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Shedding light on the base-pair opening dynamics of nucleic acids in living human cells. Nat Commun 2022; 13:7143. [PMID: 36446768 PMCID: PMC9708698 DOI: 10.1038/s41467-022-34822-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
Base-pair opening is a fundamental property of nucleic acids that plays important roles in biological functions. However, studying the base-pair opening dynamics inside living cells has remained challenging. Here, to determine the base-pair opening kinetics inside living human cells, the exchange rate constant ([Formula: see text]) of the imino proton with the proton of solvent water involved in hairpin and G-quadruplex (GQ) structures is determined by the in-cell NMR technique. It is deduced on determination of [Formula: see text] values that at least some G-C base pairs of the hairpin structure and all G-G base-pairs of the GQ structure open more frequently in living human cells than in vitro. It is suggested that interactions with endogenous proteins could be responsible for the increase in frequency of base-pair opening. Our studies demonstrate a difference in dynamics of nucleic acids between in-cell and in vitro conditions.
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Zhao S, Li X, Wen Z, Zou M, Yu G, Liu X, Mao J, Zhang L, Xue Y, Fu R, Wang S. Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy. iScience 2022; 25:105322. [DOI: 10.1016/j.isci.2022.105322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022] Open
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3
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Liu B, Shi H, Rangadurai A, Nussbaumer F, Chu CC, Erharter KA, Case DA, Kreutz C, Al-Hashimi HM. A quantitative model predicts how m 6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. Nat Commun 2021; 12:5201. [PMID: 34465779 PMCID: PMC8408185 DOI: 10.1038/s41467-021-25253-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/21/2021] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using temperature-dependent (20°C-65°C) NMR relaxation dispersion, we show that m6A pairs with uridine with the methylamino group in the anti conformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group is syn. This ability to rapidly interchange between Watson-Crick or mismatch-like forms, combined with different syn:anti isomer preferences when paired (~1:100) versus unpaired (~10:1), explains how m6A robustly slows duplex annealing without affecting melting at elevated temperatures via two pathways in which isomerization occurs before or after duplex annealing. Our model quantitatively predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions, and provides an explanation for why the modification robustly slows diverse cellular processes.
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Affiliation(s)
- Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kevin Andreas Erharter
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - 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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Marušič M, Schlagnitweit J, Petzold K. RNA Dynamics by NMR Spectroscopy. Chembiochem 2019; 20:2685-2710. [PMID: 30997719 PMCID: PMC6899578 DOI: 10.1002/cbic.201900072] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/12/2019] [Indexed: 12/22/2022]
Abstract
An ever-increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined-Lego like-than in proteins, hence the numerous revelations of RNA excited states.
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Affiliation(s)
- Maja Marušič
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
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5
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Ferris ZE, Li Q, Germann MW. Substituting Inosine for Guanosine in DNA: Structural and Dynamic Consequences. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19850032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Inosine differs from the guanosine nucleoside only by the absence of the N2 amino group. Both nucleosides also have similar electrostatic potentials. Therefore, substituting I for G has been used to probe various properties of nucleic acids and to facilitate the interpretation of binding studies. In particular, the absence of the amino group permits the assessment of its importance in the binding of ligands to the minor groove of duplex DNA. It has been known for some time that an I-C base pair is of lower stability than a regular G-C base pair, which needs to be considered when making DNA constructs containing inosine. However, it is generally assumed that both base pairs are structurally highly similar. To test this assumption in an identical sequence environment, we have determined the fine structure of two hairpin DNA substrates that differ only in the substitution of an I-C base pair for a G-C base pair. The structures have been solved using nuclear magnetic resonance (NMR) restraints in conjunction with Mardigras and molecular dynamics. The structural data are complemented with thermodynamic and dynamic data to get a comprehensive evaluation of the consequences of G-C vs I-C base pair substitutions. Our data show a strong similarity in the structures of the hairpins, but a significant difference in the melting temperatures, T m. This difference is also reflected in the drastically decreased base pair lifetime of 7.4 milliseconds compared to the G-C base pair lifetime of 155 milliseconds. The substitution of I-C for G-C is to probe for specific effect due to the amino group is satisfactory, as long as the lowered thermal stability and the drastically increased local dynamics are considered.
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Affiliation(s)
| | - Qiushi Li
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Department of Biology, Georgia State University, Atlanta, GA, USA
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6
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Buchachenko AL, Breslavskaya NN. An Insight into the Helicase Functioning Through the Hydrogen Isotope Effects. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2018. [DOI: 10.1134/s1990793117060185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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Anosova I, Kowal EA, Sisco NJ, Sau S, Liao JY, Bala S, Rozners E, Egli M, Chaput JC, Van Horn WD. Structural Insights into Conformation Differences between DNA/TNA and RNA/TNA Chimeric Duplexes. Chembiochem 2016; 17:1705-8. [PMID: 27347671 DOI: 10.1002/cbic.201600349] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 12/20/2022]
Abstract
Threose nucleic acid (TNA) is an artificial genetic polymer capable of heredity and evolution, and is studied in the context of RNA chemical etiology. It has a four-carbon threose backbone in place of the five-carbon ribose of natural nucleic acids, yet forms stable antiparallel complementary Watson-Crick homoduplexes and heteroduplexes with DNA and RNA. TNA base-pairs more favorably with RNA than with DNA but the reason is unknown. Here, we employed NMR, ITC, UV, and CD to probe the structural and dynamic properties of heteroduplexes of RNA/TNA and DNA/TNA. The results indicate that TNA templates the structure of heteroduplexes, thereby forcing an A-like helical geometry. NMR measurement of kinetic and thermodynamic parameters for individual base pair opening events reveal unexpected asymmetric "breathing" fluctuations of the DNA/TNA helix. The results suggest that DNA is unable to fully adapt to the conformational constraints of the rigid TNA backbone and that nucleic acid breathing dynamics are determined from both backbone and base contributions.
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Affiliation(s)
- Irina Anosova
- School of Molecular Sciences and the Biodesign Institute, Arizona State University, 551 E. University Dr., PSG-106, Tempe, AZ, 85287, USA
| | - Ewa A Kowal
- Department of Biochemistry, Vanderbilt University School of Medicine, Robinson Research Building 868A, Nashville, TN, 37232, USA
| | - Nicholas J Sisco
- School of Molecular Sciences and the Biodesign Institute, Arizona State University, 551 E. University Dr., PSG-106, Tempe, AZ, 85287, USA
| | - Sujay Sau
- Department of Pharmaceutical Sciences, University of California Irvine, 147 Bison Modular, Building 515, Irvine, CA, 92697, USA
| | - Jen-Yu Liao
- Department of Pharmaceutical Sciences, University of California Irvine, 147 Bison Modular, Building 515, Irvine, CA, 92697, USA
| | - Saikat Bala
- Department of Pharmaceutical Sciences, University of California Irvine, 147 Bison Modular, Building 515, Irvine, CA, 92697, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Science 2 Building 308, Binghamton, NY, 13902, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Robinson Research Building 868A, Nashville, TN, 37232, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California Irvine, 147 Bison Modular, Building 515, Irvine, CA, 92697, USA
| | - Wade D Van Horn
- School of Molecular Sciences and the Biodesign Institute, Arizona State University, 551 E. University Dr., PSG-106, Tempe, AZ, 85287, USA.
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Abstract
A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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Szulik M, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry 2015; 54:1294-305. [PMID: 25632825 PMCID: PMC4325598 DOI: 10.1021/bi501534x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.
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Affiliation(s)
- Marta
W. Szulik
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pradeep S. Pallan
- Department
of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, School of
Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boguslaw Nocek
- Bioscience
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Markus Voehler
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Surajit Banerjee
- Northeastern
Collaborative Access Team and Department of Chemistry and Chemical
Biology, Cornell University, Argonne National
Laboratory, Argonne, Illinois 60439, United
States
| | - Sonja Brooks
- Department
of Biological Sciences, Vanderbilt Institute of Chemical Biology,
and Center for Structural Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Andrzej Joachimiak
- Bioscience
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Martin Egli
- Department
of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, School of
Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brandt F. Eichman
- Department
of Biological Sciences, Vanderbilt Institute of Chemical Biology,
and Center for Structural Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States,(M.P.S.) Tel.: 615-322-2589; E-mail:
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