1
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Maste S, Sharma B, Pongratz T, Grabe B, Hiller W, Erlach MB, Kremer W, Kalbitzer HR, Marx D, Kast SM. The accuracy limit of chemical shift predictions for species in aqueous solution. Phys Chem Chem Phys 2024; 26:6386-6395. [PMID: 38315169 DOI: 10.1039/d3cp05471c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.
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Affiliation(s)
- Stefan Maste
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Tim Pongratz
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Bastian Grabe
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Wolf Hiller
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Markus Beck Erlach
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Werner Kremer
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Hans Robert Kalbitzer
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Stefan M Kast
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
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2
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Dickerhoff J, Jang J, Yang D. Best method to determine DNA G-quadruplex folding: The 1H- 13C HSQC NMR experiment. Methods 2024; 221:35-41. [PMID: 38029869 PMCID: PMC10872514 DOI: 10.1016/j.ymeth.2023.11.013] [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: 09/22/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/01/2023] Open
Abstract
NMR spectroscopy is the major method for G-quadruplex structure determination under physiologically relevant solution conditions. Unlike duplex B-DNA, in which all nucleotides adopt an anti glycosidic conformation, the core tetrad-guanines in a G-quadruplex can adopt anti or syn glycosidic conformation depending on the folding structure. An experimental method that can clearly and unambiguously determine syn and anti tetrad-Gs in a G-quadruplex is highly desirable and necessary. In the present study, we exploit the advantages of the 1H-13C HSQC experiment to determine tetrad-G's glycosidic conformation and thus folding topology of G-quadruplexes. We use several examples to demonstrate the clear and straightforward determination of the guanine glycosidic conformations and G-quadruplex folding structures. Moreover, 1H-13C HSQC data can readily identify adenine H2 resonances as well as determine unusual syn conformation in loop and flanking sequences, a challenging task by standard 2D NOESY.
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Affiliation(s)
- Jonathan Dickerhoff
- Purdue University, College of Pharmacy, Borch Department of Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave, West Lafayette, IN 47907, USA
| | - Jinho Jang
- Purdue University, College of Pharmacy, Borch Department of Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave, West Lafayette, IN 47907, USA
| | - Danzhou Yang
- Purdue University, College of Pharmacy, Borch Department of Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave, West Lafayette, IN 47907, USA; Purdue Institute for Cancer Research, 201 S University St, West Lafayette, IN 47906, USA; Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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3
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Vianney YM, Schröder N, Jana J, Chojetzki G, Weisz K. Showcasing Different G-Quadruplex Folds of a G-Rich Sequence: Between Rule-Based Prediction and Butterfly Effect. J Am Chem Soc 2023; 145:22194-22205. [PMID: 37751488 DOI: 10.1021/jacs.3c08336] [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: 09/28/2023]
Abstract
In better understanding the interactions of G-quadruplexes in a cellular or noncellular environment, a reliable sequence-based prediction of their three-dimensional fold would be extremely useful, yet is often limited by their remarkable structural diversity. A G-rich sequence related to a promoter sequence of the PDGFR-β nuclease hypersensitivity element (NHE) comprises a G3-G3-G2-G4-G3 pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical G-quadruplexes with uninterrupted G-columns can be expected, minimal base substitutions in a non-G-tract domain were shown to guide folding into either a basket-type antiparallel quadruplex, a parallel-stranded quadruplex with an interrupted G-column, a quadruplex with a V-shaped loop, or a (3+1) hybrid quadruplex. A 3D NMR structure for each of the different folds was determined. Supported by thermodynamic profiling on additional sequence variants, formed topologies were rationalized by the identification and assessment of specific critical interactions of loop and overhang residues, giving valuable insights into their contribution to favor a particular conformer. The variability of such tertiary interactions, together with only small differences in quadruplex free energies, emphasizes current limits for a reliable sequence-dependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Nina Schröder
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Gregor Chojetzki
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
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4
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Cohen RD, Wood JS, Lam YH, Buevich AV, Sherer EC, Reibarkh M, Williamson RT, Martin GE. DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking. Molecules 2023; 28:molecules28062449. [PMID: 36985422 PMCID: PMC10051451 DOI: 10.3390/molecules28062449] [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: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively.
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Affiliation(s)
- Ryan D Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Jared S Wood
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
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5
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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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6
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Peterková K, Durník I, Marek R, Plavec J, Podbevšek P. c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry. Nucleic Acids Res 2021; 49:8947-8960. [PMID: 34365512 PMCID: PMC8421218 DOI: 10.1093/nar/gkab659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Radek Marek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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7
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Reddy Sannapureddi RK, Mohanty MK, Gautam AK, Sathyamoorthy B. Characterization of DNA G-quadruplex Topologies with NMR Chemical Shifts. J Phys Chem Lett 2020; 11:10016-10022. [PMID: 33179931 DOI: 10.1021/acs.jpclett.0c02969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
G-quadruplexes are nucleic acid motifs formed by stacking of guanosine-tetrad pseudoplanes. They perform varied biological roles, and their distinctive structural features enable diverse applications. High-resolution structural characterization of G-quadruplexes is often time-consuming and expensive, calling for effective methods. Herein, we develop NMR chemical shifts and machine learning-based methodology that allows direct, rapid, and reliable analysis of canonical three-plane DNA G-quadruplexes sans isotopic enrichment. We show, for the first time, that each unique topology enforces a specific distribution of glycosidic torsion angles. Newly acquired carbon chemical shifts are exquisite probes for the dihedral angle distribution and provide immediate and unambiguous backbone topology assignment. The support vector machine learning methodology aids resonance assignment by providing plane indices for tetrad-forming guanosines. We further demonstrate the robustness by successful application of the methodology to a sequence that folds in two dissimilar topologies under different ionic conditions, providing its first atomic-level characterization.
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Affiliation(s)
| | - Manish Kumar Mohanty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Anoop Kumar Gautam
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
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8
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Abou Assi H, Rangadurai AK, Shi H, Liu B, Clay MC, Erharter K, Kreutz C, Holley CL, Al-Hashimi H. 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states. Nucleic Acids Res 2020; 48:12365-12379. [PMID: 33104789 PMCID: PMC7708057 DOI: 10.1093/nar/gkaa928] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/10/2020] [Accepted: 10/09/2020] [Indexed: 12/18/2022] Open
Abstract
2'-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3'-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of flexible RNAs containing bulges and internal loops. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of low-populated short-lived excited states by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi-value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.
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Affiliation(s)
- Hala Abou Assi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Atul K Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mary C Clay
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Erharter
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Christopher L Holley
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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9
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Lawrence C, Grishaev A. Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. RNA (NEW YORK, N.Y.) 2020; 26:2051-2061. [PMID: 32917774 PMCID: PMC7668244 DOI: 10.1261/rna.074617.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/19/2020] [Indexed: 06/01/2023]
Abstract
Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they exhibit crystal packing and counter-ion binding artifacts that prevent their use for the chemical shifts analysis. On the other hand, NMR-determined structures of RNA often are not solved at the density of restraints required to precisely define the variable degrees of freedom. In this study we sidestep the problems of direct parameterization of the RNA chemical shifts/structure relationship and examine the effects of imposing local fragmental coordinate similarity restraints based on similarities of the experimental secondary ribose 13C/1H chemical shifts instead. The effect of such chemical shift similarity (CSS) restraints on the structural accuracy is assessed via residual dipolar coupling (RDC)-based cross-validation. Improvements in the coordinate accuracy are observed for all of the six RNA constructs considered here as test cases, which argues for routine inclusion of these terms during NMR-based oligonucleotide structure determination. Such accuracy improvements are expected to facilitate derivation of the chemical shift/structure relationships for RNA.
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Affiliation(s)
- Chad Lawrence
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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10
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Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R 1ρ relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2020; 74:457-471. [PMID: 32789613 PMCID: PMC7508749 DOI: 10.1007/s10858-020-00337-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/13/2020] [Indexed: 05/30/2023]
Abstract
NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson-Crick-like conformations. As Watson-Crick-like G·T mismatches have base pairing geometries similar to Watson-Crick base pairs, we hypothesized that they would mimic Watson-Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3' and C4' nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson-Crick conformation and that transitions toward tautomeric and anionic Watson-Crick-like G·T mismatches restore the canonical Watson-Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson-Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T-, and also establish sugar carbons as new non-exchangeable probes of this exchange process.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Nymirum, 4324 S. Alston Avenue, Durham, NC, 27713, USA
| | - Isaac Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Nymirum, 4324 S. Alston Avenue, Durham, NC, 27713, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Chemistry, Duke University, Durham, NC, 27710, USA.
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11
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Krivdin LB. Computational 1 H NMR: Part 3. Biochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:15-30. [PMID: 31286566 DOI: 10.1002/mrc.4895] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
This is the third and the last part of three closely interrelated reviews dealing with computation of 1 H nuclear magnetic resonance chemical shifts and 1 H-1 H spin-spin coupling constants. Present review deals with the computation of these parameters in biologically active natural products, carbohydrates, and other molecules of biological origin focusing on stereochemical applications of computational 1 H nuclear magnetic resonance to these objects.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Department of Chemistry, Angarsk State Technical University, Angarsk, Russia
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12
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Zheng M, Hwang S, Snyder T, Aquilina J, Proni G, Paz MM, Pradhan P, Cheng SY, Champeil E. Synthesis of Mitomycin C and decarbamoylmitomycin C N 6 deoxyadenosine-adducts. Bioorg Chem 2019; 92:103280. [PMID: 31539740 DOI: 10.1016/j.bioorg.2019.103280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 01/06/2023]
Abstract
Mitomycin C (MC), an anti-cancer drug, and its analog, decarbamoylmitomycin C (DMC), are DNA-alkylating agents. MC is currently used in the clinics and its cytotoxicity is mainly due to its ability to form Interstrand Crosslinks (ICLs) which impede DNA replication and, thereby, block cancer cells proliferation. However, both MC and DMC are also able to generate monoadducts with DNA. In particular, we recently discovered that DMC, like MC, can form deoxyadenosine (dA) monoadducts with DNA. The biological role played by these monoadducts is worthy of investigation. To probe the role of these adducts and to detect them in enzymatic digests of DNA extracted from culture cells treated by both drugs, we need access to reference compounds i.e. MC and DMC dA-mononucleoside adducts. Previous biomimetic methods used to generate MC and DMC mononucleoside adducts are cumbersome and very low yielding. Here, we describe the diastereospecific chemical synthesis of both C-1 epimers of MC and DMC deoxyadenosine adducts. The key step of the synthesis involves an aromatic substitution reaction between a 6-fluoropurine 2'-deoxyribonucleoside and appropriately protected stereoisomeric triaminomitosenes to form protected-MC-dA adducts with either an S or R stereochemical configuration at the adenine-mitosene linkage. Fluoride-based deprotection methods generated the final four reference compounds: the two stereoisomeric MC-dA adducts and the two stereoisomeric DMC-dA adducts. The MC and DMC-dA adducts synthesized here will serve as standards for the detection and identification of such adducts formed in the DNA of culture cells treated with both drugs.
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Affiliation(s)
- Maggie Zheng
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA.
| | - Seokjin Hwang
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA.
| | - Timothy Snyder
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA.
| | - Jake Aquilina
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA.
| | - Gloria Proni
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA.
| | - Manuel M Paz
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Padmanava Pradhan
- The City College, 138th Street at Convent Avenue, New York, NY 10031, USA.
| | - Shu-Yuan Cheng
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA.
| | - Elise Champeil
- John Jay College of Criminal Justice, New York, 524 West 59(th) Street, New York, NY 10019, USA; The Graduate Center of the City University of New York, New York, NY 10016, USA.
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13
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Karg B, Mohr S, Weisz K. Duplex‐Guided Refolding into Novel G‐Quadruplex (3+1) Hybrid Conformations. Angew Chem Int Ed Engl 2019; 58:11068-11071. [DOI: 10.1002/anie.201905372] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Beatrice Karg
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Swantje Mohr
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Klaus Weisz
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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14
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Rangadurai A, Zhou H, Merriman DK, Meiser N, Liu B, Shi H, Szymanski ES, Al-Hashimi HM. Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? Nucleic Acids Res 2019; 46:11099-11114. [PMID: 30285154 PMCID: PMC6237737 DOI: 10.1093/nar/gky885] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022] Open
Abstract
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson–Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2′-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5–4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3–4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Nathalie Meiser
- Goethe University, Institute for Organic Chemistry and Chemical Biology, Frankfurt am Main, Germany
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.,Department of Chemistry, Duke University, Durham, NC, USA
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15
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Xia Y, Zhang H. 13C NMR chemical shift prediction of diverse chemical compounds. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:477-490. [PMID: 31155931 DOI: 10.1080/1062936x.2019.1619621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Selection of key descriptors is very important in QSPR analysis. Presence of noise in the subset of descriptors reduces the quality of predictions. A complete set is considered as perfect when it does not include irrelevant or redundant elements. This paper reports complete sets of descriptors used to develop QSPR models for 1786 13C NMR chemical shifts (δC parameters) of carbon atoms in 125 diverse chemical compounds. PBE1PBE/6-311G(2d,2p) and B3LYP/6-31G(d) basis sets were used for quantum chemistry calculations after the molecular structures were optimized with semi-empirical AM1 and B3LYP/6-31G(d). The two complete sets consisting of magnetic shielding elements (σXX, σYY, σZZ) and the chemical shift principal values (σ11, σ22, σ33) were used as the inputs for support vector machine (SVM) models of δC parameters. The four SVM models obtained have the mean root mean square (rms) errors of about 4.5-4.6 ppm. The results suggest that SVM models are accurate and acceptable compared with previous models, although our models are based on a relatively large set of compounds. Our approach is valuable in the selection of important descriptors for QSPR studies of δC parameters.
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Affiliation(s)
- Y Xia
- a China Key Laboratory of Advanced Packaging Materials and Technology of Hunan Province, School of Packaging and Materials Engineering , Hunan University of Technology , Zhuzhou , China
| | - H Zhang
- b Chinese Mechanical Engineering Society , Beijing , China
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16
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Karg B, Mohr S, Weisz K. Duplex‐gesteuerte Umfaltung in neuartige G‐Quadruplex‐(3+1)‐ Hybridkonformationen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Beatrice Karg
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Swantje Mohr
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Klaus Weisz
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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17
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Yu XL, Deng JY, Chen JF, Yang HQ. Prediction of 13C NMR Chemical Shifts of Quinolone Derivatives Based on DFT Calculations. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619050093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52. Molecules 2019; 24:molecules24071294. [PMID: 30987050 PMCID: PMC6479982 DOI: 10.3390/molecules24071294] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 11/17/2022] Open
Abstract
The potential to affect gene expression via G-quadruplex stabilization has been extended to all domains of life, including viruses. Here, we investigate the polymorphism and structures of G-quadruplexes of the human papillomavirus type 52 with UV, CD and NMR spectroscopy and gel electrophoresis. We show that oligonucleotide with five G-tracts folds into several structures and that naturally occurring single nucleotide polymorphisms (SNPs) have profound effects on the structural polymorphism in the context of G-quadruplex forming propensity, conformational heterogeneity and folding stability. With help of SNP analysis, we were able to select one of the predominant forms, formed by G-rich sequence d(G₃TAG₃CAG₄ACACAG₃T). This oligonucleotide termed HPV52(1-4) adopts a three G-quartet snap back (3 + 1) type scaffold with four syn guanine residues, two edgewise loops spanning the same groove, a no-residue V loop and a propeller type loop. The first guanine residue is incorporated in the central G-quartet and all four-guanine residues from G4 stretch are included in the three quartet G-quadruplex core. Modification studies identified several structural elements that are important for stabilization of the described G-quadruplex fold. Our results expand set of G-rich targets in viral genomes and address the fundamental questions regarding folding of G-rich sequences.
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19
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Kennedy SD, Bauer WJ, Wang W, Kielkopf CL. Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites. Biochem Biophys Res Commun 2019; 511:416-421. [PMID: 30797552 DOI: 10.1016/j.bbrc.2019.02.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 11/19/2022]
Abstract
The pre-mRNA branch point sequence (BPS) anneals with a pseudouridine-modified region of the U2 small nuclear (sn)RNA, and offers a 2' hydroxyl group of a bulged adenosine as the nucleophile for the first catalytic step of pre-mRNA splicing. To increase our structural understanding of branch site selection, we characterized a duplex containing a BPS sequence that is common among multicellular eukaryotes (5'-UACUGAC-3') and the complementary U2 snRNA site using NMR. A major conformation of the expected branch site adenosine stacked within the duplex and paired with the conserved pseudouridine of the U2 snRNA strand. In contrast, the guanosine preceding the branch site appeared flexible and had weak contacts with the surrounding nucleotides. Pseudouridine-modified and unmodified U2 snRNA-BPS-containing duplexes remained structurally similar. These results highlight the importance of auxiliary factors to achieve the active bulged conformation of the branch site nucleophile for the first step of pre-mRNA splicing.
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Affiliation(s)
- Scott D Kennedy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
| | - William J Bauer
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Wenhua Wang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
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20
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Filitcheva J, Edwards PJB, Norris GE, Filichev VV. α-2′-Deoxyguanosine can switch DNA G-quadruplex topologies from antiparallel to parallel. Org Biomol Chem 2019; 17:4031-4042. [DOI: 10.1039/c9ob00360f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-2′-Deoxyguanosine (α-dG) converts antiparallel, dimeric G-quadruplex DNA into a parallel, tetramolecular complex.
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Affiliation(s)
- Jana Filitcheva
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
| | | | - Gillian E. Norris
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - Vyacheslav V. Filichev
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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21
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Haase L, Dickerhoff J, Weisz K. DNA–RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies. Chemistry 2018; 24:15365-15371. [DOI: 10.1002/chem.201803367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/05/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Linn Haase
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Jonathan Dickerhoff
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
- Present address: Department of Medicinal Chemistry and Molecular PharmacologyCollege of PharmacyPurdue University West Lafayette IN 47907 USA
| | - Klaus Weisz
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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22
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Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. JOURNAL OF BIOMOLECULAR NMR 2018; 70:229-244. [PMID: 29675775 PMCID: PMC6048961 DOI: 10.1007/s10858-018-0177-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 05/20/2023]
Abstract
NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson-Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1A-T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3' and C4' spin relaxation in the rotating frame (R1ρ) in uniformly 13C/15N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m1A-T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state A-T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Mary C. Clay
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- To whom correspondence should be addressed. Telephone: (919) 660-1113, or
| | - Hashim M. Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- To whom correspondence should be addressed. Telephone: (919) 660-1113, or
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23
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Martínez FA, Aucar GA. Intermolecular magnetic interactions in stacked DNA base pairs. Phys Chem Chem Phys 2017; 19:27817-27827. [PMID: 28990030 DOI: 10.1039/c7cp04484d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.
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Affiliation(s)
- Fernando A Martínez
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física - Facultad de Ciencias Exactas y Naturales, UNNE, Avda Libertad 5460, W3404AAS, Corrientes, Argentina.
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24
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Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res 2017; 45:e134. [PMID: 28609788 PMCID: PMC5737546 DOI: 10.1093/nar/gkx525] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/15/2022] Open
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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Affiliation(s)
- Mary C. Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura R. Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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25
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Dickerhoff J, Haase L, Langel W, Weisz K. Tracing Effects of Fluorine Substitutions on G-Quadruplex Conformational Changes. ACS Chem Biol 2017; 12:1308-1315. [PMID: 28318229 DOI: 10.1021/acschembio.6b01096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A human telomere sequence that folds into an intramolecular (3 + 1)-hybrid G-quadruplex was modified by the incorporation of 2'-fluoro-2'-deoxyriboguanosines (FG) into syn positions of its outer tetrad. A circular dichroism and NMR spectral analysis reveals a nearly quantitative switch of the G-tetrad polarity with concerted syn↔anti transitions of all four G residues. These observations follow findings on a FG-substituted (3 + 1)-hybrid quadruplex with a different fold, suggesting a more general propensity of hybrid-type quadruplexes to undergo a tetrad polarity reversal. Two out of the three FG analogs in both modified quadruplexes adopt an S-type sugar pucker, challenging a sole contribution of N-type sugars in enforcing an anti glycosidic torsion angle associated with the tetrad flip. NMR restrained three-dimensional structures of the two substituted quadruplexes reveal a largely conserved overall fold but significant rearrangements of the overhang and loop nucleotides capping the flipped tetrad. Sugar pucker preferences of the FG analogs may be rationalized by different orientations of the fluorine atom and its resistance to be positioned within the narrow groove with its highly negative electrostatic potential and spine of water molecules.
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Affiliation(s)
- Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Linn Haase
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Walter Langel
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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26
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Fukal J, Páv O, Buděšínský M, Šebera J, Sychrovský V. The benchmark of 31P NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate. Phys Chem Chem Phys 2017; 19:31830-31841. [DOI: 10.1039/c7cp06969c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A benchmark for structural interpretation of the 31P NMR shift and the 2JP,C spin–spin coupling in the phosphate group was obtained by means of theoretical calculations and measurements in diethylphosphate and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide.
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Affiliation(s)
- Jiří Fukal
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Department of Electrotechnology
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27
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Karg B, Haase L, Funke A, Dickerhoff J, Weisz K. Observation of a Dynamic G-Tetrad Flip in Intramolecular G-Quadruplexes. Biochemistry 2016; 55:6949-6955. [PMID: 27951645 DOI: 10.1021/acs.biochem.6b00925] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A MYC sequence forming an intramolecular G-quadruplex with a parallel topology was modified by the incorporation of 8-bromoguanosine (BrG) analogues in one of its outer G-tetrads. The propensity of the BrG analogues to adopt a syn glycosidic torsion angle results in an exceptional monomolecular quadruplex conformation featuring a complete flip of one tetrad while keeping a parallel orientation of all G-tracts as shown by circular dichroism and nuclear magnetic resonance spectroscopic studies. When substituting three of the four G-tetrad residues with BrG analogues, two coexisting quadruplex conformational isomers with an all-syn and all-anti outer G-quartet are approximately equally populated in solution. A dynamic interconversion of the two quadruplexes with an exchange rate (kex) of 0.2 s-1 is demonstrated through the observation of exchange crosspeaks in rotating frame Overhauser effect spectroscopy and nuclear Overhauser effect spectroscopy experiments at 50 °C. The kinetic properties suggest disruption of the corresponding outer G-tetrad but not of the whole quadruplex core during the tetrad flip. Conformational syn-anti isomers with homopolar and heteropolar stacking interactions are nearly isoenergetic with a transition enthalpy of 18.2 kJ/mol in favor of the all-syn isomer.
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Affiliation(s)
- Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Linn Haase
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Andrea Funke
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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28
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Dickerhoff J, Appel B, Müller S, Weisz K. Zuckerseitige Wechselwirkungen in einem DNA-RNA-G-Quadruplex: Hinweise auf sequentielle C−H⋅⋅⋅O-Wasserstoffbrücken als Beitrag zur RNA-Quadruplex-Faltung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Klaus Weisz
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
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29
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Dickerhoff J, Appel B, Müller S, Weisz K. Sugar-Edge Interactions in a DNA-RNA G-Quadruplex: Evidence of Sequential C-H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding. Angew Chem Int Ed Engl 2016; 55:15162-15165. [PMID: 27860177 DOI: 10.1002/anie.201608275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/29/2016] [Indexed: 11/11/2022]
Abstract
DNA G-quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti-dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA-RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3'-side within the quadruplex core strongly suggest the presence of C8-H⋅⋅⋅O hydrogen-bonding interactions with the O2' position of the C2'-endo ribonucleotide. A geometric analysis of reported high-resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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30
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Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 2016; 23:803-10. [PMID: 27478929 PMCID: PMC5016226 DOI: 10.1038/nsmb.3270] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/05/2016] [Indexed: 12/13/2022]
Abstract
The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result,N(1)-methyladenosine and N(1)-methylguanosine, which occur in DNA as a form of alkylation damage and in RNA as post-transcriptional modifications, have dramatically different consequences. Whereas they create G-C(+) and A-T Hoogsteen base pairs in duplex DNA, thereby maintaining the structural integrity of the double helix, they block base-pairing and induce local duplex melting in RNA. These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Isaac J. Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Evgenia N. Nikolova
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California USA
| | | | - Gianmarc Grazioli
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - James McSally
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Tianyu Bai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | | | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck Austria
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
- Department of Chemistry, Duke University, Durham, North Carolina USA
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31
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Dračínský M, Šála M, Klepetářová B, Šebera J, Fukal J, Holečková V, Tanaka Y, Nencka R, Sychrovský V. Benchmark Theoretical and Experimental Study on 15N NMR Shifts of Oxidatively Damaged Guanine. J Phys Chem B 2016; 120:915-25. [DOI: 10.1021/acs.jpcb.5b11428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Blanka Klepetářová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Jakub Šebera
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
| | - Jiří Fukal
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Veronika Holečková
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Yoshiyuki Tanaka
- Faculty
of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihama-Boji, Yamashirocho, Tokushima, Tokushima 980-8578, Japan
| | - Radim Nencka
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Vladimír Sychrovský
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
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32
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Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Fiala R, Boelens R, Sklenář V, Trantírek L. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:53-62. [PMID: 26685997 PMCID: PMC4742510 DOI: 10.1007/s10858-015-0005-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.
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Affiliation(s)
- Andrea Vavrinská
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiří Zelinka
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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33
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Brown JD, Summers MF, Johnson BA. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression. JOURNAL OF BIOMOLECULAR NMR 2015; 63:39-52. [PMID: 26141454 PMCID: PMC4669054 DOI: 10.1007/s10858-015-9961-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/29/2015] [Indexed: 05/29/2023]
Abstract
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.
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Affiliation(s)
- Joshua D Brown
- Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Michael F Summers
- Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Bruce A Johnson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
- One Moon Scientific, Inc., 839 Grant Ave., Westfield, NJ, 07090, USA.
- CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
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34
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Condon D, Kennedy SD, Mort BC, Kierzek R, Yildirim I, Turner DH. Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. J Chem Theory Comput 2015; 11:2729-2742. [PMID: 26082675 PMCID: PMC4463549 DOI: 10.1021/ct501025q] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Molecular dynamics (MD) simulations for RNA tetramers r(AAAA), r(CAAU), r(GACC), and r(UUUU) are benchmarked against 1H-1H NOESY distances and 3J scalar couplings to test effects of RNA torsion parametrizations. Four different starting structures were used for r(AAAA), r(CAAU), and r(GACC), while five starting structures were used for r(UUUU). On the basis of X-ray structures, criteria are reported for quantifying stacking. The force fields, AMBER ff99, parmbsc0, parm99χ_Yil, ff10, and parmTor, all predict experimentally unobserved stacks and intercalations, e.g., base 1 stacked between bases 3 and 4, and incorrect χ, ϵ, and sugar pucker populations. The intercalated structures are particularly stable, often lasting several microseconds. Parmbsc0, parm99χ_Yil, and ff10 give similar agreement with NMR, but the best agreement is only 46%. Experimentally unobserved intercalations typically are associated with reduced solvent accessible surface area along with amino and hydroxyl hydrogen bonds to phosphate nonbridging oxygens. Results from an extensive set of MD simulations suggest that recent force field parametrizations improve predictions, but further improvements are necessary to provide reasonable agreement with NMR. In particular, intramolecular stacking and hydrogen bonding interactions may not be well balanced with the TIP3P water model. NMR data and the scoring method presented here provide rigorous benchmarks for future changes in force fields and MD methods.
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Affiliation(s)
- David
E. Condon
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Scott D. Kennedy
- Department
of Biochemistry and Biophysics, University
of Rochester, Rochester, New York 14642, United States
| | - Brendan C. Mort
- University
of Rochester Center for Integrated Research Computing, Rochester, New York 14627, United States
| | - Ryszard Kierzek
- Institute
of Bioorganic Chemistry, Polish Academy
of Sciences, 60-704 Poznan, Poland
| | - Ilyas Yildirim
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Douglas H. Turner
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
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35
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Bazzi S, Novotný J, Yurenko YP, Marek R. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands. Chemistry 2015; 21:9414-25. [PMID: 26032561 DOI: 10.1002/chem.201500743] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 01/13/2023]
Abstract
A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na(+) /K(+) ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased π-π stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands.
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Affiliation(s)
- Sophia Bazzi
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Jan Novotný
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Yevgen P Yurenko
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
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36
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Dickerhoff J, Weisz K. Flipping a G-tetrad in a unimolecular quadruplex without affecting its global fold. Angew Chem Int Ed Engl 2015; 54:5588-91. [PMID: 25775974 DOI: 10.1002/anie.201411887] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/22/2015] [Indexed: 11/07/2022]
Abstract
A unimolecular G-quadruplex with a hybrid-type topology and propeller, diagonal, and lateral loops was examined for its ability to undergo structural changes upon specific modifications. Substituting 2'-deoxy-2'-fluoro analogues with a propensity to adopt an anti glycosidic conformation for two or three guanine deoxyribonucleosides in syn positions of the 5'-terminal G-tetrad significantly alters the CD spectral signature of the quadruplex. An NMR analysis reveals a polarity switch of the whole tetrad with glycosidic conformational changes detected for all four guanine nucleosides in the modified sequence. As no additional rearrangement of the overall fold occurs, a novel type of G-quadruplex is formed with guanosines in the four columnar G-tracts lined up in either an all-syn or an all-anti glycosidic conformation.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)
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37
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Dickerhoff J, Weisz K. Flipping a G-Tetrad in a Unimolecular Quadruplex Without Affecting Its Global Fold. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Carvalho ATP, Gouveia ML, Raju Kanna C, Wärmländer SKTS, Platts J, Kamerlin SCL. Theoretical modelling of epigenetically modified DNA sequences. F1000Res 2015; 4:52. [PMID: 26448859 DOI: 10.12688/f1000research.6148.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2015] [Indexed: 11/20/2022] Open
Abstract
We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.
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Affiliation(s)
| | - Maria Leonor Gouveia
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, S-751 85, Sweden
| | - Charan Raju Kanna
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
| | | | - Jamie Platts
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
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39
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Carvalho ATP, Gouveia ML, Raju Kanna C, Wärmländer SKTS, Platts J, Kamerlin SCL. Theoretical modelling of epigenetically modified DNA sequences. F1000Res 2015; 4:52. [PMID: 26448859 PMCID: PMC4582758 DOI: 10.12688/f1000research.6148.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2015] [Indexed: 12/20/2022] Open
Abstract
We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.
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Affiliation(s)
| | - Maria Leonor Gouveia
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, S-751 85, Sweden
| | - Charan Raju Kanna
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
| | | | - Jamie Platts
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
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40
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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41
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Dairaku T, Furuita K, Sato H, Šebera J, Yamanaka D, Otaki H, Kikkawa S, Kondo Y, Katahira R, Matthias Bickelhaupt F, Fonseca Guerra C, Ono A, Sychrovský V, Kojima C, Tanaka Y. Direct detection of the mercury–nitrogen bond in the thymine–HgII–thymine base-pair with 199Hg NMR spectroscopy. Chem Commun (Camb) 2015; 51:8488-91. [DOI: 10.1039/c5cc02423d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
One-bond 199Hg–15N J-coupling.
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42
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Victora A, Möller HM, Exner TE. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes. Nucleic Acids Res 2014; 42:e173. [PMID: 25404135 PMCID: PMC4267612 DOI: 10.1093/nar/gku1006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
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Affiliation(s)
- Andrea Victora
- Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457 Konstanz, Germany
| | - Heiko M Möller
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam OT Golm, Germany
| | - Thomas E Exner
- Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457 Konstanz, Germany Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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Abramov G, Goldbourt A. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 59:219-230. [PMID: 24875850 DOI: 10.1007/s10858-014-9840-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply the magic-angle spinning (MAS) solid-state NMR (SSNMR) technique to study a uniformly (13)C and (15)N labeled wild-type T7 phage. We describe the details of the large-scale preparation and purification of an isotopically enriched phage sample under fully hydrated conditions, and show a complete (13)C and a near-complete (15)N nucleotide-type specific assignment of the sugar and base moieties in the 40 kbp dsDNA of T7 using two-dimensional (13)C-(13)C and (15)N-(13)C correlation experiments. The chemical shifts are interpreted as reporters of a B-form conformation of the encapsulated dsDNA. While MAS SSNMR was found to be extremely useful in determining the structures of proteins in native-like environments, its application to nucleic acids has lagged behind, leaving a missing (13)C and (15)N chemical shift database. This work therefore expands the (13)C and (15)N database of real B-form DNA systems, and opens routes to characterize more complex nucleic acid systems by SSNMR.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 69978, Ramat Aviv, Tel Aviv, Israel
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Morag O, Abramov G, Goldbourt A. Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell. J Am Chem Soc 2014; 136:2292-301. [PMID: 24447194 DOI: 10.1021/ja412178n] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.
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Affiliation(s)
- Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Ramat Aviv 69978, Tel Aviv, Israel
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Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J. Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J Chem Theory Comput 2013; 10:463-80. [PMID: 26579924 DOI: 10.1021/ct400837p] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.
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Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC, Central European Institute of Technology , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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Frank AT, Bae SH, Stelzer AC. Prediction of RNA 1H and 13C chemical shifts: a structure based approach. J Phys Chem B 2013; 117:13497-506. [PMID: 24033307 DOI: 10.1021/jp407254m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of NMR-derived chemical shifts in protein structure determination and prediction has received much attention, and, as such, many methods have been developed to predict protein chemical shifts from three-dimensional (3D) coordinates. In contrast, little attention has been paid to predicting chemical shifts from RNA coordinates. Using the random forest machine learning approach, we developed RAMSEY, which is capable of predicting both (1)H and protonated (13)C chemical shifts from RNA coordinates. In this report, we introduce RAMSEY, assess its accuracy, and demonstrate the sensitivity of RAMSEY-predicted chemical shifts to RNA 3D structure.
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Affiliation(s)
- Aaron T Frank
- Nymirum , 3510 West Liberty Road, Ann Arbor, Michigan 48103, United States
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Aeschbacher T, Schmidt E, Blatter M, Maris C, Duss O, Allain FHT, Güntert P, Schubert M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucleic Acids Res 2013; 41:e172. [PMID: 23921634 PMCID: PMC3794610 DOI: 10.1093/nar/gkt665] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson–Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs.
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Affiliation(s)
- Thomas Aeschbacher
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, 60438 Frankfurt am Main, Germany and Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012; 14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
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