007/s11172-012-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Sierant M, Yang X, Nawrot B. Sirna Analogs Containing Phosphorodithioate Substitutions. PHOSPHORUS SULFUR 2013. [DOI: 10.1080/10426507.2012.745079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Malgorzata Sierant
- a Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Lodz , Poland
| | | | - Barbara Nawrot
- a Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Lodz , Poland
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24
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Yan G, Wang Y, He X, Wang K, Liu J, Du Y. A highly sensitive label-free electrochemical aptasensor for interferon-gamma detection based on graphene controlled assembly and nuclease cleavage-assisted target recycling amplification. Biosens Bioelectron 2013; 44:57-63. [PMID: 23391707 DOI: 10.1016/j.bios.2013.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/05/2013] [Accepted: 01/07/2013] [Indexed: 11/15/2022]
Abstract
We report here a highly sensitive and label-free electrochemical aptasensing technology for detection of interferon-gamma (IFN-γ) based on graphene controlled assembly and enzyme cleavage-assisted target recycling amplification strategy. In this work, in the absence of IFN-γ, the graphene could not be assembled onto the 16-mercaptohexadecanoic acid (MHA) modified gold electrode because the IFN-γ binding aptamer was strongly adsorbed on the graphene due to the strong π-π interaction. Thus the electronic transmission was blocked (eT OFF). However, the presence of target IFN-γ and DNase I led to desorption of aptamer from the graphene surface and further cleavage of the aptamer, thereby releasing the IFN-γ. The released IFN-γ could then re-attack other aptamers on the graphene, resulting in the successive release of the aptamers from the graphene. At the same time, the "naked" graphene could be assembled onto the MHA modified gold electrode with hydrophobic interaction and π-conjunction, mediating the electron transfer between the electrode and the electroactive indicator. Then, measurable electrochemical signals were generated (eT ON), which was related to the concentration of the IFN-γ. By taking advantages of graphene and enzyme cleavage-assisted target recycling amplification, the developed label-free electrochemical aptasensing technology showed a linear response to concentration of IFN-γ range from 0.1 to 0.7 pM. The detection limit of IFN-γ was determined to be 0.065 pM. Moreover, this aptasensor shows good selectivity toward the target in the presence of other relevant proteins. Our strategy thus opens new opportunities for label-free and amplified detection of other kinds of proteins.
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Affiliation(s)
- Genping Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, PR China
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25
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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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26
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Singh R, Vince R. 2-Azabicyclo[2.2.1]hept-5-en-3-one: Chemical Profile of a Versatile Synthetic Building Block and its Impact on the Development of Therapeutics. Chem Rev 2012; 112:4642-86. [DOI: 10.1021/cr2004822] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rohit Singh
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
| | - Robert Vince
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
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27
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Guga P, Koziołkiewicz M. Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 2012; 8:1642-81. [PMID: 21922655 DOI: 10.1002/cbdv.201100130] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, PL-90-363 Łódź.
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28
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Tang D, Tang J, Li Q, Su B, Chen G. Ultrasensitive aptamer-based multiplexed electrochemical detection by coupling distinguishable signal tags with catalytic recycling of DNase I. Anal Chem 2011; 83:7255-9. [PMID: 21888312 DOI: 10.1021/ac201891w] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work reports an aptamer-based, disposable, and multiplexed sensing platform for simultaneous electrochemical determination of small molecules, employing adenosine triphosphate (ATP) and cocaine as the model target analytes. The multiplexed sensing strategy is based on target-induced release of distinguishable redox tag-conjugated aptamers from a magnetic graphene platform. The electronic signal of the aptasensors could be further amplified by coupling DNase I with catalytic recycling of self-produced reactants. The assay was based on the change in the current at the various peak potentials in the presence of the corresponding signal tags. Experimental results revealed that the multiplexed electrochemical aptasensor enabled the simultaneous monitoring of ATP and cocaine in a single run with wide working ranges and low detection limits (LODs: 0.1 pM for ATP and 1.5 pM for cocaine). This concept offers promise for rapid, simple, and cost-effective analysis of biological samples.
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