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Herbert C, Valesyan S, Kist J, Limbach PA. Analysis of RNA and Its Modifications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:47-68. [PMID: 38594935 DOI: 10.1146/annurev-anchem-061622-125954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Ribonucleic acids (RNAs) are key biomolecules responsible for the transmission of genetic information, the synthesis of proteins, and modulation of many biochemical processes. They are also often the key components of viruses. Synthetic RNAs or oligoribonucleotides are becoming more widely used as therapeutics. In many cases, RNAs will be chemically modified, either naturally via enzymatic systems within a cell or intentionally during their synthesis. Analytical methods to detect, sequence, identify, and quantify RNA and its modifications have demands that far exceed requirements found in the DNA realm. Two complementary platforms have demonstrated their value and utility for the characterization of RNA and its modifications: mass spectrometry and next-generation sequencing. This review highlights recent advances in both platforms, examines their relative strengths and weaknesses, and explores some alternative approaches that lie at the horizon.
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Affiliation(s)
- Cassandra Herbert
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Satenik Valesyan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Jennifer Kist
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
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Kadlecová Z, Kalíková K, Tesařová E, Gilar M. Phosphorothioate oligonucleotides separation in ion-pairing reversed-phase liquid chromatography: effect of temperature. J Chromatogr A 2022; 1681:463473. [PMID: 36113338 DOI: 10.1016/j.chroma.2022.463473] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 11/15/2022]
Abstract
Analysis of diastereomers of phosphorothioate oligonucleotides in ion-pairing reversed-phase liquid chromatography is affected not only by the character and concentration of ion-pairing system, but also by the separation temperature. In this work, eight ion-pairing systems at two concentrations buffered with acetic acid were used with octadecyl column to investigate the effects of temperature (in the range from 20 °C to 90 °C) on retention, diastereomeric separation, resolution of mers of different length and resolution of oligonucleotides with different number of phosphorothioate linkages. It was observed that elevated temperature suppresses the diastereomeric separation and oligonucleotide peaks become narrower. This improves the resolution of n and n-1 mers at elevated temperature. Plots of ln k (k = retention factor) versus reciprocal absolute temperature show that for 100 mM ion-pairing systems the increase in temperature does not lead to simple decrease in oligonucleotides retention as generally observed in reversed-phase liquid chromatography. The aim of this work is to improve chromatographic method for analysis of phosphorothioate oligonucleotides.
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Affiliation(s)
- Zuzana Kadlecová
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 12800, Prague, Czech Republic
| | - Květa Kalíková
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 12800, Prague, Czech Republic.
| | - Eva Tesařová
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 12800, Prague, Czech Republic
| | - Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, United States of America.
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V G, Basuri PP, Sahini K, C N N. Retention behaviour of analytes in reversed phase high performance liquid chromatography - A review. Biomed Chromatogr 2022:e5482. [PMID: 35962484 DOI: 10.1002/bmc.5482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022]
Abstract
The understanding of principles that drive the separation in reversed phase chromatography plays an important role in the prediction of elution of solutes in RP-HPLC. The separation in RP-HPLC is based on the principle of adsorption and partition. In addition, the log P value, pKa value of the drug, chromatographic parameters like mobile phase pH, buffer concentration, organic modifier and mobile phase additives also influence the retention and selectivity of the analyte. It is found that hydrophobic, electrostatic, hydrogen bonding and other specific interactions between the stationary phase and the solutes along with the hydrophobicity of an analyte molecule (log P) modify the retention behaviour of the analytes. This article gives special attention to the influence of ionization and ion interaction on the separation of analytes. The drug molecules with different log P value containing protonated and deprotonated acids, bases and zwitterions are selected as examples and this article addresses various issues related to method development, relationships between analyte retention and mobile phase pH and pKa value of the analyte. The advances in this regard, with highlights on topics such as mechanisms of retention and various factors that influence the retention behaviour of analytes is also updated with suitable examples.
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Affiliation(s)
- Ganesh V
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| | - P Poorna Basuri
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| | - K Sahini
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| | - Nalini C N
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
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Kadlecová Z, Kalíková K, Tesařová E, Gilar M. Phosphorothioate oligonucleotides separation in ion-pairing reversed-phase liquid chromatography: effect of ion-pairing system. J Chromatogr A 2022; 1676:463201. [DOI: 10.1016/j.chroma.2022.463201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023]
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Chen Y, Luo L, Feng P, Xu B, Wei X. Effective and repeatable chromatographic separation of 5 nucleotides in infant formula milk powder by ion-pair high-performance liquid chromatography-ultraviolet. J Dairy Sci 2022; 105:2840-2848. [PMID: 35181132 DOI: 10.3168/jds.2021-21133] [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: 08/09/2021] [Accepted: 12/27/2021] [Indexed: 11/19/2022]
Abstract
A robust method using HPLC-UV was developed to improve the accuracy and repeatability of a quantitative method to detect 5 nucleotides (cytidine-monophosphate, uridine monophosphate, adenosine monophosphate, guanine monophosphate, and inosine monophosphate) in infant formulas. The results showed that efficient separation could not be achieved without strict conditions. The proposed method displayed a strong linear relationship (R2 > 0.9999) of single nucleotide in infant formula milk powder in the range of 10 to 1,000 mg/kg, a steady recovery (80.0% ∼110.0%) with relative standard deviation from 0.5% to 3.5%, under strict conditions of hydrophilic C18 column with di-isopropyl at 62.5 ± 2.5°C (± standard deviation), 0.65 ± 0.1 mg/mL tetrabutylammonium bisulfate, and mobile phase of pH of 2.75 ± 0.02. By applying this method on a series of milk products in the Chinese market, we found a few of them exceeded the legal limits of nucleotides.
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Affiliation(s)
- Yuanjia Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lin Luo
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Peiyan Feng
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Baojun Xu
- Food Science and Technology Program, BNU-HKBU United International College, Zhuhai, Guangdong 519087, China
| | - Xiaoqun Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Donegan M, Nguyen JM, Gilar M. Effect of ion-pairing reagent hydrophobicity on liquid chromatography and mass spectrometry analysis of oligonucleotides. J Chromatogr A 2022; 1666:462860. [PMID: 35123169 DOI: 10.1016/j.chroma.2022.462860] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
We performed a systematic study of thirteen alkylamines used as ion-pairing reagents for ion-pair reversed-phase liquid chromatography (IP RP LC) separations of oligonucleotides on a C18 column. We proposed a method to classify the hydrophobicity of alkylamines by their retention in RP LC. The IP reagent hydrophobicity correlated with the retention and resolution of oligonucleotides in the corresponding IP mobile phases. The baseline resolution was achieved up to 30 mer for hydrophilic, or up to 50 mer for hydrophobic IP reagents. Hydrophobic alkylamines permitted useful oligonucleotide separations at relatively low buffer concentrations, such as 5-10 mM alkylamine-acetate IP systems. These buffers were compatible with mass spectrometry detection, however, replacement of acetic acid with hexafluoroisopropanol in the mobile phase improved the MS signal by 2-3 orders of magnitude. Experiments with native and chemically modified oligonucleotides highlighted the mixed-mode nature of IP RP LC. When using hydrophobic IP reagents, the ionic retention mechanism of oligonucleotides is enhanced while hydrophobic retention is diminished.
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Affiliation(s)
| | | | - Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA.
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Jia W, Yang Y, Liu S, Shi L. Molecular mechanisms of the irradiation-induced accumulation of polyphenols in star anise (Illicium verum Hook. f.). J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104233] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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