1
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Schnieders R, Knezic B, Zetzsche H, Sudakov A, Matzel T, Richter C, Hengesbach M, Schwalbe H, Fürtig B. NMR Spectroscopy of Large Functional RNAs: From Sample Preparation to Low-Gamma Detection. ACTA ACUST UNITED AC 2020; 82:e116. [PMID: 32960489 DOI: 10.1002/cpnc.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
NMR spectroscopy is a potent method for the structural and biophysical characterization of RNAs. The application of NMR spectroscopy is restricted in RNA size and most often requires isotope-labeled or even selectively labeled RNAs. Additionally, new NMR pulse sequences, such as the heteronuclear-detected NMR experiments, are introduced. We herein provide detailed protocols for the preparation of isotope-labeled RNA for NMR spectroscopy via in vitro transcription. This protocol covers all steps, from the preparation of DNA template to the transcription of milligram RNA quantities. Moreover, we present a protocol for a chemo-enzymatic approach to introduce a single modified nucleotide at any position of any RNA. Regarding NMR methodology, we share protocols for the implementation of a suite of heteronuclear-detected NMR experiments including 13 C-detected experiments for ribose assignment and amino groups, the CN-spin filter heteronuclear single quantum coherence (HSQC) for imino groups and the 15 N-detected band-selective excitation short transient transverse-relaxation-optimized spectroscopy (BEST-TROSY) experiment. © 2020 The Authors. Basic Protocol 1: Preparation of isotope-labeled RNA samples with in vitro transcription using T7 RNAP, DEAE chromatography, and RP-HPLC purification Alternate Protocol 1: Purification of isotope-labeled RNA from in vitro transcription with preparative PAGE Alternate Protocol 2: Purification of isotope-labeled RNA samples from in vitro transcription via centrifugal concentration Support Protocol 1: Preparation of DNA template from plasmid Support Protocol 2: Preparation of PCR DNA as template Support Protocol 3: Preparation of T7 RNA Polymerase (T7 RNAP) Support Protocol 4: Preparation of yeast inorganic pyrophosphatase (YIPP) Basic Protocol 2: Preparation of site-specific labeled RNAs using a chemo-enzymatic synthesis Support Protocol 5: Synthesis of modified nucleoside 3',5'-bisphosphates Support Protocol 6: Preparation of T4 RNA Ligase 2 Support Protocol 7: Setup of NMR spectrometer for heteronuclear-detected NMR experiments Support Protocol 8: IPAP and DIPAP for homonuclear decoupling Basic Protocol 3: 13 C-detected 3D (H)CC-TOCSY, (H)CPC, and (H)CPC-CCH-TOCSY experiments for ribose assignment Basic Protocol 4: 13 C-detected 2D CN-spin filter HSQC experiment Basic Protocol 5: 13 C-detected C(N)H-HDQC experiment for the detection of amino groups Support Protocol 9: 13 C-detected CN-HSQC experiment for amino groups Basic Protocol 6: 13 C-detected "amino"-NOESY experiment Basic Protocol 7: 15 N-detected BEST-TROSY experiment.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
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2
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Asadi-Atoi P, Barraud P, Tisne C, Kellner S. Benefits of stable isotope labeling in RNA analysis. Biol Chem 2020; 400:847-865. [PMID: 30893050 DOI: 10.1515/hsz-2018-0447] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. They contain a variety of chemical modifications and many RNAs fold into complex structures. Here, we review recent progress in the analysis of RNA modification and structure on the basis of stable isotope labeling techniques. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the key tools and many breakthrough developments were made possible by the analysis of stable isotope labeled RNA. Therefore, we discuss current stable isotope labeling techniques such as metabolic labeling, enzymatic labeling and chemical synthesis. RNA structure analysis by NMR is challenging due to two major problems that become even more salient when the size of the RNA increases, namely chemical shift overlaps and line broadening leading to complete signal loss. Several isotope labeling strategies have been developed to provide solutions to these major issues, such as deuteration, segmental isotope labeling or site-specific labeling. Quantification of modified nucleosides in RNA by MS is only possible through the application of stable isotope labeled internal standards. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), it is now possible to analyze the dynamic processes of post-transcriptional RNA modification and demodification. The trend, in both NMR and MS RNA analytics, is without doubt shifting from the analysis of snapshot moments towards the development and application of tools capable of analyzing the dynamics of RNA structure and modification profiles.
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Affiliation(s)
- Paria Asadi-Atoi
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Pierre Barraud
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261, CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Carine Tisne
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261, CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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3
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Schnieders R, Keyhani S, Schwalbe H, Fürtig B. More than Proton Detection-New Avenues for NMR Spectroscopy of RNA. Chemistry 2020; 26:102-113. [PMID: 31454110 PMCID: PMC6973061 DOI: 10.1002/chem.201903355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleic acid oligonucleotides (RNAs) play pivotal roles in cellular function (riboswitches), chemical biology applications (SELEX-derived aptamers), cell biology and biomedical applications (transcriptomics). Furthermore, a growing number of RNA forms (long non-coding RNAs, circular RNAs) but also RNA modifications are identified, showing the ever increasing functional diversity of RNAs. To describe and understand this functional diversity, structural studies of RNA are increasingly important. However, they are often more challenging than protein structural studies as RNAs are substantially more dynamic and their function is often linked to their structural transitions between alternative conformations. NMR is a prime technique to characterize these structural dynamics with atomic resolution. To extend the NMR size limitation and to characterize large RNAs and their complexes above 200 nucleotides, new NMR techniques have been developed. This Minireview reports on the development of NMR methods that utilize detection on low-γ nuclei (heteronuclei like 13 C or 15 N with lower gyromagnetic ratio than 1 H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1 H coherences, detected by 13 C NMR spectroscopy. Furthermore, 13 C and 15 N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-γ nuclei detection experiments in RNA.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
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4
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Tan Y, Li Y, Tang F. Nucleic Acid Aptamer: A Novel Potential Diagnostic and Therapeutic Tool for Leukemia. Onco Targets Ther 2019; 12:10597-10613. [PMID: 31824168 PMCID: PMC6900352 DOI: 10.2147/ott.s223946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/14/2019] [Indexed: 12/23/2022] Open
Abstract
Leukemia immunotherapy has been dominant via using synthetic antibodies to target cluster of differentiation (CD) molecules, nevertheless inevitable cytotoxicity and immunogenicity would limit its development. Recently, increasing reports have focused on nucleic acid aptamers, a class of high-affinity nucleic acid ligands. Aptamers purportedly serve as “chemical antibodies”, have negligible cytotoxicity and low immunogenicity, and would be widely applied for the therapy and diagnosis of various diseases, especially leukemia. In the preclinical applications, nucleic acid aptamers have displayed the augmented specificity and selectivity via recognizing targets on leukemia cells based on unique three-dimensional conformations. As small molecules with nucleic acid characteristics, aptamers need to be chemically modified to resist nuclease degradation, renal clearance and improve binding affinities. Moreover, aptamers can be linked with neoteric detection techniques to enhance sensitivity and selectivity of diagnosis and therapy. In this review, we summarized aptamers’ preparation, chemical modification and conjugation, and discussed the application of aptamers in diagnosis and treatment of leukemia through highly specifically recognizing target molecules. Significantly, the application prospect of aptamers in fusion genes would be introduced.
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Affiliation(s)
- Yuan Tan
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yuejin Li
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Faqing Tang
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
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5
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Schnieders R, Wolter AC, Richter C, Wöhnert J, Schwalbe H, Fürtig B. Novel
13
C‐detected NMR Experiments for the Precise Detection of RNA Structure. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Antje C. Wolter
- Institute for Molecular BiosciencesCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Jens Wöhnert
- Institute for Molecular BiosciencesCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
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6
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Schnieders R, Wolter AC, Richter C, Wöhnert J, Schwalbe H, Fürtig B. Novel 13 C-detected NMR Experiments for the Precise Detection of RNA Structure. Angew Chem Int Ed Engl 2019; 58:9140-9144. [PMID: 31131949 PMCID: PMC6617721 DOI: 10.1002/anie.201904057] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Indexed: 12/20/2022]
Abstract
Up to now, NMR spectroscopic investigations of RNA have utilized imino proton resonances as reporters for base pairing and RNA structure. The nucleobase amino groups are often neglected, since most of their resonances are broadened beyond detection due to rotational motion around the C-NH2 bond. Here, we present 13 C-detected NMR experiments for the characterization of all RNA amino groups irrespective of their motional behavior. We have developed a C(N)H-HDQC experiment that enables the observation of a complete set of sharp amino resonances through the detection of proton-NH2 double quantum coherences. Further, we present an "amino"-NOESY experiment to detect NOEs to amino protons, which are undetectable by any other conventional NOESY experiment. Together, these experiments allow the exploration of additional chemical shift information and inter-residual proton distances important for high-resolution RNA secondary and tertiary structure determination.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Antje C Wolter
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
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7
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RNA structure refinement using NMR solvent accessibility data. Sci Rep 2017; 7:5393. [PMID: 28710477 PMCID: PMC5511288 DOI: 10.1038/s41598-017-05821-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022] Open
Abstract
NMR spectroscopy is a powerful technique to study ribonucleic acids (RNAs) which are key players in a plethora of cellular processes. Although the NMR toolbox for structural studies of RNAs expanded during the last decades, they often remain challenging. Here, we show that solvent paramagnetic relaxation enhancements (sPRE) induced by the soluble, paramagnetic compound Gd(DTPA-BMA) provide a quantitative measure for RNA solvent accessibility and encode distance-to-surface information that correlates well with RNA structure and improves accuracy and convergence of RNA structure determination. Moreover, we show that sPRE data can be easily obtained for RNAs with any isotope labeling scheme and is advantageous regarding sample preparation, stability and recovery. sPRE data show a large dynamic range and reflect the global fold of the RNA suggesting that they are well suited to identify interaction surfaces, to score structural models and as restraints in RNA structure determination.
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8
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Wolter AC, Weickhmann AK, Nasiri AH, Hantke K, Ohlenschläger O, Wunderlich CH, Kreutz C, Duchardt‐Ferner E, Wöhnert J. Ein stabil protoniertes Adenin‐Nukleotid mit einem extrem verschobenen p
K
a
‐Wert stabilisiert die Tertiärstruktur eines GTP‐bindenden RNA‐Aptamers. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Antje C. Wolter
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) Goethe-Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt/Main Deutschland
| | - A. Katharina Weickhmann
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) Goethe-Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt/Main Deutschland
| | - Amir H. Nasiri
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) Goethe-Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt/Main Deutschland
| | - Katharina Hantke
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) Goethe-Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt/Main Deutschland
| | - Oliver Ohlenschläger
- Leibniz Institut für Alternsforschung (Fritz-Lipmann-Institut) Beutenbergstraße 11 07745 Jena Deutschland
| | - Christoph H. Wunderlich
- Institut für Organische Chemie Centre for Molecular Biosciences (CMBI) Universität Innsbruck Innrain 80/82 6020 Innsbruck Österreich
| | - Christoph Kreutz
- Institut für Organische Chemie Centre for Molecular Biosciences (CMBI) Universität Innsbruck Innrain 80/82 6020 Innsbruck Österreich
| | - Elke Duchardt‐Ferner
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) Goethe-Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt/Main Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) Goethe-Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt/Main Deutschland
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9
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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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10
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Wolter AC, Weickhmann AK, Nasiri AH, Hantke K, Ohlenschläger O, Wunderlich CH, Kreutz C, Duchardt-Ferner E, Wöhnert J. A Stably Protonated Adenine Nucleotide with a Highly Shifted pK a Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer. Angew Chem Int Ed Engl 2016; 56:401-404. [PMID: 27885761 DOI: 10.1002/anie.201609184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/01/2016] [Indexed: 12/23/2022]
Abstract
RNA tertiary structure motifs are stabilized by a wide variety of hydrogen-bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pKa values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP-binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pKa value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pKa for A nucleotides in single-stranded RNA. This is the largest pKa shift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pKa shifts observed for amino acid side chains in proteins. Both RNA pre-folding and ligand binding contribute to the pKa shift.
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Affiliation(s)
- Antje C Wolter
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
| | - A Katharina Weickhmann
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
| | - Amir H Nasiri
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
| | - Katharina Hantke
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
| | - Oliver Ohlenschläger
- Leibniz Institut für Alternsforschung (Fritz-Lipmann-Institut), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph H Wunderlich
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
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Khosa S, Hoeppner A, Gohlke H, Schmitt L, Smits SHJ. Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance. PLoS One 2016; 11:e0149903. [PMID: 26930060 PMCID: PMC4773095 DOI: 10.1371/journal.pone.0149903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/05/2016] [Indexed: 01/22/2023] Open
Abstract
Lantibiotics are antimicrobial peptides produced by Gram-positive bacteria. Interestingly, several clinically relevant and human pathogenic strains are inherently resistant towards lantibiotics. The expression of the genes responsible for lantibiotic resistance is regulated by a specific two-component system consisting of a histidine kinase and a response regulator. Here, we focused on a response regulator involved in lantibiotic resistance, NsrR from Streptococcus agalactiae, and determined the crystal structures of its N-terminal receiver domain and C-terminal DNA-binding effector domain. The C-terminal domain exhibits a fold that classifies NsrR as a member of the OmpR/PhoB subfamily of regulators. Amino acids involved in phosphorylation, dimerization, and DNA-binding were identified and demonstrated to be conserved in lantibiotic resistance regulators. Finally, a model of the full-length NsrR in the active and inactive state provides insights into protein dimerization and DNA-binding.
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Affiliation(s)
- Sakshi Khosa
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Astrid Hoeppner
- X-Ray Facility and Crystal Farm, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
- * E-mail:
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