1
|
Ozaki M, Kuwayama T, Shimotsuma M, Hirose T. Separation and purification of short-, medium-, and long-stranded RNAs by RP-HPLC using different mobile phases and C 18 columns with various pore sizes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1948-1956. [PMID: 38445900 DOI: 10.1039/d4ay00114a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Nucleic acids, which have been employed in medicines for various diseases, are attracting attention as a new pharmaceutical model. Depending on the target substances, nucleic acid medicines with various nucleic acid chain lengths (several tens of nucleotides [nt] to several thousands of nt) exist. The purification of synthesized nucleic acids is crucial as various impurities remain in the crude product after synthesis. Presently, reversed-phase high-performance liquid chromatography (RP-HPLC) represents an effective purification method for nucleic acids. However, the information regarding the HPLC conditions for separating and purifying nucleic acids of various chain lengths is insufficient. Thus, this technical note describes the separation and purification of short-, medium-, and long-stranded nucleic acids (several tens of nt to thousands of nt) by RP-HPLC with various mobile phases and octadecyl-based columns with various pore sizes, such as normal (9-12 nm), wide (30 nm), and super wide (>30 nm) pores.
Collapse
Affiliation(s)
- Makoto Ozaki
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tomomi Kuwayama
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Motoshi Shimotsuma
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tsunehisa Hirose
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| |
Collapse
|
2
|
Stoll D, Sylvester M, Meston D, Sorensen M, Maloney TD. Development of multiple heartcutting two-dimensional liquid chromatography with ion-pairing reversed-phase separations in both dimensions for analysis of impurities in therapeutic oligonucleotides. J Chromatogr A 2024; 1714:464574. [PMID: 38103311 DOI: 10.1016/j.chroma.2023.464574] [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] [Received: 09/07/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Oligonucleotides constitute an emerging and highly complex bioanalytical challenge and it is becoming increasingly clear that 1D methodologies are unable to fully resolve all possible impurities present in these samples. 2D-LC therefore constitutes a perfect solution wherein critical pairs can be sampled from a steep gradient 1D and separated in a shallower 2D gradient. Herein, we provide a facile 2D-LC method development approach to quickly generate high selectivity gradients utilizing ion pairing reverse phase (IPRP-IPRP). In particular we demonstrate how to iteratively generate a 12 % gradient from two training runs and then to utilize that data to predict retentions of analytes with a 2 % gradient with retention prediction errors as low as 3 and 11 %, respectively. This iterative method development workflow was applied to impurity profiling down to 1:1000 for the full-length product and phosphorothioate modified impurities. Additionally, we demonstrated the elucidation of critical pairs in complex crude pharmaceutical oligonucleotide samples by applying tailored high selectivity gradients in the second dimension. It was found that the iterative retention modeling approach allows fast and facile 2D-LC method development for complex oligonucleotide separations.
Collapse
Affiliation(s)
- Dwight Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, USA.
| | - Maria Sylvester
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, USA
| | - Daniel Meston
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, USA
| | - Matt Sorensen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Todd D Maloney
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| |
Collapse
|
3
|
Li F, Chen S, Studzińska S, Lämmerhofer M. Polybutylene terephthalate-based stationary phase for ion-pair-free reversed-phase liquid chromatography of small interfering RNA. Part 2: Use for selective comprehensive two-dimensional liquid chromatography. J Chromatogr A 2023; 1701:464069. [PMID: 37216850 DOI: 10.1016/j.chroma.2023.464069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/06/2023] [Accepted: 05/13/2023] [Indexed: 05/24/2023]
Abstract
With the increasing numbers of nucleic acid-based pharmaceuticals like antisense oligonucleotides (ASO), small interfering ribonucleic acid (siRNA) entering the market, research facilities, pharmaceutical industries and also regulatory authorities have been looking for efficient analytical methods for these synthetic oligonucleotides (ON). Besides of conventional one-dimensional (1D) reversed-phase liquid chromatography with or without ion-pairing (IP-RP-LC, RP-LC), hydrophilic liquid chromatography (HILIC) and mixed-mode chromatography (MMC), two-dimensional (2D) approaches combining two orthogonal chromatographic techniques also become more relevant due to the high structural complexity of oligonucleotides. Recently, we tested a polybutylene terephthalate(PBT)-based stationary phase under ion-pairing free RP mode for the liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS) analysis of siRNA (Patisiran). In this study, retention profile and chromatographic orthogonality, respectively, were compared to other LC-modes like HILIC, IP-RPLC, another ion-pair free cholesterol-bonded RPLC and MMC considering their normalized retention times. Finally, because of higher orthogonality, the ion-pairing free PBT-bonded RPLC as first dimension (1D) was hyphenated with HILIC in the second dimension (2D) in a selective comprehensive 2D-LC setup leading to an enhanced resolution for peak purity evaluation of the main ON entities.
Collapse
Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Shenkai Chen
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Sylwia Studzińska
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarin Str., PL-87-100 Toruń, Poland
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| |
Collapse
|
4
|
Rahman Chowdhury T, Taufiq T, Ishida K, Ariful Islam M, Kasahara Y, Osawa T, Obika S. Synthesis and biophysical properties of tetravalent PEG-conjugated antisense oligonucleotide. Bioorg Med Chem 2023; 78:117149. [PMID: 36587552 DOI: 10.1016/j.bmc.2022.117149] [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] [Received: 11/16/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
This study was aimed at developing a novel platform for tetravalent conjugation of 4-arm polyethylene glycol (PEG) with an antisense oligonucleotide (ASO). The ASO technology has several limitations, such as low cellular uptake, poor nuclease stability, and short half-life. PEG-conjugated ASOs may result in an improvement in the pharmacokinetic behavior of the drug. Moreover, PEGylation can reduce enzymatic degradation and renal excretion of the conjugates, thereby, increasing its blood stability and retention time. In this study, we successfully synthesized PEG-ASO conjugate consisting of 4-arm-PEG and four molecules of ASO (4-arm-PEG-tetra ASO). Its hybridization ability with complementary RNA, enzymatic stability, and in vitro gene silencing ability were evaluated. No significant difference in hybridization ability was observed between 4-arm-PEG-tetra ASO and the parent ASO. In addition, gene silencing activity of the 4-arm-PEG-tetra ASO was observed in vitro. However, the in vitro activity of the 4-arm-PEG-tetra ASO was slightly reduced as that of the parent ASO. Moreover, the 4-arm-PEG-tetra ASO showed appreciable stability in cellular extract, suggesting that it hybridizes with mRNA in its intact form, without being cleaved in the cell, and exhibits ASO activity.
Collapse
Affiliation(s)
- Taslima Rahman Chowdhury
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Tahia Taufiq
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenta Ishida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University (OTRI), 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
5
|
Studzińska S, Li F, Szumski M, Buszewski B, Lämmerhofer M. Cholesterol Stationary Phase in the Separation and Identification of siRNA Impurities by Two-Dimensional Liquid Chromatography-Mass Spectrometry. Int J Mol Sci 2022; 23:ijms232314960. [PMID: 36499291 PMCID: PMC9738757 DOI: 10.3390/ijms232314960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The aim of this research was to develop a simple and efficient ion-pair reagent-free chromatographic method for the separation and qualitative determination of oligonucleotide impurities, exemplified by synthesis of raw products of the two single strands of patisiran siRNA. The stationary phases with mixed hydrophobic/hydrophilic properties (cholesterol and alkylamide) were firstly used for this purpose with reversed-phased high-performance liquid chromatography. Several different chromatographic parameters were tested for their impact on impurities separation: type, concentration, pH of salt, as well as organic solvent type in the mobile phase. The pH was the most influential factor on the separation and signal intensities in mass spectrometry detection. Finally, the optimized method included the application of cholesterol stationary phase, with mobile phase containing 20 mM ammonium formate (pH 6.5) and methanol. It allowed good separation and the identification of most impurities within 25 min. Since not all closely related impurities could be fully resolved from the main peak in this oligonucleotide impurity profiling, two-dimensional liquid chromatography was used for peak purity determination of the target oligonucleotides. The Ethylene Bridged Hybrid (BEH) Amide column in hydrophilic interaction liquid chromatography was applied in the second dimension, allowing additional separation of three closely related impurities.
Collapse
Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., 87-100 Toruń, Poland
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +48-56-6114753
| | - Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michał Szumski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 4 Wilenska St., 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., 87-100 Toruń, Poland
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| |
Collapse
|
6
|
Lokras A, Chakravarty A, Rades T, Christensen D, Franzyk H, Thakur A, Foged C. Simultaneous quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems. Int J Pharm 2022; 626:122171. [PMID: 36070841 DOI: 10.1016/j.ijpharm.2022.122171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Robust, sensitive, and versatile analytical methods are essential for quantification of RNA drug cargos loaded into nanoparticle-based delivery systems. However, simultaneous quantification of multiple RNA cargos co-loaded into nanoparticles remains a challenge. Here, we developed and validated the use of ion-pair reversed-phase high-performance liquid chromatography combined with UV detection (IP-RP-HPLC-UV) for simultaneous quantification of single- and double-stranded RNA cargos. Complete extraction of RNA cargo from the nanoparticle carrier was achieved using a phenol:chloroform:isoamyl alcohol mixture. Separations were performed using either a C18 or a PLRP-S column, eluted with 0.1 M triethylammonium acetate (TEAA) solution as ion-pairing reagent (eluent A), and 0.1 M TEAA containing 25 % (v/v) CH3CN as eluent B. These methods were applied to quantify mRNA and polyinosinic:polycytidylic acid co-loaded into lipid-polymer hybrid nanoparticles, and single-stranded oligodeoxynucleotide donors and Alt-R CRISPR single guide RNAs co-loaded into lipid nanoparticles. The developed methods were sensitive (limit of RNA quantification < 60 ng), linear (R2 > 0.997), and accurate (≈ 100 % recovery of RNA spiked in nanoparticles). Hence, the present study may facilitate convenient quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems.
Collapse
Affiliation(s)
- Abhijeet Lokras
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Akash Chakravarty
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Thomas Rades
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Dennis Christensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen Ø, Denmark
| | - Aneesh Thakur
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Camilla Foged
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark.
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Evaluating the interplay among stationary phases/ion-pairing reagents/sequences for liquid chromatography mass spectrometry analysis of oligonucleotides. Anal Biochem 2021; 625:114194. [PMID: 33910045 DOI: 10.1016/j.ab.2021.114194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 03/27/2021] [Indexed: 11/22/2022]
Abstract
The correlation among stationary phases, ion-pairing reagents (IPR) and sequences for ion-pair reversed-phase liquid chromatography mass spectrometry (IP-RP LC-MS) analysis of oligonucleotide (ODN) remains unclear. The present study aimed to evaluate such correlation using particle-packed C18 columns in order to search for the optimal combination among them. Five C18 columns packed with core-shell silica, polymer, porous silica and hybrid particles, respectively, were evaluated for the analysis of synthetic and chemically modified ODNs with six different IPRs. Our results showed that silica-based porous particles, compared to other particles, retained ODN the strongest no matter which IPR was used. Meanwhile, among the six IPRs hexylamine (HA) produced the longest retention for all ODNs, regardless of the types of C18 particles. For the separation of ODNs, C18 columns performed similarly under identical LC conditions. However, the separation ability of C18 columns is highly dependent on the type of IPR and ODN sequences. Moreover, the type of particles has little impact on the signals of ODNs for the majority of synthetic sequences, but such impact could be dramatic for chemically modified sequences. On the other hand, both the type of IPR and ODN sequence have a significant effect on MS signals for synthetic and chemically modified ODNs.
Collapse
|
9
|
Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
Collapse
Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | | |
Collapse
|
10
|
Bartlett MG, Omuro S. Evaluation of alkylamines and stationary phases to improve LC-MS of oligonucleotides. Biomed Chromatogr 2020; 35:e5045. [PMID: 33283300 DOI: 10.1002/bmc.5045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022]
Abstract
This study evaluated four bridged-ethylene hybrid (BEH) columns containing C18 (130 Å), peptide C18 (300 Å), phenyl, or a mixed-mode charged surface hybrid (CSH C18 ) using a wide range of antisense oligonucleotide therapeutics. The BEH C18 , peptide, and phenyl columns were all capable of providing significant retention of oligonucleotide samples across multiple ion-pairing systems using alkylamines and 1,1,1,3,3,3,-hexafluoroisopropanol (HFIP). The retention of the oligonucleotides varied depending on the choice of alkylamine, with the order of retention being dimethylcyclohexylamine > diisopropylethylamine > triethylamine. The selectivity of these columns for several closely eluting impurities was similar. Although overall the C18 , peptide, and phenyl columns were all found to be capable of analyzing oligonucleotide therapeutics, the phenyl column was found to be the most retentive and the C18 column provided the best peak shape. The CSH C18 column was found to be degraded by the alkylamine-HFIP mobile phase despite the mobile phase being within the pH stability range of the column.
Collapse
Affiliation(s)
- Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - Shogo Omuro
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
11
|
Kučera R, Sčensná A, Miletín M, Zimčík P. The chromatographic behaviour of new double-labelled oligodeoxynucleotide probes containing azaphthalocyanine dye as a quencher with respect to evaluation of their purity. Biomed Chromatogr 2020; 35:e5033. [PMID: 33226652 DOI: 10.1002/bmc.5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/12/2020] [Accepted: 11/19/2020] [Indexed: 11/07/2022]
Abstract
The influence of experimental conditions on chromatographic behaviour of promising oligodeoxynucleotide double-labelled molecular probes containing an azaphthalocyanine macrocycle as a perspective dark quencher was studied. A recently introduced new stationary phase based on styrene-divinylbenzene copolymer was tested. The planar and hydrophobic structure of the azaphthalocyanine is considerably different from those of currently used fluorophores and quenchers. Thus, the most challenging issue was the separation of the double-labelled probe from its main impurity represented by a mono-labelled probe, containing only the azaphthalocyanine macrocycle. The absorbance measurement cannot simply determine this impurity, and its presence fundamentally compromises the biological assay. The commonly used gradient elution was not suitable and isocratic conditions seemed to be more appropriate. The azaphthalocyanine moiety influences the properties of the modified oligodeoxynucleotides substantially, and thus their chromatographic behaviour was determined predominantly by this quencher. Acetonitrile was the preferred organic solvent for the analysis of probes containing the azaphthalocyanine quencher and the effect of ion-pairing reagents was dependent on the probe structure. The temperature seemed to be an effective parameter for fine-tuning of the separation and mass transfer improvement. Generally, our findings could be helpful in method development for purity evaluation of double-labelled oligodeoxynucleotide probes and semipreparative methods.
Collapse
Affiliation(s)
- Radim Kučera
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Anna Sčensná
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Miroslav Miletín
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Petr Zimčík
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| |
Collapse
|
12
|
Li F, Su X, Bäurer S, Lämmerhofer M. Multiple heart-cutting mixed-mode chromatography-reversed-phase 2D-liquid chromatography method for separation and mass spectrometric characterization of synthetic oligonucleotides. J Chromatogr A 2020; 1625:461338. [PMID: 32709362 DOI: 10.1016/j.chroma.2020.461338] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/20/2023]
Abstract
Until today, ion-pair reversed-phase chromatography is still the dominating method for analytical characterization of synthetic oligonucleotides. Its hyphenation with mass spectrometry, however, has some drawbacks such as ion-suppression in electrospray ionization. To overcome this problem, we present in this work a multiple heart-cutting (MHC) two-dimensional liquid chromatography (2D-LC) method with ultra-violet (UV) and electrospray ionization (ESI) mass spectrometry (MS) detection. A reversed-phase/weak anion-exchange (RP/WAX) stationary phase in the first dimension (1D) provides the selectivity for separation of structurally closely related oligonucleotide sequences and deletions (shortmers), respectively, using a mixed pH/triethylammonium phosphate buffer gradient at constant organic modifier content. Heart cuts of the oligonucleotide peaks are transferred to the second dimension (2D) via a multiple heart-cutting valve which is equipped with two loop decks. The 2D RP column is used for desalting via a diverter valve. Active solvent modulation enables to refocus the oligonucleotide peak into a sharp zone by 2D RP entirely free of non-volatile buffer components and ion-pair agents. Oligonucleotides can thus be sensitively detected by ESI-QTOF-MS under MS-compatible conditions.
Collapse
Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaoli Su
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefanie Bäurer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| |
Collapse
|
13
|
Simultaneous separation of small interfering RNA and lipids using ion-pair reversed-phase liquid chromatography. J Chromatogr A 2019; 1601:145-154. [DOI: 10.1016/j.chroma.2019.04.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 11/23/2022]
|
14
|
Kanavarioti A. HPLC methods for purity evaluation of man-made single-stranded RNAs. Sci Rep 2019; 9:1019. [PMID: 30705318 PMCID: PMC6356003 DOI: 10.1038/s41598-018-37642-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
Synthetic RNA oligos exhibit purity decreasing as a function of length, because the efficiency of the total synthesis is the numerical product of the individual step efficiencies, typically below 98%. Analytical methods for RNAs up to the 60 nucleotides (nt) have been reported, but they fall short for purity evaluation of 100nt long, used as single guide RNA (sgRNA) in CRISPR technology, and promoted as pharmaceuticals. In an attempt to exploit a single HPLC method and obtain both identity as well as purity, ion-pair reversed-phase chromatography (IP-RP) at high temperature in the presence of an organic cosolvent is the current analytical strategy. Here we report that IP-RP is less suitable compared to the conventional ion-exchange (IEX) for analysis of 100nt RNAs. We demonstrate the relative stability of RNA in the denaturing/basic IEX mobile phase, lay out a protocol to determine the on-the-column stability of any RNA, and establish the applicability of this method for quality testing of sgRNA, tRNA, and mRNA. Unless well resolving HPLC methods are used for batch-to-batch evaluation of man-made RNAs, process development will remain shortsighted, and observed off-target effects in-vitro or in-vivo may be partially related to low purity and the presence of shorter sequences.
Collapse
Affiliation(s)
- Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95762, USA.
| |
Collapse
|
15
|
Li N, El Zahar NM, Saad JG, van der Hage ERE, Bartlett MG. Alkylamine ion-pairing reagents and the chromatographic separation of oligonucleotides. J Chromatogr A 2018; 1580:110-119. [PMID: 30409418 DOI: 10.1016/j.chroma.2018.10.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/11/2018] [Accepted: 10/19/2018] [Indexed: 11/17/2022]
Abstract
Alkylamines are commonly used to improve both chromatographic and mass spectral performance of electrospray ionization liquid chromatography mass spectrometry based methods for the analysis of oligonucleotides. Recently several new alkylamines have been introduced to enhance the electrospray mass spectral response for oligonucleotides; however, the chromatographic properties of these new alkylamines have not been rigorously assessed. We have investigated the retention, peak width, resolution and general chromatographic performance of fifteen different alkylamines for the separation of a model DNA, RNA and an antisense therapeutic oligonucleotide. Eleven of the fifteen alkylamines were shown to provide similar chromatographic performance across all three classes of oligonucleotides. Based on these findings, a model for the mechanism of retention of oligonucleotides using alkylamines and hexafluoroisopropanol mobile phases is proposed. Depending on the concentrations of alkylamines and pH adjustment, oligonucleotides can be retained by micellar chromatography and not the generally held ion-pairing mechanism. This conclusion is supported by light scattering, transmission electron microscopy and ion mobility experiments detecting three micron aggregates in the mobile phase at concentrations that are routinely used for LC-MS analysis of oligonucleotides. These aggregates are not detected at lower alkylamine concentrations where the retention mechanism follows an ion-pairing mechanism. The formation of these aggregates appears to be dependent on the pH of the mobile phase.
Collapse
Affiliation(s)
- Ning Li
- Department of Pharmaceutical Analysis, School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, China; Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA
| | - N M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abassia, Cairo, 11566, Egypt
| | - Jack G Saad
- Micromeritics Instrument Company, 4356 Communications Drive, Norcross, GA, 30093, USA
| | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA.
| |
Collapse
|
16
|
Sasaki T, Kudalkar SN, Bertoletti N, Anderson KS. DRONE: Direct Tracking of DNA Cytidine Deamination and Other DNA Modifying Activities. Anal Chem 2018; 90:11735-11740. [PMID: 30256094 PMCID: PMC6410358 DOI: 10.1021/acs.analchem.8b01405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enzymes that catalyze DNA modifying activities including cytidine deamination and cytosine methylation play important biological roles and have been implicated pathologically in diseases such as cancer. Here, we report Direct Resolution of ONE dalton difference (DRONE), an ultra high performance liquid chromatography (UHPLC)-based analytical method to track a single dalton change in the cytosine-to-uracil conversion catalyzed by the human apolipoprotein B m-RNA editing catalytic polypeptide-like 3 (APOBEC3) cytidine deaminases, implicated in cancer and antiviral defense. Additionally, we demonstrate broad applicability by tracking other important DNA modifications and assessing epigenetic enzyme inhibition. We have extended our methodology to obtain data on two distinct deamination events in the same oligonucleotide substrate designed from a putative APOBEC substrate, diversifying the utility of the described method. DRONE provides an important foundation for in-depth analysis of DNA-modifying enzymes and versatile detection of novel DNA modifications of interest.
Collapse
Affiliation(s)
- Tomoaki Sasaki
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| | - Shalley N. Kudalkar
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| | - Karen S. Anderson
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| |
Collapse
|
17
|
Li L, Qin Y, Ma B, Cui H, Qiao P, Jiang H, Zhang M. Direct and simultaneous determination of methionine sulfoxide and pyroglutamic acid impurities in Compound Amino Acid Injection-18 AA by ion-pair reversed-phase HPLC. SEPARATION SCIENCE PLUS 2018. [DOI: 10.1002/sscp.201800059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Li Li
- Kangda College of Nanjing Medical University; Lianyungang China
| | - Yaru Qin
- Kangda College of Nanjing Medical University; Lianyungang China
| | - Bingyuan Ma
- Kangda College of Nanjing Medical University; Lianyungang China
| | - Hongyan Cui
- Kangda College of Nanjing Medical University; Lianyungang China
| | - Ping Qiao
- Kangda College of Nanjing Medical University; Lianyungang China
| | - He Jiang
- Kangda College of Nanjing Medical University; Lianyungang China
| | - Ming Zhang
- Kangda College of Nanjing Medical University; Lianyungang China
| |
Collapse
|
18
|
Li L, Leone T, Foley JP, Welch CJ. Separation of small interfering RNA stereoisomers using reversed-phase ion-pairing chromatography. J Chromatogr A 2017; 1500:84-88. [DOI: 10.1016/j.chroma.2017.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/25/2022]
|
19
|
Studzińska S, Bocian S, Siecińska L, Buszewski B. Application of phenyl-based stationary phases for the study of retention and separation of oligonucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1060:36-43. [PMID: 28595118 DOI: 10.1016/j.jchromb.2017.05.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/15/2017] [Accepted: 05/27/2017] [Indexed: 12/11/2022]
Abstract
The main goal of our work was to apply three different phenyl-bonded stationary phases in ion pair chromatography for the analysis of synthetic oligonucleotides of various sequences. The influence of the stationary phase structure and the impact of ion-pairing reagent concentration on the retention of oligonucleotides were tested. Moreover the influence of oligonucleotide sequence on their interactions with phenyl-based stationary phases was also investigated. Such complex studies for analysis of oligonucleotides with these adsorbents were done for the first time. Investigations were implemented in the Quantitative Structure Retention Relationships analysis in order to improve the discussion on the retention mechanism of analyzed compounds. The retention of oligonucleotides was the lowest for polar embedded phenyl stationary phase, however its selectivity was high and allowed for complete separation of studied compounds in the shortest time. It was shown that the low retention factor value was observed for oligonucleotides forming secondary structures, such as hairpin loops. Moreover obtained data showed that except for electrostatic and hydrophobic interactions, π-π also influences on the retention mechanism. These interactions cause higher retention factor values for phenyl-based stationary phases compared to octadecyl ones.
Collapse
Affiliation(s)
- Sylwia Studzińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland.
| | - Szymon Bocian
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Lena Siecińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland
| |
Collapse
|
20
|
Application of a cholesterol stationary phase in the analysis of phosphorothioate oligonucleotides by means of ion pair chromatography coupled with tandem mass spectrometry. Talanta 2016; 154:270-7. [PMID: 27154674 DOI: 10.1016/j.talanta.2016.03.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 12/14/2022]
Abstract
The main aim of this study was the investigation of the influence of several ion pair reagents towards both the retention and the mass spectrometry sensitivity of phosphorothioate oligonucleotides. A cholesterol stationary phase was applied for the first time in the analysis of this group of compounds. The mobile phase composition was modified by changing the concentration and the type of amines and acetates or 1,1,1,3,3,3-hexafluoroisopropanol. It has been shown that the increase of amines concentration results in the retention factor increase for each oligonucleotide, on each adsorbent. The only exception was the mobile phase composed of triethylamine and 1,1,1,3,3,3-hexafluoroisopropanol. This is a consequence of interactions taking place between a cholesterol molecule and an alcohol. This effect was convenient when the mass spectrometry detection was applied, since it allowed an increase in the sensitivity. Moreover, optimization of the mobile phase composition and its impact on the efficiency of ionization process and on the sensitivity in mass spectrometry were also presented. The optimization of this new method, based on cholesterol stationary phase coupled with mass spectrometry detection, was finally applied for the determination of phosphorothioate oligonucleotides impurity in a real sample.
Collapse
|