1
|
Porcelli F, Casavola AR, Grottesi A, Schiumarini D, Avaldi L. Probing the conformational dynamics of an Ago-RNA complex in water/methanol solution. Phys Chem Chem Phys 2024; 26:2497-2508. [PMID: 38170800 DOI: 10.1039/d3cp05530b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Argonaute (Ago) proteins mediate target recognition guiding miRNA to bind complementary mRNA primarily in the seed region. However, additional pairing can occur beyond the seed, forming a supplementary duplex that can contribute to the guide-target affinity. In order to shed light on the connection, between protein-RNA interactions and miRNA-mRNA seed and supplementary duplex mobility, we carried out molecular dynamics simulations at the microsecond time-scale using a different approach compared to the ones normally used. Until now, theoretical investigations with classical MD on Ago-RNA complexes have been focused primarily on pure water solvent, which mimics the natural environment of biological molecules. Here, we explored the conformational space of a human Ago2 (hAgo2) bound to the seed + supplementary miRNA-mRNA duplex, using the solvent environment as a molecular probe. MD simulations have been performed in a mixture of water/MeOH at a molar ratio of 70 : 30 as well as in pure water for comparison. Our findings revealed that the mixed solvent promotes protein RNA association, principally enhancing salt-linkages between basic amino acid side-chains and acidic phosphates of the sugar-phosphate backbone. The primary effect registered was the restriction of supplementary duplex flexibility and the stabilization of the miRNA 3' terminus. Interestingly, we observed that the influence of the solvent appears to have almost no impact on the conformation of the seed duplex.
Collapse
Affiliation(s)
- Francesco Porcelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| | - Anna Rita Casavola
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| | | | - Donatella Schiumarini
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| |
Collapse
|
2
|
Lippens JL, Timmons HC, Welch C, Kulkarni A, Flick TG. Rapid Intact Mass Analysis and Evaluation of the Separation Potential of Microfluidic Capillary Electrophoresis Mass Spectrometry for Oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2491-2497. [PMID: 37823612 DOI: 10.1021/jasms.3c00217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Oligonucleotide characterization is a rapidly advancing field in the biopharmaceutical industry. Understanding critical quality attributes, such as intact mass and impurities, requires a toolbox of analytical techniques, which commonly includes liquid chromatography-mass spectrometry (LC-MS). Oligonucleotide LC-MS analysis frequently requires sample run times upward of 15 min to achieve separation of multiple oligonucleotide species. Additionally, LC methods frequently employ mobile phase additives such as triethylamine and 1,1,1,3,3,3-hexafluoro-2-propanol that are not always desired for use in MS instrumentation. Here, microfluidic capillary electrophoresis mass spectrometry (CE-MS) via ZipChip technology was employed to enable rapid intact mass analysis of oligonucleotide single strands. Baseline separation of equal length oligonucleotides was achieved in less than 4 min. Additionally, the potential of the ZipChip platform for separation of oligonucleotide full-length products (FLPs) and their impurities was evaluated.
Collapse
Affiliation(s)
- Jennifer L Lippens
- Pivotal Attribute Sciences, Amgen, Thousand Oaks, California 91320, United States
| | - Heath C Timmons
- Pivotal Attribute Sciences, Amgen, Thousand Oaks, California 91320, United States
| | - Crystal Welch
- 908 Devices, Boston, Massachusetts 94720-1460, United States
| | - Aditya Kulkarni
- 908 Devices, Boston, Massachusetts 94720-1460, United States
| | - Tawnya G Flick
- Pivotal Attribute Sciences, Amgen, Thousand Oaks, California 91320, United States
| |
Collapse
|
3
|
Kuo YA, Jung C, Chen YA, Kuo HC, Zhao OS, Nguyen TD, Rybarski JR, Hong S, Chen YI, Wylie DC, Hawkins JA, Walker JN, Shields SWJ, Brodbelt JS, Petty JT, Finkelstein IJ, Yeh HC. Massively Parallel Selection of NanoCluster Beacons. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204957. [PMID: 35945159 PMCID: PMC9588665 DOI: 10.1002/adma.202204957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/18/2022] [Indexed: 06/15/2023]
Abstract
NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here, a high-throughput selection method is reported that takes advantage of repurposed next-generation-sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs, respectively. Based on these findings, a "zipper-bag" model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high-throughput screening with machine-learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.
Collapse
Affiliation(s)
- Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Yu-An Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Oliver S Zhao
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Trung D Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Dennis C Wylie
- Computational Biology and Bioinformatics, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, 78712, USA
| | - John A Hawkins
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Samuel W J Shields
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, SC, 29617, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, 78712, USA
| |
Collapse
|
4
|
Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
Collapse
Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
5
|
Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
Collapse
Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
| |
Collapse
|
6
|
Sutton JM, El Zahar NM, Bartlett MG. Oligonucleotide Anion Adduct Formation Using Negative Ion Electrospray Ion-Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:497-508. [PMID: 33476148 DOI: 10.1021/jasms.0c00380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Improving the mobile phase of electrospray oligonucleotides has been a major focus in the field of oligonucleotides. These improved mobile phases should reduce the charge state envelope of oligonucleotides coupled with electrospray ionization, which is key to reducing spectral complexity and increasing sensitivity. Traditional mobile phase compositions with fluorinated alcohol and alkylamine, like hexafluoroisopropanol (HFIP) and triethylamine (TEA), have a large amount of cationic adduction and many charge states. Utilizing different fluorinated alcohol and alkylamine combinations, like nonafluoro-tert-butyl alcohol (NFTB) and octylamine (OA), can selectively reduce the charge states analyzed. Other classes of biomolecules have been analyzed with anionic salts to stabilize complexes, increase the molecular peak detection, and even provide unique structural information about these molecules; however, there have been no studies using anionic salts with oligonucleotides. Our experiments systematically study the stability and binding of ammonium anionic salt. We show that anions selectively bind low charge states of these oligonucleotides. Ion-mobility measurements are made to determine the collision cross section (CCS) of these oligonucleotides with anion adduction. We utilize both a nucleic acid exact hard sphere simulation (EHSS) calibration and a protein calibration. We are able to show that NFTB/OA is a good choice for the study of oligonucleotides with reduced charge states for the binding of anionic salts and the determination of CCS using ion mobility.
Collapse
Affiliation(s)
- J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 West Green Street, Athens, Georgia 30602-2352, United States
| | - Noha M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 West Green Street, Athens, Georgia 30602-2352, United States
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abassia, Cairo 11566, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University, Ras-Sedr, South Sinai Governorate 46612, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 West Green Street, Athens, Georgia 30602-2352, United States
| |
Collapse
|
7
|
Sutton JM, Guimaraes GJ, Annavarapu V, van Dongen WD, Bartlett MG. Current State of Oligonucleotide Characterization Using Liquid Chromatography-Mass Spectrometry: Insight into Critical Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1775-1782. [PMID: 32812756 DOI: 10.1021/jasms.0c00179] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As interests increase in oligonucleotide therapeutics, there has been a greater need for analytical techniques to properly analyze and quantitate these biomolecules. This article looks into some of the existing chromatographic approaches for oligonucleotide analysis, including anion exchange, hydrophilic interaction liquid chromatography, and ion pair chromatography. Some of the key advantages and challenges of these chromatographic techniques are discussed. Colloid formation in mobile phases of alkylamines and fluorinated alcohols, a recently discovered analytical challenge, is discussed. Mass spectrometry is the method of choice to directly obtain structural information about oligonucleotide therapeutics. Mass spectrometry sensitivity challenges are reviewed, including comparison to other oligonucleotide techniques, salt adduction, and the multiple charge state envelope. Ionization of oligonucleotides through the charge residue model, ion evaporation model, and chain ejection model are analyzed. Therapeutic oligonucleotides have to undergo approval from major regulatory agencies, and the impurities and degradation products must be well-characterized to be approved. Current accepted thresholds for oligonucleotide impurities are reported. Aspects of the impurities and degradation products from these types of molecules are discussed as well as optimal analytical strategies to determine oligonucleotide related substances. Finally, ideas are proposed on how the field of oligonucleotide therapeutics may improve to aid in future analysis.
Collapse
Affiliation(s)
- J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | - Guilherme J Guimaraes
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | - Vidya Annavarapu
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| |
Collapse
|