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Hirsch M, Hofmann L, Yakobov I, Kahremany S, Sameach H, Shenberger Y, Gevorkyan-Airapetov L, Ruthstein S. An efficient EPR spin-labeling method enables insights into conformational changes in DNA. BIOPHYSICAL REPORTS 2024; 4:100168. [PMID: 38945453 PMCID: PMC11298882 DOI: 10.1016/j.bpr.2024.100168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Electron paramagnetic resonance (EPR) is a powerful tool for elucidating both static and dynamic conformational alterations in macromolecules. However, to effectively utilize EPR for such investigations, the presence of paramagnetic centers, known as spin labels, is required. The process of spin labeling, particularly for nucleotides, typically demands intricate organic synthesis techniques. In this study, we introduce a unique addition-elimination reaction method with a simple spin-labeling process, facilitating the monitoring of structural changes within nucleotide sequences. Our investigation focuses on three distinct labeling positions with a DNA sequence, allowing the measurement of distance between two spin labels. The experimental mean distances obtained agreed with the calculated distances, underscoring the efficacy of this straightforward spin-labeling approach in studying complex biological processes such as transcription mechanism using EPR measurements.
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Affiliation(s)
- Melanie Hirsch
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Idan Yakobov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Shirin Kahremany
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Hila Sameach
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel.
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2
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Gauger M, Heinz M, Halbritter ALJ, Stelzl LS, Erlenbach N, Hummer G, Sigurdsson ST, Prisner TF. Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations. Angew Chem Int Ed Engl 2024; 63:e202402498. [PMID: 38530284 DOI: 10.1002/anie.202402498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20-base-pair-long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm- and singly fluorine-labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state-of-the-art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high-precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.
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Affiliation(s)
- Maximilian Gauger
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
| | - Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
| | | | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University, 55128, Mainz, Germany
- KOMET 1, Institute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128, Mainz, Germany
- Institute of Quantitative and Computational Bioscience (IQCB), Johannes Gutenberg University Mainz, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 1, 60438, Frankfurt am Main, Germany
| | | | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
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3
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Persaud KE, Sahu RR, Neary MC, Kapdi AR, Lakshman MK. Two short approaches to the COVID-19 drug β-D- N4-hydroxycytidine and its prodrug molnupiravir. Org Biomol Chem 2024; 22:735-740. [PMID: 38168802 DOI: 10.1039/d3ob02039h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Molnupiravir, the prodrug for β-D-N4-hydroxycytidine (NHC), is marketed by Merck as Lagevrio™ against mild-moderate COVID-19, under FDA emergency use authorization. It is the first oral drug against the disease. This work describes two synthetic approaches to NHC and molnupiravir by amide activation in uridine with a peptide-coupling agent and with a 4-chloropyrimidinone nucleoside intermediate.
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Affiliation(s)
- Kevin E Persaud
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Rajesh R Sahu
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India
| | - Michelle C Neary
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
| | - Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
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4
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Liu ZQ. Is it still worth renewing nucleoside anticancer drugs nowadays? Eur J Med Chem 2024; 264:115987. [PMID: 38056297 DOI: 10.1016/j.ejmech.2023.115987] [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: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Nucleoside has situated the convergence point in the discovery of novel drugs for decades, and a large number of nucleoside derivatives have been constructed for screening novel pharmacological properties at various experimental platforms. Notably, nearly 20 nucleosides are approved to be used in the clinic treatment of various cancers. Nevertheless, the blossom of synthetic nucleoside analogs in comparison with the scarcity of nucleoside anticancer drugs leads to a question: Is it still worth insisting on the screening of novel anticancer drugs from nucleoside derivatives? Hence, this review attempts to emphasize the importance of nucleoside analogs in the discovery of novel anticancer drugs. Firstly, we introduce the metabolic procedures of nucleoside anticancer drug (such as 5-fluorouracil) and summarize the designing of novel nucleoside anticancer candidates based on clinically used nucleoside anticancer drugs (such as gemcitabine). Furthermore, we collect anticancer properties of some recently synthesized nucleoside analogs, aiming at emphasizing the availability of nucleoside analogs in the discovery of anticancer drugs. Finally, a variety of synthetic strategies including the linkage of sugar moiety with nucleobase scaffold, modifications on the sugar moiety, and variations on the nucleobase structure are collected to exhibit the abundant protocols in the achievement of nucleoside analogs. Taken the above discussions collectively, nucleoside still advantages for the finding of novel anticancer drugs because of the clearly metabolic procedures, successfully clinic applications, and abundantly synthetic routines.
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Affiliation(s)
- Zai-Qun Liu
- Department of Organic Chemistry, College of Chemistry, Jilin University, Changchun, 130021, People's Republic of China.
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5
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Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
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Kaiser F, Endeward B, Collauto A, Scheffer U, Prisner TF, Göbel MW. Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block. Chemistry 2022; 28:e202201822. [PMID: 35903916 PMCID: PMC9804336 DOI: 10.1002/chem.202201822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/05/2023]
Abstract
The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.
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Affiliation(s)
- Frank Kaiser
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Burkhard Endeward
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Alberto Collauto
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Thomas F. Prisner
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael W. Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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