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Oligonucleotides Isolation and Separation—A Review on Adsorbent Selection. Int J Mol Sci 2022; 23:ijms23179546. [PMID: 36076941 PMCID: PMC9455468 DOI: 10.3390/ijms23179546] [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: 07/26/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotides have many important applications, including as primers in polymerase chain reactions and probes for DNA sequencing. They are proposed as a diagnostic and prognostic tool for various diseases and therapeutics in antisense therapy. Accordingly, it is necessary to develop liquid chromatography and solid phase extraction methods to separate oligonucleotides and isolate them from biological samples. Many reviews have been written about the determination of these compounds using the separation technique or sample preparation for their isolation. However, presumably, there are no articles that critically review the adsorbents used in liquid chromatography or solid phase extraction. The present publication reviews the literature from the last twenty years related to supports (silica, polymers, magnetic nanoparticles) and their modifications. The discussed issues concern reversed phase (alkyl, aromatic, cholesterol, mixed ligands), ion-exchange (strong and weak ones), polar (silica, polyhydroxy, amide, zwitterionic), and oligonucleotide-based adsorbents.
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Sutton JM, Kim J, El Zahar NM, Bartlett MG. BIOANALYSIS AND BIOTRANSFORMATION OF OLIGONUCLEOTIDE THERAPEUTICS BY LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:334-358. [PMID: 32588492 DOI: 10.1002/mas.21641] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/05/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Since 2016, eight new oligonucleotide therapies have been approved which has led to increased interest in oligonucleotide analysis. There is a particular need for powerful bioanalytical tools to study the metabolism and biotransformation of these molecules. This review provides the background on the biological basis of these molecules as currently used in therapies. The article also reviews the current state of analytical methodology including state of the art sample preparation techniques, liquid chromatography-mass spectrometry methods, and the current limits of detection/quantitation. Finally, the article summarizes the challenges in oligonucleotide bioanalysis and provides future perspectives for this emerging field. © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- James Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
| | - Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
| | - Noha M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Cairo, 11566, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
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Nuckowski Ł, Dzieszkowski K, Rafiński Z, Studzińska S. Application of Magnetic Nanoparticles Coated with Crosslinked Zwitterionic Poly(ionic liquid)s for the Extraction of Oligonucleotides. MATERIALS (BASEL, SWITZERLAND) 2021; 14:3146. [PMID: 34201146 PMCID: PMC8226603 DOI: 10.3390/ma14123146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/16/2022]
Abstract
Magnetic nanoparticles coated with zwitterionic poly(ionic liquid)s were applied for dispersive solid-phase extraction of oligonucleotides. The materials were synthesized by miniemulsion copolymerization of ionic liquids and divinylbenzene on magnetic nanoparticles. The functional monomers contain a positively charged imidazolium ring and one of the anionic groups: derivatives of acetate, malonate, or butyl sulfonate ions. Adsorption of unmodified DNA oligonucleotide on obtained materials was possible in ion-exchange (IE) and hydrophilic interactions (HI) mode. The adsorption in IE was possible at low pH and was almost complete. The adsorption in HI mode required the usage of appropriate addition of organic solvent but did not provide full adsorption. Studies on the desorption of the analytes included determining the impact of ammonium acetate concentration and pH and organic solvents addition on the recovery. The material containing acetic fragments as an anionic group was selected for the final procedure with the use of 10 mM ammonium acetate (pH = 9.5)/methanol (50/50, v/v) as an elution solution. The magnetic dispersive solid-phase extraction procedure was tested for the oligonucleotides with various modifications and lengths. Moreover, it was applied to extract DNA oligonucleotide and its synthetic metabolites from enriched human plasma without any pre-purification, with recoveries greater than 80%.
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Affiliation(s)
- Łukasz Nuckowski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland;
| | - Krzysztof Dzieszkowski
- Chair of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland; (K.D.); (Z.R.)
| | - Zbigniew Rafiński
- Chair of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland; (K.D.); (Z.R.)
| | - Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland;
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Kim J, El Zahar NM, Bartlett MG. In vitro metabolism of 2'-ribose unmodified and modified phosphorothioate oligonucleotide therapeutics using liquid chromatography mass spectrometry. Biomed Chromatogr 2020; 34:e4839. [PMID: 32246854 DOI: 10.1002/bmc.4839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/18/2020] [Accepted: 03/30/2020] [Indexed: 01/06/2023]
Abstract
Antisense oligonucleotides (ASOs) have been touted as an emerging therapeutic class to treat genetic disorders and infections. The evaluation of metabolic stability of ASOs during biotransformation is critical due to concerns regarding drug safety. Because the effects of the modifications in ASOs on their metabolic stabilities are different from unmodified ASOs, studies that afford an understanding of these effects as well as propose proper methods to determine modified and unmodified ASO metabolites are imperative. An LC-tandem mass spectrometry method offering good selectivity with a high-quality separation using 30 mm N,N-dimethylcyclohexylamine and 100 mm 1,1,1,3,3,3-hexafluoro-2-propanol was utilized to identify each oligonucleotide metabolite. Subsequently, the method was successfully applied to a variety of in vitro systems including endo/exonuclease digestion, mouse liver homogenates, and then liver microsomes, after which the metabolic stability of unmodified versus modified ASOs was compared. Typical patterns of chain-shortened metabolites generated by mainly 3'-exonucleases were observed in phosphodiester and phosphorothioate ASOs, and endonuclease activity was identically observed in gapmers that showed relatively more resistance to nuclease degradation. Overall, the degradation of each ASO occurred more slowly corresponding to the degree of chemical modifications, while 5'-exonuclease activities were only observed in gapmers incubated in mouse liver homogenates. Our findings provide further understanding of the impact of modifications on the metabolic stability of ASOs, which facilitates the development of future ASO therapeutics.
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Affiliation(s)
- Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA, USA
| | - Noha M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA, USA.,Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA, USA
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Kim J, Basiri B, Hassan C, Punt C, van der Hage E, den Besten C, Bartlett MG. Metabolite Profiling of the Antisense Oligonucleotide Eluforsen Using Liquid Chromatography-Mass Spectrometry. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:714-725. [PMID: 31422288 PMCID: PMC6704339 DOI: 10.1016/j.omtn.2019.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 11/26/2022]
Abstract
Eluforsen (previously known as QR-010) is a 33-mer 2′-O-methyl modified phosphorothioate antisense oligonucleotide targeting the F508del mutation in the gene encoding CFTR protein of cystic fibrosis patients. In this study, eluforsen was incubated with endo- and exonucleases and mouse liver homogenates to elucidate its in vitro metabolism. Mice and monkeys were used to determine in vivo liver and lung metabolism of eluforsen following inhalation. We developed a liquid chromatography-mass spectrometry method for the identification and semi-quantitation of the metabolites of eluforsen and then applied the method for in vitro and in vivo metabolism studies. Solid-phase extraction was used following proteinase K digestion for sample preparation. Chain-shortened metabolites of eluforsen by 3′ exonuclease were observed in mouse liver in an in vitro incubation system and by either 3′ exonuclease or 5′ exonuclease in liver and lung samples from an in vivo mouse and monkey study. This study provides approaches for further metabolite characterization of 2′-ribose-modified phosphorothioate oligonucleotides in in vitro and in vivo studies to support the development of oligonucleotide therapeutics.
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Affiliation(s)
- Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
| | - Babak Basiri
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
| | | | - Carine Punt
- ProQR Therapeutics N.V., Leiden, the Netherlands
| | | | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA.
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Nuckowski Ł, Kaczmarkiewicz A, Studzińska S. Review on sample preparation methods for oligonucleotides analysis by liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1090:90-100. [PMID: 29803869 DOI: 10.1016/j.jchromb.2018.05.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/10/2018] [Accepted: 05/17/2018] [Indexed: 02/01/2023]
Abstract
Antisense oligonucleotides have been successfully investigated for the treatment of different types of diseases. Detection and determination of antisense oligonucleotides and their metabolites are necessary for drug development and evaluation. This review focuses mainly on the first step of the analysis of oligonucleotides i.e. the sample preparation stage, and in particular on the techniques used for liquid chromatography and liquid chromatography coupled with mass spectrometry. Exceptional sample preparation techniques are required as antisense oligonucleotides need to be determined in complex biological matrices. The text discusses general issues in oligonucleotide sample preparation and approaches to their solution. The most popular techniques i.e. protein precipitation, protein enzyme digestion and liquid-liquid extraction are reviewed. Solid phase extraction methods are discussed and the issues connected with the application of each method are highlighted. Other newly reported promising techniques are also described. Finally, there is a summary of actually used techniques and the indication of the direction of future research.
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Affiliation(s)
- Łukasz Nuckowski
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Anna Kaczmarkiewicz
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Sylwia Studzińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87 100 Toruń, Poland.
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Beverly M, Dell A, Parmar P, Houghton L. Label-free analysis of mRNA capping efficiency using RNase H probes and LC-MS. Anal Bioanal Chem 2016; 408:5021-30. [PMID: 27193635 DOI: 10.1007/s00216-016-9605-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/01/2016] [Accepted: 04/26/2016] [Indexed: 12/25/2022]
Abstract
A label-free method for determining the 5'-end cap identity and orientation of a messenger RNA (mRNA) is described. Biotin-tagged probes that were complementary to the 5' end of target mRNA were used with RNase H to cleave the 5' end of the mRNA. The cleaved end sequence was isolated using streptavidin-coated magnetic beads and then analyzed by LC-MS. Quantitative and qualitative information on the 5' cap was determined from the unique mass of the isolated cleaved sequence. This approach, combined with the use of 5' RNA pyrophosphohydrolase, was also used to ascertain the orientation of the 5' cap. The assay showed low-picomole sensitivity for detecting capping reaction impurities. Uncapped triphosphate mRNA, spiked into 100 pmol of capped mRNA, could be detected over the tested range of 0.5 to 25 % with a linear response. The capping efficiency of several vaccinia-capped mRNA preparations was determined to be between 88 and 98 % depending on the modification type and length of the mRNA. mRNA of 2.2K and 9K nucleotides in length and containing the modified nucleotides pseudouridine and 5-methylcytidine were all successfully analyzed, demonstrating the utility of the technique to study mRNA capping. Graphical abstract mRNA 5' end analysis with RNAse H cleavage and capture probe.
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Affiliation(s)
- Michael Beverly
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA.
| | - Amy Dell
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
| | - Parul Parmar
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
| | - Leslie Houghton
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
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Abstract
Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.
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Batkai S, Thum T. Analytical approaches in microRNA therapeutics. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 964:146-52. [DOI: 10.1016/j.jchromb.2014.03.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/17/2014] [Accepted: 03/19/2014] [Indexed: 02/06/2023]
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Lin YZ, Wang TH, Lin YS, Kuan WC, Lee WC. A novel method to prepare magnetic polymer-based anion exchangers and their application. J Appl Polym Sci 2014. [DOI: 10.1002/app.40725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yu-Zong Lin
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center; National Chung Cheng University; Min-Hsiung Chia-Yi 621 Taiwan
| | - Tzu-Hsien Wang
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center; National Chung Cheng University; Min-Hsiung Chia-Yi 621 Taiwan
| | - Yu-Sheng Lin
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center; National Chung Cheng University; Min-Hsiung Chia-Yi 621 Taiwan
| | - Wei-Chih Kuan
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center; National Chung Cheng University; Min-Hsiung Chia-Yi 621 Taiwan
| | - Wen-Chien Lee
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center; National Chung Cheng University; Min-Hsiung Chia-Yi 621 Taiwan
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Chen B, Mason SF, Bartlett MG. The effect of organic modifiers on electrospray ionization charge-state distribution and desorption efficiency for oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:257-264. [PMID: 23325666 DOI: 10.1007/s13361-012-0509-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/21/2012] [Accepted: 09/26/2012] [Indexed: 06/01/2023]
Abstract
The chemical composition of the solution has a critical impact on the electrospray desorption efficiency of oligonucleotides. Several physiochemical properties of various organic modifiers were investigated with respect to their role in the desorption process of oligonucleotides. The Henry's Law Constant, which reflects the volatility of alkylamines, was found to have a prominent effect on both the electrospray charge state distribution and desorption efficiency of oligonucleotides. Alkylamines with higher k(H,cc)(aq/gas) values such as hexylamine, piperidine, and imidazole reduced the charge state distribution by forming complexes with the oligonucleotide and dissociating from it in the gas phase, while alkylamines with extremely low k(H,cc)(aq/gas) values reduced the electrospray charge state distribution by facilitating ion emission at an earlier stage of the electrospray desorption process. Ion-pairing agents with moderate k(H,cc)(aq/gas) values do not alter the electrospray charge state distribution of oligonucleotides and their ability to enhance oligonucleotide ionization followed the order of decreasing k(H,cc)(aq/gas) values. The Henry's Law Constant also correlated to the impact of the acidic modifiers on oligonucleotide ionization efficiency. Ionization enhancement effects were observed with hexafluoroisopropanol, and this effect was attributed to its low k(H,cc)(aq/gas) and moderate acidity. The comprehensive effects of both alkylamine and hexafluoroisoproapnol on the electrospray ionization desorption of oligonucleotides were also evaluated, and acid-base equilibrium was found to play a critical role in determining these effects.
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Affiliation(s)
- Buyun Chen
- Department of Pharmaceutical and Biomedical Science, College of Pharmacy, The University of Georgia, Athens, GA 30602-2352, USA
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