1
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Currie J, Dahlberg JR, Lundberg E, Thunberg L, Eriksson J, Schweikart F, Nilsson GA, Örnskov E. Stability indicating ion-pair reversed-phase liquid chromatography method for modified mRNA. J Pharm Biomed Anal 2024; 245:116144. [PMID: 38636193 DOI: 10.1016/j.jpba.2024.116144] [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: 11/24/2023] [Revised: 03/11/2024] [Accepted: 03/29/2024] [Indexed: 04/20/2024]
Abstract
Modified messenger RNA (mRNA) represents a rapidly emerging class of therapeutic drug product. Development of robust stability indicating methods for control of product quality are therefore critical to support successful pharmaceutical development. This paper presents an ion-pair reversed-phase liquid chromatography (IP-RPLC) method to characterise modified mRNA exposed to a wide set of stress-inducing conditions, relevant for pharmaceutical development of an mRNA drug product. The optimised method could be used for separation and analysis of large RNA, sized up to 1000 nucleotides. Column temperature, mobile phase flow rate and ion-pair selection were each studied and optimised. Baseline separations of the model RNA ladder sample were achieved using all examined ion-pairing agents. We established that the optimised method, using 100 mM Triethylamine, enabled the highest resolution separation for the largest fragments in the RNA ladder (750/1000 nucleotides), in addition to the highest overall resolution for the selected modified mRNA compound (eGFP mRNA, 996 nucleotides). The stability indicating power of the method was demonstrated by analysing the modified eGFP mRNA, upon direct exposure to heat, hydrolytic conditions and treatment with ribonucleases. Our results showed that the formed degradation products, which appeared as shorter RNA fragments in front of the main peak, could be well monitored, using the optimised method, and the relative stability of the mRNA under the various stressed conditions could be assessed.
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Affiliation(s)
- Jonathan Currie
- Innovation Strategies and External Liaison, Pharmaceutical Technology and Development, Operations & IT, AstraZeneca, Gothenburg, Sweden
| | - Jacob R Dahlberg
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ester Lundberg
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Thunberg
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonas Eriksson
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Fritz Schweikart
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Gunilla A Nilsson
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Eivor Örnskov
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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2
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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.
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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.
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3
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Separation of long-stranded RNAs by RP-HPLC using an octadecyl-based column with super-wide pores. ANAL SCI 2023; 39:417-425. [PMID: 36566342 PMCID: PMC9789886 DOI: 10.1007/s44211-022-00253-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022]
Abstract
Messenger ribonucleic acids (mRNAs) have been used in vaccines for various diseases and are attracting attention as a new pharmaceutical paradigm. The purification of mRNAs is necessary because various impurities, such as template DNAs and transcription enzymes, remain in the crude product after mRNA synthesis. Among the various purification methods, reversed-phase high-performance liquid chromatography (RP-HPLC) is currently attracting attention. Herein, we optimized the pore size of the packing materials, the mobile phase composition, and the temperature of the process; we also evaluated changes in the separation patterns of RNA strands of various lengths via RP-HPLC. Additionally, single-stranded (50-1000 nucleotides in length) and double-stranded (80-500 base pairs in length) RNAs were separated while their non-denatured states were maintained by performing the analysis at 60 °C using triethylammonium acetate as the mobile phase and octadecyl-based RNA-RP1 with super-wide pores (> 30 nm) as the column. Furthermore, impurities in a long-stranded RNA of several thousand nucleotides synthesized by in vitro transcription were successfully separated using an RNA-RP1 column. The columns used in this study are expected to separate various RNA strands and the impurities contained in them.
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4
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Rentel C, Gaus H, Bradley K, Luu N, Kolkey K, Mai B, Madsen M, Pearce M, Bock B, Capaldi D. Assay, Purity, and Impurity Profile of Phosphorothioate Oligonucleotide Therapeutics by Ion Pair-High-Performance Liquid Chromatography-Mass Spectrometry. Nucleic Acid Ther 2022; 32:206-220. [PMID: 35238617 DOI: 10.1089/nat.2021.0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relatively large molecular size, diastereoisomeric nature, and complex impurity profiles of therapeutic phosphorothioate oligonucleotides create significant analytical challenges for the quality control laboratory. To overcome the lack of selectivity inherent to traditional chromatographic approaches, an ion pair liquid chromatography-mass spectrometry (LCMS) method combining ultraviolet and mass spectrometry quantification was developed and validated for >35 different oligonucleotide drug substances and products, including several commercialized drugs. The selection of chromatographic and spectrometric conditions, data acquisition and processing, critical aspects of sample and buffer preparation and instrument maintenance, and results from method validation experiments are discussed.
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Affiliation(s)
- Claus Rentel
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Hans Gaus
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Kym Bradley
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Nhuy Luu
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Kimmy Kolkey
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Bao Mai
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Mark Madsen
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Megan Pearce
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Brandon Bock
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Daniel Capaldi
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
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5
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Akamatsu M, Yamashita T, Teramoto S, Huang Z, Lynch J, Toda T, Niu L, Kwak S. Testing of the therapeutic efficacy and safety of AMPA receptor RNA aptamers in an ALS mouse model. Life Sci Alliance 2022; 5:5/4/e202101193. [PMID: 35022247 PMCID: PMC8761490 DOI: 10.26508/lsa.202101193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
In motor neurons of sporadic amyotrophic lateral sclerosis (ALS) patients, the RNA editing at the glutamine/arginine site of the GluA2 subunit of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors is defective or incomplete. As a result, AMPA receptors containing the abnormally expressed, unedited isoform of GluA2 are highly Ca2+-permeable, and are responsible for mediating abnormal Ca2+ influx, thereby triggering motor neuron degeneration and cell death. Thus, blocking the AMPA receptor-mediated, abnormal Ca2+ influx is a potential therapeutic strategy for treatment of sporadic ALS. Here, we report a study of the efficacy and safety of two RNA aptamers targeting AMPA receptors on the ALS phenotype of AR2 mice. A 12-wk continuous, intracerebroventricular infusion of aptamers to AR2 mice reduced the progression of motor dysfunction, normalized TDP-43 mislocalization, and prevented death of motor neurons. Our results demonstrate that the use of AMPA receptor aptamers as a novel class of AMPA receptor antagonists is a promising strategy for developing an ALS treatment approach.
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Affiliation(s)
- Megumi Akamatsu
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takenari Yamashita
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sayaka Teramoto
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Neurology, Tokyo Medical University, Tokyo, Japan
| | - Zhen Huang
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, USA
| | - Janet Lynch
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, USA
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Li Niu
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, USA
| | - Shin Kwak
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan .,Department of Neurology, Tokyo Medical University, Tokyo, Japan
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6
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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.
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7
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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.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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8
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Jaremko W, Huang Z, Karl N, Pierce VD, Lynch J, Niu L. A kainate receptor-selective RNA aptamer. J Biol Chem 2020; 295:6280-6288. [PMID: 32161119 PMCID: PMC7212664 DOI: 10.1074/jbc.ra119.011649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/21/2020] [Indexed: 11/06/2022] Open
Abstract
Kainate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are two major, closely related receptor subtypes in the glutamate ion channel family. Excessive activities of these receptors have been implicated in a number of central nervous system diseases. Designing potent and selective antagonists of these receptors, especially of kainate receptors, is useful for developing potential treatment strategies for these neurological diseases. Here, we report on two RNA aptamers designed to individually inhibit kainate and AMPA receptors. To improve the biostability of these aptamers, we also chemically modified these aptamers by substituting their 2'-OH group with 2'-fluorine. These 2'-fluoro aptamers, FB9s-b and FB9s-r, were markedly resistant to RNase-catalyzed degradation, with a half-life of ∼5 days in rat cerebrospinal fluid or serum-containing medium. Furthermore, FB9s-r blocked AMPA receptor activity. Aptamer FB9s-b selectively inhibited GluK1 and GluK2 kainate receptor subunits, and also GluK1/GluK5 and GluK2/GluK5 heteromeric kainate receptors with equal potency. This inhibitory profile makes FB9s-b a powerful template for developing tool molecules and drug candidates for treatment of neurological diseases involving excessive activities of the GluK1 and GluK2 subunits.
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Affiliation(s)
- William Jaremko
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Zhen Huang
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Nicholas Karl
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Vincen D Pierce
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Janet Lynch
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Li Niu
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
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9
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A review on native and denaturing purification methods for non-coding RNA (ncRNA). J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:71-79. [PMID: 31071581 DOI: 10.1016/j.jchromb.2019.04.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
Abstract
Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.
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10
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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.
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Affiliation(s)
- Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95762, USA.
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11
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Baronti L, Karlsson H, Marušič M, Petzold K. A guide to large-scale RNA sample preparation. Anal Bioanal Chem 2018; 410:3239-3252. [PMID: 29546546 PMCID: PMC5937877 DOI: 10.1007/s00216-018-0943-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022]
Abstract
RNA is becoming more important as an increasing number of functions, both regulatory and enzymatic, are being discovered on a daily basis. As the RNA boom has just begun, most techniques are still in development and changes occur frequently. To understand RNA functions, revealing the structure of RNA is of utmost importance, which requires sample preparation. We review the latest methods to produce and purify a variation of RNA molecules for different purposes with the main focus on structural biology and biophysics. We present a guide aimed at identifying the most suitable method for your RNA and your biological question and highlighting the advantages of different methods. Graphical abstract In this review we present different methods for large-scale production and purification of RNAs for structural and biophysical studies.
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Affiliation(s)
- Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden
| | - Hampus Karlsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden
| | - Maja Marušič
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden.
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12
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Huang Z, Wen W, Wu A, Niu L. Chemically Modified, α-Amino-3-hydroxy-5-methyl-4-isoxazole (AMPA) Receptor RNA Aptamers Designed for in Vivo Use. ACS Chem Neurosci 2017; 8:2437-2445. [PMID: 28872832 DOI: 10.1021/acschemneuro.7b00211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glutamate ion channels have three subtypes, that is, α-amino-3-hydroxy-5-methyl-4-isoxazole (AMPA), kainate, and N-methyl-d-aspartate (NMDA) receptors. Excessive activity of these receptor subtypes either individually or collectively is involved in various neurological disorders. RNA aptamers as antagonists of these receptors are potential therapeutics. For developing aptamer therapeutics, the RNA aptamers must be chemically modified to become ribonuclease-resistant or stable in biological fluids. Using systematic evolution of ligands by exponential enrichment (SELEX) and a chemically modified library, prepared enzymatically (i.e., the library contains RNAs with 2'-fluoro modified nucleoside triphosphates or ATPs, CTPs and UTPs, but regular GTPs), we have isolated an aptamer. The short aptamer (69 nucleotides) FN1040s selectively inhibits the GluA1 and GluA2Qflip AMPA receptor subunits, whereas the full-length aptamer (101 nucleotides) FN1040 additionally inhibits GluK1, but not GluK2, kainate receptor, and GluN1a/2A and GluN1a/2B, the two major native NMDA receptors. The two aptamers show similar potency (2-4 μM) and are stable with a half-life of at least 2 days in serum-containing medium or cerebrospinal fluid. Therefore, these two aptamers are amenable for in vivo use.
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Affiliation(s)
- Zhen Huang
- Department of Chemistry and
Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222, United States
| | - Wei Wen
- Department of Chemistry and
Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222, United States
| | - Andrew Wu
- Department of Chemistry and
Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222, United States
| | - Li Niu
- Department of Chemistry and
Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222, United States
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13
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Jaremko WJ, Huang Z, Wen W, Wu A, Karl N, Niu L. Identification and characterization of RNA aptamers: A long aptamer blocks the AMPA receptor and a short aptamer blocks both AMPA and kainate receptors. J Biol Chem 2017; 292:7338-7347. [PMID: 28325839 PMCID: PMC5418036 DOI: 10.1074/jbc.m116.774752] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Indexed: 11/06/2022] Open
Abstract
AMPA and kainate receptors, along with NMDA receptors, represent different subtypes of glutamate ion channels. AMPA and kainate receptors share a high degree of sequence and structural similarities, and excessive activity of these receptors has been implicated in neurological diseases such as epilepsy. Therefore, blocking detrimental activity of both receptor types could be therapeutically beneficial. Here, we report the use of an in vitro evolution approach involving systematic evolution of ligands by exponential enrichment with a single AMPA receptor target (i.e. GluA1/2R) to isolate RNA aptamers that can potentially inhibit both AMPA and kainate receptors. A full-length or 101-nucleotide (nt) aptamer selectively inhibited GluA1/2R with a KI of ∼5 μm, along with GluA1 and GluA2 AMPA receptor subunits. Of note, its shorter version (55 nt) inhibited both AMPA and kainate receptors. In particular, this shorter aptamer blocked equally potently the activity of both the GluK1 and GluK2 kainate receptors. Using homologous binding and whole-cell recording assays, we found that an RNA aptamer most likely binds to the receptor's regulatory site and inhibits it noncompetitively. Our results suggest the potential of using a single receptor target to develop RNA aptamers with dual activity for effectively blocking both AMPA and kainate receptors.
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Affiliation(s)
- William J Jaremko
- From the Department of Chemistry and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Zhen Huang
- From the Department of Chemistry and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Wei Wen
- From the Department of Chemistry and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Andrew Wu
- From the Department of Chemistry and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Nicholas Karl
- From the Department of Chemistry and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
| | - Li Niu
- From the Department of Chemistry and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York 12222
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14
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Zhang Q, Lv H, Wang L, Chen M, Li F, Liang C, Yu Y, Jiang F, Lu A, Zhang G. Recent Methods for Purification and Structure Determination of Oligonucleotides. Int J Mol Sci 2016; 17:E2134. [PMID: 27999357 PMCID: PMC5187934 DOI: 10.3390/ijms17122134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures. The excellent features, such as high specificity and affinity for target proteins, small size, chemical stability, low immunogenicity, facile chemical synthesis, versatility in structural design and engineering, and accessible for site-specific modifications with functional moieties, make aptamers attractive molecules in the fields of clinical diagnostics and biopharmaceutical therapeutics. However, difficulties in purification and structural identification of aptamers remain a major impediment to their broad clinical application. In this mini-review, we present the recently attractive developments regarding the purification and identification of aptamers. We also discuss the advantages, limitations, and prospects for the major methods applied in purifying and identifying aptamers, which could facilitate the application of aptamers.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Chromatography, High Pressure Liquid/methods
- Chromatography, Ion Exchange/methods
- Chromatography, Reverse-Phase/methods
- Crystallography, X-Ray/methods
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/ultrastructure
- Electrophoresis, Gel, Two-Dimensional/methods
- Nuclear Magnetic Resonance, Biomolecular/methods
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Affiliation(s)
- Qiulong Zhang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Huanhuan Lv
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Lili Wang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Man Chen
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Fangfei Li
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Chao Liang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Yuanyuan Yu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Feng Jiang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Aiping Lu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Ge Zhang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
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15
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Qiao JQ, Liang C, Wei LC, Cao ZM, Lian HZ. Retention of nucleic acids in ion-pair reversed-phase high-performance liquid chromatography depends not only on base composition but also on base sequence. J Sep Sci 2016; 39:4502-4511. [DOI: 10.1002/jssc.201600701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/04/2016] [Accepted: 09/28/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Jun-qin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis; Nanjing University; Nanjing China
| | - Chao Liang
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis; Nanjing University; Nanjing China
| | - Lan-chun Wei
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis; Nanjing University; Nanjing China
| | - Zhao-ming Cao
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis; Nanjing University; Nanjing China
| | - Hong-zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis; Nanjing University; Nanjing China
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16
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Björkbom A, Lelyveld VS, Zhang S, Zhang W, Tam CP, Blain JC, Szostak JW. Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms. J Am Chem Soc 2015; 137:14430-8. [PMID: 26495937 PMCID: PMC7547889 DOI: 10.1021/jacs.5b09438] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass spectrometry (MS) is a powerful technique for characterizing noncanonical nucleobases and other chemical modifications in small RNAs, yielding rich chemical information that is complementary to high-throughput indirect sequencing. However, mass spectra are often prohibitively complex when fragment ions are analyzed following either solution phase hydrolysis or gas phase fragmentation. For all but the simplest cases, ions arising from multiple fragmentation events, alternative fragmentation pathways, and diverse salt adducts frequently obscure desired single-cut fragment ions. Here we show that it is possible to take advantage of predictable regularities in liquid chromatographic (LC) separation of optimized RNA digests to greatly simplify the interpretation of complex MS data. A two-dimensional analysis of extracted compound chromatograms permits straightforward and robust de novo sequencing, using a novel Monte Carlo algorithm that automatically generates bidirectional paired-end reads, pinpointing the position of modified nucleotides in a sequence. We demonstrate that these advances permit routine LC-MS sequencing of RNAs containing noncanonical nucleotides, and we furthermore examine the applicability of this approach to the study of oligonucleotides containing artificial modifications as well as those commonly observed in post-transcriptionally modified RNAs.
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Affiliation(s)
- Anders Björkbom
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States.,Åbo Akademi University , Department of Biosciences, Artillerigatan 6, FI-20520 Åbo, Finland
| | - Victor S Lelyveld
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Shenglong Zhang
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Weicheng Zhang
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Chun Pong Tam
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - J Craig Blain
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States
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17
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Kawamura K, Ikoma K, Maruoka Y, Hisamoto H. Separation Behavior of Short Oligonucleotides by Ion-Pair Reversed-Phase Capillary Liquid Chromatography Using a Silica-Based Monolithic Column Applied to Simple Detection of SNPs. Chromatographia 2015. [DOI: 10.1007/s10337-015-2855-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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18
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Huang Z, Lin CY, Jaremko W, Niu L. HPLC purification of RNA aptamers up to 59 nucleotides with single-nucleotide resolution. Methods Mol Biol 2015; 1297:83-93. [PMID: 25895997 DOI: 10.1007/978-1-4939-2562-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An RNA sample is usually heterogeneous. RNA heterogeneity refers to difference in length or size (i.e., number of nucleotides [nt]), sequence, or alternative but coexisting conformations. Separation and purification of RNA is generally required for investigating the structure and function of RNA, such as RNA catalysis and RNA structure determination by nuclear magnetic resonance or crystallography. Separation and purification of RNA is also required for using RNAs as functional probes and therapeutics as well as building blocks for RNA nanoparticles. Previously established protocols are limited in separating RNAs longer than 25 nt by single-nucleotide resolution. When the length of RNAs becomes longer, single-nucleotide separation of RNAs becomes more challenging. Here we describe protocols, by the use of ion-pair, reverse-phase high-performance liquid chromatography (HPLC), to extend our ability to separate regular RNAs up to 59 nt with single-nucleotide resolution. For chemically modified RNAs at 2' positions on the ribose, we can resolve RNAs of similar sizes even with a 26 Da difference. This is much less than 320 Da, an average single-nucleotide molecular weight difference.
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Affiliation(s)
- Zhen Huang
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA
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19
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Gong L, McCullagh JSO. Comparing ion-pairing reagents and sample dissolution solvents for ion-pairing reversed-phase liquid chromatography/electrospray ionization mass spectrometry analysis of oligonucleotides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:339-350. [PMID: 24395501 DOI: 10.1002/rcm.6773] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/19/2013] [Accepted: 10/20/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE A sensitive and selective liquid chromatography/mass spectrometry (LC/MS) method is essential for quality control of synthetic oligonucleotides. However, researchers are still searching for improvements to ion-pairing reagents for ion-pairing reversed-phase LC/MS. This study performed a comprehensive comparison of six ion-pairing reagents to determine their performance as mobile phase modifiers for oligonucleotide LC/MS. METHODS The study was performed using a Waters ultra-performance liquid chromatography (UPLC®) system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer by using a UPLC® OST column (2.1 mm × 100 mm, 1.7 µm). Buffer systems containing ion-pairing reagents (triethylamine, tripropylamine, hexylamine, N,N-dimethylbutylamine, dibutylamine, N,N-diisopropylethylamine) and hexafluoro-2-propanol were compared by measuring the adduct ion formation, chromatographic separation, and MS signal intensity of four oligonucleotides (10mer to 40mer). The effect of dissolution solvents on MS signal intensity and adduct ion formation was also investigated. RESULTS Results showed that the type of dissolution solvent can have a signficiant impact on adduct ion formation with oligonucleotides. Results also showed that the maximum separation for small, medium and large oligonucleotides occured when using tripropylamine, N,N-dimethylbutylamine, and dibutylamine, respectively. However, on average 15 mM hexylamine and 50 mM hexafluoro-2-propanol provided the best chromtatographic performance (resolution values: 14.1 ± 0.34, 11.0 ± 0.17, and 6.4 ± 0.11 for the pairs of oligonucleotides T10 & T15, T15 & T25, and T25 & T40, respectively (3 replicates)). CONCLUSIONS The impact of dissolution solvent on the MS signal of oligonucleotides depends on the type of ion-pairing reagent. Buffer combining 15 mM hexylamine and 50 mM hexafluoro-2-propanol produced the highest overall performance for oligonucleotides (10mer to 40mer) with respect to chromatographic resolution and mass detection.
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Affiliation(s)
- Lingzhi Gong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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20
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Flores JK, Walshe JL, Ataide SF. RNA and RNA–Protein Complex Crystallography and its Challenges. Aust J Chem 2014. [DOI: 10.1071/ch14319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA biology has changed completely in the past decade with the discovery of non-coding RNAs. Unfortunately, obtaining mechanistic information about these RNAs alone or in cellular complexes with proteins has been a major problem. X-ray crystallography of RNA and RNA–protein complexes has suffered from the major problems encountered in preparing and purifying them in large quantity. Here, we review the available techniques and methods in vitro and in vivo used to prepare and purify RNA and RNA–protein complex for crystallographic studies. We also discuss the future directions necessary to explore the vast number of RNA species waiting for their atomic-resolution structure to be determined.
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21
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Lin CY, Huang Z, Jaremko W, Niu L. High-performance liquid chromatography purification of chemically modified RNA aptamers. Anal Biochem 2013; 449:106-8. [PMID: 24373999 DOI: 10.1016/j.ab.2013.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/11/2013] [Accepted: 12/16/2013] [Indexed: 12/16/2022]
Abstract
2'-Fluoro modified RNAs are useful as potential therapeutics and as special substrates for studying RNA function. 2'-Fluoro modified RNAs generally need to be purified after they are prepared either enzymatically or by solid-phase synthesis. Here we introduce a protocol by which 2'-fluoro modified RNAs with 57 and 58 nucleotides can be resolved and purified using ion-pair, reverse-phase high-performance liquid chromatography (HPLC). Because the size of our RNA samples is in the range of many known RNA aptamers of therapeutic values, our protocol should be generally useful.
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Affiliation(s)
- Chi-Yen Lin
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
| | - Zhen Huang
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
| | - William Jaremko
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
| | - Li Niu
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA.
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