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Bender V, Fuchs L, Süss R. RP-HPLC-CAD method for the rapid analysis of lipids used in lipid nanoparticles derived from dual centrifugation. Int J Pharm X 2024; 7:100255. [PMID: 38766478 PMCID: PMC11101883 DOI: 10.1016/j.ijpx.2024.100255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The use of lipids as suitable excipients for drug carrier systems has been established for years. Liposomes or lipid nanoparticles (LNPs) in general have been shown capable of delivering both hydrophilic and hydrophobic drugs. The Covid-19 pandemic and the resulting vaccines have significantly increased interest in the potential for these lipid-based systems, which can carry different types of therapeutic RNAs. LNPs used for the transfection of RNA are usually a multi-component mixture of phospholipids and other lipids. Essential components are positively charged or ionizable lipids such as DOTAP or SM-102, but also uncharged helper lipids such as cholesterol, DOPE, DSPC, DMG-PEG2000 or DSPE-PEG2000. Due to the differences in charge, simultaneous detection is a challenge. Here, we present a reversed-phase high-performance liquid chromatography charged-aerosol-detector method (RP-HPLC-CAD method) using a C-18 column for the simultaneous determination of charged and uncharged lipids. Our method has been validated according to the ICH-Q2 (R2) guideline for accuracy, precision, specificity and working range, including the limit of detection (LOD) and quantification (LOQ), as well as the calibration range. We were able to show satisfactory results in both precision and accuracy. The working range also shows great potential with a calibration range from 9.375 to 1000 μg/ml, LODs <1.85 μg/ml and LOQs <6.16 μg/ml. This method represents a fast and reproducible procedure for quantifying the lipids mentioned. In combination with the novel approach for the production of LNPs using dual centrifugation (DC), it offers the possibility of extremely rapid production of RNA-loaded LNPs, and the immediate analysis for their lipid components.
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Affiliation(s)
- Valentin Bender
- Department of Pharmaceutics, Institute of Pharmaceutical Sciences, University of Freiburg, Sonnenstraße 5, 79104 Freiburg, Germany
| | - Leon Fuchs
- Department of Pharmaceutics, Institute of Pharmaceutical Sciences, University of Freiburg, Sonnenstraße 5, 79104 Freiburg, Germany
| | - Regine Süss
- Department of Pharmaceutics, Institute of Pharmaceutical Sciences, University of Freiburg, Sonnenstraße 5, 79104 Freiburg, Germany
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2
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Togawa H, Okubo T, Nonaka Y, Yamaguchi T, Obika S. Retention behavior of short double-stranded oligonucleotide and its potential impurities by anion-exchange chromatography under non-denaturing conditions. J Chromatogr A 2023; 1691:463808. [PMID: 36706652 DOI: 10.1016/j.chroma.2023.463808] [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: 11/17/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
Small interfering RNA (siRNA), consisting of two complementary single-stranded RNAs with overhanging bases, is being adopted as a potent and specific inhibitor of target gene expression. However, non-duplexed single strands and undesired double strands composed of impurities (e.g., n-1 mer) could be produced in addition to the target double strand in the siRNA manufacturing process. Compared to the liquid chromatography analysis of single strands, the analysis of the duplexes under non-denaturing conditions is challenging, since restricted chromatographic conditions are required to maintain the Watson-Crick hydrogen bonds. This study reports the analysis of double-stranded oligomers having approximately 20 base pairs with some overhanging bases as non-denatured forms by anion-exchange chromatography (AEX). Optimization of the chromatographic conditions could potentially achieve the adequate separation of excess single strands from the double strand. Non-optimal duplexes, such as duplexes with long overhangs or bulge structures, were prepared by intentionally deleting terminal or middle nucleotide(s) of either the sense or the antisense strand, and these non-optimal duplexes were eluted at different retention times in most of the cases. Interestingly, under alkaline chromatographic conditions (pH 9.0), non-optimal duplexes containing a shortmer tended to exhibit a stronger retention than their parent duplexes, although they possessed a less negative charge. This study demonstrated some retention behavior of double strands with overhangs by AEX under non-denaturing conditions.
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Affiliation(s)
- Hiroyuki Togawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takashi Okubo
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Yumi Nonaka
- CERI Kurume, Chemicals Evaluation and Research Institute, Japan, 3-2-7 Miyanojin, Kurume, Fukuoka 839-0801, Japan
| | - Takao Yamaguchi
- 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.
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Talap J, Zhao J, Shen M, Song Z, Zhou H, Kang Y, Sun L, Yu L, Zeng S, Cai S. Recent advances in therapeutic nucleic acids and their analytical methods. J Pharm Biomed Anal 2021; 206:114368. [PMID: 34571322 DOI: 10.1016/j.jpba.2021.114368] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022]
Abstract
Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.
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Affiliation(s)
- Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jing Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zihan Song
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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5
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Goyon A, Yehl P, Zhang K. Characterization of therapeutic oligonucleotides by liquid chromatography. J Pharm Biomed Anal 2020; 182:113105. [PMID: 32004766 DOI: 10.1016/j.jpba.2020.113105] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/21/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022]
Abstract
Marketed therapies in the pharmaceutical landscape are rapidly evolving and getting more diverse. Small molecule medicines have dominated in the past while antibodies have grown dramatically in recent years. However, the failure of traditional small and large molecules in accessing certain targets has led to increased R&D efforts to develop alternative modalities. Therapeutic oligonucleotides (ONs) can accurately be directed against their ribonucleic acid (RNA) target and represent a promising approach in previously untreated diseases. Established automated synthesis of ONs coupled with chemical improvements and the advance of new drug delivery technologies has recently brought ONs to a heightened level of interest. The first part of the present review describes the different classes of oligonucleotides, namely antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA (miRNA), aptamer and immunostimulatory ON, with a focus on their delivery systems relevant for future analytical characterization. The second part reviews the typical impurities in therapeutic ON products. The third part discusses the use of historical methods anion exchange chromatography (AEX), ion-pair reversed phase liquid chromatography (IP-RP), mixed-mode chromatography (MMC) and recent analytical methodologies of hydrophilic interaction liquid chromatography (HILIC), two-dimensional liquid chromatography (2D-LC) mass spectrometry for the characterization of ASO and siRNA modalities. The effects of physicochemical properties of RPLC columns and ion-pair agents on ON separation are specifically addressed with possible future directions for method development provided. Finally, some innovative analytical developments for the analysis of siRNAs and their delivery materials to pave the way toward the use of multi-attribute methods in the near future are discussed.
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Affiliation(s)
- Alexandre Goyon
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Peter Yehl
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Ghodke PP, Guengerich FP. Impact of 1, N 6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair. J Biol Chem 2020; 295:6092-6107. [PMID: 32213600 DOI: 10.1074/jbc.ra120.012829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
Incorporation of ribonucleotides into DNA can severely diminish genome integrity. However, how ribonucleotides instigate DNA damage is poorly understood. In DNA, they can promote replication stress and genomic instability and have been implicated in several diseases. We report here the impact of the ribonucleotide rATP and of its naturally occurring damaged analog 1,N 6-ethenoadenosine (1,N 6-ϵrA) on translesion synthesis (TLS), mediated by human DNA polymerase η (hpol η), and on RNase H2-mediated incision. Mass spectral analysis revealed that 1,N 6-ϵrA in DNA generates extensive frameshifts during TLS, which can lead to genomic instability. Moreover, steady-state kinetic analysis of the TLS process indicated that deoxypurines (i.e. dATP and dGTP) are inserted predominantly opposite 1,N 6-ϵrA. We also show that hpol η acts as a reverse transcriptase in the presence of damaged ribonucleotide 1,N 6-ϵrA but has poor RNA primer extension activities. Steady-state kinetic analysis of reverse transcription and RNA primer extension showed that hpol η favors the addition of dATP and dGTP opposite 1,N 6-ϵrA. We also found that RNase H2 recognizes 1,N 6-ϵrA but has limited incision activity across from this lesion, which can lead to the persistence of this detrimental DNA adduct. We conclude that the damaged and unrepaired ribonucleotide 1,N 6-ϵrA in DNA exhibits mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N 6-ϵrA is incompletely incised by RNase H2.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37323-0146
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37323-0146.
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O'Shea J, Theile CS, Das R, Babu IR, Charisse K, Manoharan M, Maier MA, Zlatev I. An efficient deprotection method for 5′-[O,O-bis(pivaloyloxymethyl)]-(E)-vinylphosphonate containing oligonucleotides. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Two-dimensional liquid chromatography-mass spectrometry for the characterization of modified oligonucleotide impurities. Anal Biochem 2018; 556:45-52. [PMID: 29936097 DOI: 10.1016/j.ab.2018.06.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
A 2D-LC system coupled with a TOF mass spectrometer has been evaluated for its capabilities to provide enhanced characterization of oligonucleotide impurities. To address loop limitations in the total volume (40 μL) sampled across 1D peaks, a column trap was incorporated between the 1D and 2D columns. The main advantages of the column trap include reduction of the total number of sequential 2D runs required to fully sample broad 1D peaks, and most importantly, reduction of the error in quantitative determination of the components in broad 1D peaks by avoiding the numerical stitching of data from several 2D runs. Comprehensive RP x IP provided orthogonal separation despite its lower 1D resolution. In contrast, IP x IP did not provide orthogonal separation. RP x IP using the direct on-line extended heart-cutting system with the column trap showed additional benefits, in the elimination of off-line fractionation and sample handling errors and was successfully applied in a pH stability study of a crude oligonucleotide. SAX x IP successfully separated the isobaric "n+16" doublet of the "n + O" and "[n + S-O]" impurity species, a feat not currently possible by mass spectrometry alone or 1D-LC, demonstrating the importance of the added capabilities of the 2D-LC approach.
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Liu C, Yamaguchi Y, Zhu X, Li Z, Ni Y, Dou X. Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions. Electrophoresis 2015; 36:1651-7. [PMID: 25867445 DOI: 10.1002/elps.201500018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 11/10/2022]
Abstract
The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double-stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polymer with different concentrations and molecular weights (Mws). Migration mechanism of dsRNA during CE was studied by the mobility and resolution length (RL) plots. We found that the RL depended on not only the concentration of HEC, but also the Mw of HEC. For instance, RL of small dsRNA fragment was more influenced by concentration of high Mw HEC than large dsRNA fragment and RL of large dsRNA fragment was more influenced by concentration of low Mw HEC than small dsRNA fragment. In addition, we found electrophoretic evidence that the structure of dsRNA was more compact than dsDNA with the same length. In practice, we succeeded to separate the glyceraldehyde 3-phosphate dehydrogenase siRNA in the mixture of the siRNA ladder marker within 4 min.
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Affiliation(s)
- Chenchen Liu
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yoshinori Yamaguchi
- Institute of Photonics and Biomedicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, P. R. China.,Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka, Suita-city, Osaka, Japan
| | - Xifang Zhu
- School of Optoelectronic Engineering, Changzhou Institute of Technology, Changzhou, Jiangsu, P. R. China
| | - Zhenqing Li
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yi Ni
- Institute of Photonics and Biomedicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, P. R. China
| | - Xiaoming Dou
- Institute of Photonics and Biomedicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, P. R. China.,School of Optoelectronic Engineering, Changzhou Institute of Technology, Changzhou, Jiangsu, P. R. China
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10
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Affiliation(s)
- Dirk Haussecker
- Department of Medical Biotechnology, College of Natural Sciences, Dongguk University, Seoul, Korea
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11
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Noll B, Seiffert S, Hertel F, Debelak H, Hadwiger P, Vornlocher HP, Roehl I. Purification of small interfering RNA using nondenaturing anion-exchange chromatography. Nucleic Acid Ther 2011; 21:383-93. [PMID: 22017541 DOI: 10.1089/nat.2011.0317] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A manufacturing and purification process for duplex oligonucleotides was established, which shortens and simplifies currently used procedures, yielding a product of higher purity. The reported procedure is based on nondenaturing anion-exchange (AEX) chromatography, which is performed on the annealed duplex rather than the individual single strands. The duplex is formed early in the process by annealing of the crude single strands directly after solid-phase synthesis. Two 30 μmol manufacturing runs using duplex purification were performed on 2 different AEX resins and compared with a manufacturing run of the same scale using conventional single-strand chromatography. The same pooling strategy was employed for all purifications. Content of optimal duplex (duplex exclusively comprising full-length single strands) was 90.5% and 90.2% for the batches obtained by duplex purification and 86.1% for the batch obtained by single-strand purification. Maximum chromatographic recoveries were 67% for the duplex purification and 68% for the single-strand purification. Hence, the manufacture of small interfering RNA (siRNA) using duplex purification was simpler and faster than conventional single-strand purification and provided better purity and similar yield of final siRNA.
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Noll B, Seiffert S, Vornlocher HP, Roehl I. Characterization of small interfering RNA by non-denaturing ion-pair reversed-phase liquid chromatography. J Chromatogr A 2011; 1218:5609-17. [PMID: 21737080 DOI: 10.1016/j.chroma.2011.06.057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/31/2011] [Accepted: 06/11/2011] [Indexed: 01/27/2023]
Abstract
Small interfering RNAs (siRNA) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. siRNA are typically formed by annealing of two complementary single stranded oligoribonucleotides. Compared to purity determination of non-hybridized single strands by denaturing chromatographic methods, characterization of the hybridized duplex is challenging. Here we are reporting a non-denaturing ion pairing-reversed phase (IP-RP) chromatography method capable of separating optimal duplex (full-length single strands only) from non-optimal duplex variants (containing shortmers, longmers and 2',5'-isomers) using ultraviolet- and mass spectrometric detection. The impact of different annealing conditions on siRNA composition was investigated. Optimized annealing conditions lead to a significant increase in optimal duplex, while total duplex content remained constant. The non-denaturing method reported herein showed high mass spectrometric sensitivity and superior separation efficiencies compared to other IP-RP buffer systems. The method is useful for in-process control and release testing of therapeutic double stranded nucleic acids such as siRNA.
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