1
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Chapman J, Paukner M, Leser M, Teng KW, Koide S, Holder M, Armache KJ, Becker C, Ueberheide B, Brenowitz M. Systematic Fe(II)-EDTA Method of Dose-Dependent Hydroxyl Radical Generation for Protein Oxidative Footprinting. Anal Chem 2023; 95:18316-18325. [PMID: 38049117 PMCID: PMC10734636 DOI: 10.1021/acs.analchem.3c02319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
Correlating the structure and dynamics of proteins with biological function is critical to understanding normal and dysfunctional cellular mechanisms. We describe a quantitative method of hydroxyl radical generation via Fe(II)-ethylenediaminetetraacetic acid (EDTA)-catalyzed Fenton chemistry that provides ready access to protein oxidative footprinting using equipment commonly found in research and process control laboratories. Robust and reproducible dose-dependent oxidation of protein samples is observed and quantitated by mass spectrometry with as fine a single residue resolution. An oxidation analysis of lysozyme provides a readily accessible benchmark for our method. The efficacy of our oxidation method is demonstrated by mapping the interface of a RAS-monobody complex, the surface of the NIST mAb, and the interface between PRC2 complex components. These studies are executed using standard laboratory tools and a few pennies of reagents; the mass spectrometry analysis can be streamlined to map the protein structure with single amino acid residue resolution.
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Affiliation(s)
- Jessica
R. Chapman
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
| | - Max Paukner
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Micheal Leser
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Kai Wen Teng
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
| | - Shohei Koide
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Marlene Holder
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Karim-Jean Armache
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Chris Becker
- Protein
Metrics Inc., Cupertino, California 95014, United States
| | - Beatrix Ueberheide
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Michael Brenowitz
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department
of Molecular Pharmacology, Albert Einstein
College of Medicine, Bronx, New York 10461, United States
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2
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Patel S, Sexton AN, Strine MS, Wilen CB, Simon MD, Pyle AM. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nat Commun 2023; 14:3426. [PMID: 37296103 PMCID: PMC10255950 DOI: 10.1038/s41467-023-38623-1] [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: 09/12/2022] [Accepted: 05/09/2023] [Indexed: 06/12/2023] Open
Abstract
Compact RNA structural motifs control many aspects of gene expression, but we lack methods for finding these structures in the vast expanse of multi-kilobase RNAs. To adopt specific 3-D shapes, many RNA modules must compress their RNA backbones together, bringing negatively charged phosphates into close proximity. This is often accomplished by recruiting multivalent cations (usually Mg2+), which stabilize these sites and neutralize regions of local negative charge. Coordinated lanthanide ions, such as terbium (III) (Tb3+), can also be recruited to these sites, where they induce efficient RNA cleavage, thereby revealing compact RNA 3-D modules. Until now, Tb3+ cleavage sites were monitored via low-throughput biochemical methods only applicable to small RNAs. Here we present Tb-seq, a high-throughput sequencing method for detecting compact tertiary structures in large RNAs. Tb-seq detects sharp backbone turns found in RNA tertiary structures and RNP interfaces, providing a way to scan transcriptomes for stable structural modules and potential riboregulatory motifs.
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Affiliation(s)
- Shivali Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Anna Marie Pyle
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
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3
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Amirloo B, Staroseletz Y, Yousaf S, Clarke DJ, Brown T, Aojula H, Zenkova MA, Bichenkova EV. "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates. Nucleic Acids Res 2021; 50:651-673. [PMID: 34967410 PMCID: PMC8789077 DOI: 10.1093/nar/gkab1273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge-loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge-loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
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Affiliation(s)
- Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Sameen Yousaf
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Harmesh Aojula
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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4
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McKenzie-Coe A, Montes NS, Jones LM. Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins. Chem Rev 2021; 122:7532-7561. [PMID: 34633178 DOI: 10.1021/acs.chemrev.1c00432] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.
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Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicholas S Montes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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5
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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6
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Xie J, Frank AT. RNA Ensembles from Solvent Accessibility Data: Application to the SAM-I Riboswitch Aptamer Domain. J Phys Chem B 2021; 125:3486-3493. [PMID: 33818089 DOI: 10.1021/acs.jpcb.0c11503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Riboswitches are regulatory ribonucleic acid (RNA) elements that act as ligand-dependent conformational switches that recognize their cognate ligand via a binding pocket located in their aptamer domain. In the apo form, the aptamer domain is dynamic, requiring an ensemble representation of its structure. Here, as a proof-of-concept, we used solvent accessibility information to construct a pair of dynamical ensembles of the aptamer domain of the well-studied S-adenosylmethionine (SAM) class-I riboswitch in the absence (-SAM) and presence (+SAM) of SAM. To achieve this, we first generated a large conformational library and then reweighted conformers in the library using solvent-accessible surface area (SASA) data derived from recently reported light-activated structural examination of RNA (LASER) reactivities measured in the -SAM and +SAM states of the riboswitch. The differences in the resulting -SAM and +SAM ensembles are consistent with a SAM-dependent reshaping of the free-energy landscape of the aptamer domain. Within our -SAM ensemble, we identified a "transient" state that is missing a critical long-range contact, leading us to speculate that it may be representative of a folding intermediate. Further structural analysis also revealed that the transient state harbors a hidden binding pocket that is distinct from the SAM-binding pocket and is predicted by docking calculations to selectively bind small-molecule ligands. The SASA-based method we applied to the SAM-I riboswitch aptamer domain is general and could be used to construct dynamical ensembles for other riboswitch aptamer domains and, more broadly, other classes of structured RNAs.
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Affiliation(s)
- Jingru Xie
- Physics Department, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aaron T Frank
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Chemistry Department, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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8
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Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke DH. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Res 2020; 48:2709-2722. [PMID: 31943114 PMCID: PMC7049723 DOI: 10.1093/nar/gkz1224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit RT in enzymatic and viral replication assays. Some aptamers inhibit RT from only a few viral clades, while others show broad-spectrum inhibition. Biophysical determinants of recognition specificity are poorly understood. We investigated the interface between HIV-1 RT and a broad–spectrum UCAA-family aptamer. SAR and hydroxyl radical probing identified aptamer structural elements critical for inhibition and established the role of signature UCAA bulge motif in RT-aptamer interaction. HDX footprinting on RT ± aptamer shows strong contacts with both subunits, especially near the C-terminus of p51. Alanine scanning revealed decreased inhibition by the aptamer for mutants P420A, L422A and K424A. 2D proton nuclear magnetic resonance and SAXS data provided constraints on the solution structure of the aptamer and enable computational modeling of the docked complex with RT. Surprisingly, the aptamer enhanced proteolytic cleavage of precursor p66/p66 by HIV-1 protease, suggesting that it stabilizes the productive conformation to allow maturation. These results illuminate features at the RT-aptamer interface that govern recognition specificity by a broad-spectrum antiviral aptamer, and they open new possibilities for accelerating RT maturation and interfering with viral replication.
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Affiliation(s)
- Phuong D M Nguyen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Liming Qiu
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Dong Zhang
- Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA
| | - Steve Tuske
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
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9
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Mailler E, Paillart JC, Marquet R, Smyth RP, Vivet-Boudou V. The evolution of RNA structural probing methods: From gels to next-generation sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1518. [PMID: 30485688 DOI: 10.1002/wrna.1518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023]
Abstract
RNA molecules are important players in all domains of life and the study of the relationship between their multiple flexible states and the associated biological roles has increased in recent years. For several decades, chemical and enzymatic structural probing experiments have been used to determine RNA structure. During this time, there has been a steady improvement in probing reagents and experimental methods, and today the structural biologist community has a large range of tools at its disposal to probe the secondary structure of RNAs in vitro and in cells. Early experiments used radioactive labeling and polyacrylamide gel electrophoresis as read-out methods. This was superseded by capillary electrophoresis, and more recently by next-generation sequencing. Today, powerful structural probing methods can characterize RNA structure on a genome-wide scale. In this review, we will provide an overview of RNA structural probing methodologies from a historical and technical perspective. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Methods > RNA Analyses in vitro and In Silico RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Elodie Mailler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Roland Marquet
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | - Redmond P Smyth
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | - Valerie Vivet-Boudou
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
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10
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Extracting information from RNA SHAPE data: Kalman filtering approach. PLoS One 2018; 13:e0207029. [PMID: 30462682 PMCID: PMC6248965 DOI: 10.1371/journal.pone.0207029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/23/2018] [Indexed: 01/26/2023] Open
Abstract
RNA SHAPE experiments have become important and successful sources of information for RNA structure prediction. In such experiments, chemical reagents are used to probe RNA backbone flexibility at the nucleotide level, which in turn provides information on base pairing and therefore secondary structure. Little is known, however, about the statistics of such SHAPE data. In this work, we explore different representations of noise in SHAPE data and propose a statistically sound framework for extracting reliable reactivity information from multiple SHAPE replicates. Our analyses of RNA SHAPE experiments underscore that a normal noise model is not adequate to represent their data. We propose instead a log-normal representation of noise and discuss its relevance. Under this assumption, we observe that processing simulated SHAPE data by directly averaging different replicates leads to bias. Such bias can be reduced by analyzing the data following a log transformation, either by log-averaging or Kalman filtering. Application of Kalman filtering has the additional advantage that a prior on the nucleotide reactivities can be introduced. We show that the performance of Kalman filtering is then directly dependent on the quality of that prior. We conclude the paper with guidelines on signal processing of RNA SHAPE data.
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11
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Murugan E, J NJ, Ariraman M, Rajendran S, Kathirvel J, Akshata CR, Kumar K. Core-Shell Nanostructured Fe 3O 4-Poly(styrene- co-vinylbenzyl chloride) Grafted PPI Dendrimers Stabilized with AuNPs/PdNPs for Efficient Nuclease Activity. ACS OMEGA 2018; 3:13685-13693. [PMID: 30411048 PMCID: PMC6217652 DOI: 10.1021/acsomega.8b01326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Four different novel magnetic core-shell nanocomposites stabilized with Au/Pd nanoparticles (NPs) were prepared by a simple procedure and demonstrated their catalytic activity for effective cleavage of pBR322 DNA. Initially, the Fe3O4-poly(styrene-divinylbenzene-vinylbenzyl chloride) (ST-DVB-VBC) matrix functionalized with 3-aminobenzoic acid was prepared and grafted with PPI-G(2) and PPI-G(3) dendrimers. Each core-shell matrix was immobilized with AuNPs and PdNPs separately. The resulting composites were characterized by FT-IR, UV-vis, SEM, TEM, XRD, VSM, XPS, Raman, and TGA. The magnetic core-shell nanocomposites at concentrations from 30 to 50 μM were employed separately to study DNA cleavage by agarose gel electrophoresis. Among the four magnetic core-shell nanocomposites, Fe3O4-poly(ST-DVB-VBC)-PPI-G(3)-AuNPs showed higher activity than others for DNA cleavage, and formed Form-II and -III DNA. When the concentration of Fe3O4-poly(ST-DVB-VBC)-PPI-G(3)-AuNPs was increased from 40 to 45 and 45 to 50 μM, Form-III (linear) DNA was observed with 10 and 22%, respectively, in addition to Form-II. This observation suggests formation of linear DNA from the supercoiled DNA via nicked DNA-intermediated consecutive cleaving process. The magnetic core-shell nanocomposites were stable and monodispersed, and exhibited rapid magnetic response. These properties are crucial for their application in biomolecular separations and targeted drug-delivery in the future.
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Affiliation(s)
- Eagambaram Murugan
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
| | - Nimita Jebaranjitham J
- PG
Department of Chemistry, Women’s
Christian College (An Autonomous Institution Affiliated to University
of Madras), College Road, Chennai 600 006, India
| | - Mathivathanan Ariraman
- Department
of Chemical Engineering, National Chung
Hsing University, Taichung
City 402, Taiwan
| | - Saravanan Rajendran
- Escuela
Universitaria de Ingeniería Mecánica (EUDIM), Universidad de Tarapacá, Avda. General Velásquez, 1775 Arica, Chile
| | - Janankiraman Kathirvel
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
| | - C. R. Akshata
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
| | - Kalpana Kumar
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
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12
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Limpikirati P, Liu T, Vachet RW. Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions. Methods 2018; 144:79-93. [PMID: 29630925 PMCID: PMC6051898 DOI: 10.1016/j.ymeth.2018.04.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
Using mass spectrometry (MS) to obtain information about a higher order structure of protein requires that a protein's structural properties are encoded into the mass of that protein. Covalent labeling (CL) with reagents that can irreversibly modify solvent accessible amino acid side chains is an effective way to encode structural information into the mass of a protein, as this information can be read-out in a straightforward manner using standard MS-based proteomics techniques. The differential reactivity of proteins under two or more conditions can be used to distinguish protein topologies, conformations, and/or binding sites. CL-MS methods have been effectively used for the structural analysis of proteins and protein complexes, particularly for systems that are difficult to study by other more traditional biochemical techniques. This review provides an overview of the non-specific CL approaches that have been combined with MS with a particular emphasis on the reagents that are commonly used, including hydroxyl radicals, carbenes, and diethylpyrocarbonate. We describe the reagent and protein factors that affect the reactivity of amino acid side chains. We also include details about experimental design and workflow, data analysis, recent applications, and some future prospects of CL-MS methods.
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Affiliation(s)
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, MA 01003, United States.
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13
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Ledda M, Aviran S. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures. Genome Biol 2018; 19:28. [PMID: 29495968 PMCID: PMC5833111 DOI: 10.1186/s13059-018-1399-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions.
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Affiliation(s)
- Mirko Ledda
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
- Integrative Genetics and Genomics Graduate Group, UC Davis, 1 Shields Ave, Davis, 95616 USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
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14
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Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR, Furche F, Hadad CM, Spitale RC. Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nat Chem Biol 2018; 14:276-283. [PMID: 29334380 PMCID: PMC6203945 DOI: 10.1038/nchembio.2548] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/15/2017] [Indexed: 12/30/2022]
Abstract
The discovery of functional RNAs that are critical for normal and disease physiology continues to expand at a breakneck pace. Many RNA functions are controlled by the formation of specific structures, and an understanding of each structural component is necessary to elucidate its function. Measuring solvent accessibility intracellularly with experimental ease is an unmet need in the field. Here, we present a novel method for probing nucleobase solvent accessibility, Light Activated Structural Examination of RNA (LASER). LASER depends on light activation of a small molecule, nicotinoyl azide (NAz), to measure solvent accessibility of purine nucleobases. In vitro, this technique accurately monitors solvent accessibility and identifies rapid structural changes resulting from ligand binding in a metabolite-responsive RNA. LASER probing can further identify cellular RNA-protein interactions and unique intracellular RNA structures. Our photoactivation technique provides an adaptable framework to structurally characterize solvent accessibility of RNA in many environments.
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Affiliation(s)
- Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
| | - Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
| | - Jojo Joseph
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus Ohio 43210
| | - Mikko Muuronen
- Department of Chemistry, University of California, Irvine. Irvine, California 92697
| | - William H. Coldren
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus Ohio 43210
| | - Nan Dai
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Ivan R. Corrêa
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine. Irvine, California 92697
| | - Christopher M. Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus Ohio 43210
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
- Department of Chemistry, University of California, Irvine. Irvine, California 92697
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15
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Chea EE, Jones LM. Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting. Analyst 2018; 143:798-807. [DOI: 10.1039/c7an01323j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins in live cells.
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Affiliation(s)
- Emily E. Chea
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
| | - Lisa M. Jones
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
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16
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Chakraborty S, Krishnan Y. A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Res 2017; 45:9694-9705. [PMID: 28934477 PMCID: PMC5766152 DOI: 10.1093/nar/gkx613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
The miR-17-92a cluster, also known as 'oncomiR-1', is an RNA transcript that plays a pivotal regulatory role in cellular processes, including the cell cycle, proliferation and apoptosis. Its dysregulation underlies the development of several cancers. Oncomir-1 comprises six constituent miRNAs, each processed with different efficiencies as a function of both developmental time and tissue type. The structural mechanisms that regulate such differential processing are unknown, and this has impeded our understanding of the dysregulation of oncomiR-1 in pathophysiology. By probing the sensitivity of each nucleotide in oncomiR-1 to reactive small molecules, we present a secondary structural map of this RNA at single-nucleotide resolution. The secondary structure and solvent accessible regions of oncomiR-1 reveal that most of its primary microRNA domains are suboptimal substrates for Drosha-DGCR8, and therefore resistant to microprocessing. The structure indicates that the binding of trans-acting factors is required to remodel the tertiary organization and unmask cryptic primary microRNA domains to facilitate their processing into pre-microRNAs.
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Affiliation(s)
- Saikat Chakraborty
- National Centre for Biological Sciences-TIFR, Bangalore, Karnataka 560065, India
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL 60637, USA
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17
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Dawn of the in vivo RNA structurome and interactome. Biochem Soc Trans 2017; 44:1395-1410. [PMID: 27911722 DOI: 10.1042/bst20160075] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/19/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale. In this review, molecular tools and NGS methods used for RNA structure probing are presented, novel insights uncovered by RNA structurome and interactome studies are highlighted, and perspectives on current challenges and potential future directions are discussed. A more complete understanding of the RNA structures and interactions in vivo will help illuminate the novel roles of RNA in gene regulation, development, and diseases.
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18
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Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017; 45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
| | - Stefanie Geigle
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
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19
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Zhu Y, Serra A, Guo T, Park JE, Zhong Q, Sze SK. Application of Nanosecond Laser Photolysis Protein Footprinting to Study EGFR Activation by EGF in Cells. J Proteome Res 2017; 16:2282-2293. [DOI: 10.1021/acs.jproteome.7b00154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yi Zhu
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Aida Serra
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Tiannan Guo
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Jung Eun Park
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Qing Zhong
- Department
of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
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20
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Fernandez N, Cordiner RA, Young RS, Hug N, Macias S, Cáceres JF. Genetic variation and RNA structure regulate microRNA biogenesis. Nat Commun 2017; 8:15114. [PMID: 28466845 PMCID: PMC5418625 DOI: 10.1038/ncomms15114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast and gastric cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing. Our results are compatible with a model whereby a genetic variant in pri-mir-30c-1 leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 resulting in increased levels of miR-30c. These data highlight that primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.
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Affiliation(s)
- Noemi Fernandez
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ross A. Cordiner
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert S. Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Javier F. Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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21
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Zhang J, Li D, Zhang J, Chen D, Murchie AIH. Osmium tetroxide as a probe of RNA structure. RNA (NEW YORK, N.Y.) 2017; 23:483-492. [PMID: 28115596 PMCID: PMC5340912 DOI: 10.1261/rna.057539.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/09/2017] [Indexed: 05/20/2023]
Abstract
Structured RNAs have a central role in cellular function. The capability of structured RNAs to adopt fixed architectural structures or undergo dynamic conformational changes contributes to their diverse role in the regulation of gene expression. Although numerous biophysical and biochemical tools have been developed to study structured RNAs, there is a continuing need for the development of new methods for the investigation of RNA structures, especially methods that allow RNA structure to be studied in solution close to its native cellular conditions. Here we use osmium tetroxide (OsO4) as a chemical probe of RNA structure. In this method, we have used fluorescence-based sequencing technologies to detect OsO4 modified RNA. We characterized the requirements for OsO4 modification of RNA by investigating three known structured RNAs: the M-box, glycine riboswitch RNAs, and tRNAasp Our results show that OsO4 predominantly modifies RNA at uracils that are conformationally exposed on the surface of the RNA. We also show that changes in OsO4 reactivity at flexible positions in the RNA correlate with ligand-driven conformational changes in the RNA structure. Osmium tetroxide modification of RNA will provide insights into the structural features of RNAs that are relevant to their underlying biological functions.
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Affiliation(s)
- Jing Zhang
- Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Danbin Li
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jun Zhang
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Dongrong Chen
- Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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22
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Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. QUANTITATIVE BIOLOGY 2017; 5:3-24. [PMID: 28717530 PMCID: PMC5510538 DOI: 10.1007/s40484-017-0093-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data. RESULTS We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy. CONCLUSIONS To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.
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Affiliation(s)
| | | | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA 95616, USA
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23
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Silva GADS, Amorim AL, Souza BD, Gabriel P, Terenzi H, Nordlander E, Neves A, Peralta RA. Synthesis and characterization of FeIII(μ-OH)ZnII complexes: effects of a second coordination sphere and increase in the chelate ring size on the hydrolysis of a phosphate diester and DNA. Dalton Trans 2017; 46:11380-11394. [DOI: 10.1039/c7dt02035j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Effects of a second coordination sphere and of the chelate ring size in FeIII(μ-OH)ZnII complexes properties and catalysis.
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Affiliation(s)
| | - André Luiz Amorim
- Departamento de Química
- Universidade Federal de Santa Catarina
- 88040-900 Florianópolis
- Brazil
| | - Bernardo de Souza
- Departamento de Química
- Universidade Federal de Santa Catarina
- 88040-900 Florianópolis
- Brazil
| | - Philipe Gabriel
- Centro de Biologia Molecular Estrutural
- Departamento de Bioquímica
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural
- Departamento de Bioquímica
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Ebbe Nordlander
- Inorganic Chemistry Research Group
- Chemical Physics
- Center for Chemistry and Chemical Engineering
- Lund University
- SE-221 00 Lund
| | - Ademir Neves
- Departamento de Química
- Universidade Federal de Santa Catarina
- 88040-900 Florianópolis
- Brazil
| | - Rosely A. Peralta
- Departamento de Química
- Universidade Federal de Santa Catarina
- 88040-900 Florianópolis
- Brazil
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24
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Deng F, Ledda M, Vaziri S, Aviran S. Data-directed RNA secondary structure prediction using probabilistic modeling. RNA (NEW YORK, N.Y.) 2016; 22:1109-1119. [PMID: 27251549 PMCID: PMC4931104 DOI: 10.1261/rna.055756.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations.
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Affiliation(s)
- Fei Deng
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Mirko Ledda
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Sana Vaziri
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
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25
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Hulscher RM, Bohon J, Rappé MC, Gupta S, D'Mello R, Sullivan M, Ralston CY, Chance MR, Woodson SA. Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting. Methods 2016; 103:49-56. [PMID: 27016143 PMCID: PMC4921310 DOI: 10.1016/j.ymeth.2016.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/09/2016] [Accepted: 03/21/2016] [Indexed: 01/01/2023] Open
Abstract
The assembly of the Escherichia coli ribosome has been widely studied and characterized in vitro. Despite this, ribosome biogenesis in living cells is only partly understood because assembly is coupled with transcription, modification and processing of the pre-ribosomal RNA. We present a method for footprinting and isolating pre-rRNA as it is synthesized in E. coli cells. Pre-rRNA synthesis is synchronized by starvation, followed by nutrient upshift. RNA synthesized during outgrowth is metabolically labeled to facilitate isolation of recent transcripts. Combining this technique with two in vivo RNA probing methods, hydroxyl radical and DMS footprinting, allows the structure of nascent RNA to be probed over time. Together, these can be used to determine changes in the structures of ribosome assembly intermediates as they fold in vivo.
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Affiliation(s)
- Ryan M Hulscher
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Jen Bohon
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Mollie C Rappé
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rhijuta D'Mello
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Michael Sullivan
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Corie Y Ralston
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mark R Chance
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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26
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Vasilieva E, Niederschulte J, Song Y, Harris GD, Koeller KJ, Liao P, Bashkin JK, Dupureur CM. Interactions of two large antiviral polyamides with the long control region of HPV16. Biochimie 2016; 127:103-14. [PMID: 27155361 DOI: 10.1016/j.biochi.2016.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/30/2016] [Indexed: 02/07/2023]
Abstract
PA1 and PA25 are large hairpin polyamides that are effective in nearly eliminating HPV16 episomes (DNA) in cell culture, and PA25 has broad spectrum activity against three cancer-causing forms of HPV (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177-186). Described here are the interactions of these PAs with sequences in the long control region (LCR) of HPV16 (7348-122). Using an FeEDTA conjugate of PA1 (designed to recognize 5'-W2GW7-3'; W = A or T), 34 affinity cleavage (AC) patterns were detected for this fragment. These sites can be rationalized with sequences featuring perfect, single, double, triple and quadruple mismatches. Quantitative DNase I footprinting analysis indicates that perfect sites bind PA1 with Kds between 0.7 and 2.2 nM. Kds for single, double, triple and quadruple mismatch sites range from 1-3 nM-20 nM. Using AC and EDTA conjugates, we report that unlike smaller 8-ring hairpin PAs, introduction of a chiral turn in this large polyamide has no effect on binding orientation (forward vs. reverse). Despite its design to recognize 5'-W2GW5GW4-3' via two Im residues, a motif not represented in this HPV sequence, a PA25-EDTA conjugate yielded 31 affinity cleavage sites on the region. Low nM Kds for PA25 without EDTA indicates a high tolerance for triple and quadruple mismatches. While there is extensive coverage of the sequence examined, AC cleavage patterns for the two PAs show discrete binding events and do not overlap significantly. This indicates that within the context of A/T rich sequences, these PAs do not recognize a simple shared sequence-related feature of the DNA. These insights continue to inform the complex nature of large hairpin PA-DNA interactions and antiviral behavior.
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Affiliation(s)
- Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Jacquelyn Niederschulte
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Yang Song
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - George Davis Harris
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Kevin J Koeller
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Puhong Liao
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - James K Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Cynthia M Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA.
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27
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Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL. Predicting RNA secondary structures from sequence and probing data. Methods 2016; 103:86-98. [PMID: 27064083 DOI: 10.1016/j.ymeth.2016.04.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/29/2016] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information.
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Affiliation(s)
- Ronny Lorenz
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Michael T Wolfinger
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; Medical University of Vienna, Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria.
| | - Andrea Tanzer
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Ivo L Hofacker
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
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28
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Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A. Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci 2016; 17:ijms17010132. [PMID: 26805815 PMCID: PMC4730372 DOI: 10.3390/ijms17010132] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 12/31/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.
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Affiliation(s)
- Kun Yan
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yasir Arfat
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Dijie Li
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Fan Zhao
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Zhihao Chen
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Chong Yin
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yulong Sun
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Lifang Hu
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Tuanmin Yang
- Department of Bone Disease Oncology, Hong-Hui Hospital, Xi'an Jiaotong University College of Medicine, South Door slightly Friendship Road 555, Xi'an 710054, China.
| | - Airong Qian
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
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29
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Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. Sci Rep 2016; 6:19016. [PMID: 26751501 PMCID: PMC4707467 DOI: 10.1038/srep19016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/02/2015] [Indexed: 01/11/2023] Open
Abstract
Noncoding RNAs (ncRNAs) represent a big class of important RNA molecules. Given the large number of ncRNAs, identifying their functional sites is becoming one of the most important topics in the post-genomic era, but available computational methods are limited. For the above purpose, we previously presented a tertiary structure based method, Rsite, which first calculates the distance metrics defined in Methods with the tertiary structure of an ncRNA and then identifies the nucleotides located within the extreme points in the distance curve as the functional sites of the given ncRNA. However, the application of Rsite is largely limited because of limited RNA tertiary structures. Here we present a secondary structure based computational method, Rsite2, based on the observation that the secondary structure based nucleotide distance is strongly positively correlated with that derived from tertiary structure. This makes it reasonable to replace tertiary structure with secondary structure, which is much easier to obtain and process. Moreover, we applied Rsite2 to three ncRNAs (tRNA (Lys), Diels-Alder ribozyme, and RNase P) and a list of human mitochondria transcripts. The results show that Rsite2 works well with nearly equivalent accuracy as Rsite but is much more feasible and efficient. Finally, a web-server, the source codes, and the dataset of Rsite2 are available at http://www.cuialb.cn/rsite2.
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30
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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31
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Somarowthu S. Progress and Current Challenges in Modeling Large RNAs. J Mol Biol 2015; 428:736-747. [PMID: 26585404 DOI: 10.1016/j.jmb.2015.11.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/03/2015] [Accepted: 11/08/2015] [Indexed: 12/21/2022]
Abstract
Recent breakthroughs in next-generation sequencing technologies have led to the discovery of several classes of non-coding RNAs (ncRNAs). It is now apparent that RNA molecules are not only just carriers of genetic information but also key players in many cellular processes. While there has been a rapid increase in the number of ncRNA sequences deposited in various databases over the past decade, the biological functions of these ncRNAs are largely not well understood. Similar to proteins, RNA molecules carry out a function by forming specific three-dimensional structures. Understanding the function of a particular RNA therefore requires a detailed knowledge of its structure. However, determining experimental structures of RNA is extremely challenging. In fact, RNA-only structures represent just 1% of the total structures deposited in the PDB. Thus, computational methods that predict three-dimensional RNA structures are in high demand. Computational models can provide valuable insights into structure-function relationships in ncRNAs and can aid in the development of functional hypotheses and experimental designs. In recent years, a set of diverse RNA structure prediction tools have become available, which differ in computational time, input data and accuracy. This review discusses the recent progress and challenges in RNA structure prediction methods.
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Affiliation(s)
- Srinivas Somarowthu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, Kline Biology Tower, New Haven, CT 06511, USA.
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32
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Ghosh S, Greenberg MM. Correlation of Thermal Stability and Structural Distortion of DNA Interstrand Cross-Links Produced from Oxidized Abasic Sites with Their Selective Formation and Repair. Biochemistry 2015; 54:6274-83. [PMID: 26426430 DOI: 10.1021/acs.biochem.5b00860] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C4'-oxidized (C4-AP) and C5'-oxidized abasic sites (DOB) that are produced following abstraction of a hydrogen atom from the DNA backbone reversibly form cross-links selectively with dA opposite a 3'-adjacent nucleotide, despite the comparable proximity of an opposing dA. A previous report on UvrABC incision of DNA substrates containing stabilized analogues of the ICLs derived from C4-AP and DOB also indicated that the latter is repaired more readily by nucleotide excision repair [Ghosh, S., and Greenberg, M. M. (2014) Biochemistry 53, 5958-5965]. The source for selective cross-link formation was probed by comparing the reactivity of ICL analogues of C4-AP and DOB that mimic the preferred and disfavored cross-links with that of reagents that indirectly detect distortion by reacting with the nucleobases. The disfavored C4-AP and DOB analogues were each more reactive than the corresponding preferred cross-link substrates, suggesting that the latter are more stable, which is consistent with selective ICL formation. In addition, the preferred DOB analogue is more reactive than the respective C4-AP ICL, which is consistent with its more efficient incision by UvrABC. The conclusions drawn from the chemical probing experiments are corroborated by UV melting studies. The preferred ICLs exhibit melting temperatures higher than those of the corresponding disfavored isomers. These studies suggest that oxidized abasic sites form reversible interstrand cross-links with dA opposite the 3'-adjacent thymidine because these products are more stable and the thermodynamic preference is reflected in the transition states for their formation.
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Affiliation(s)
- Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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33
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Blythe AJ, Fox AH, Bond CS. The ins and outs of lncRNA structure: How, why and what comes next? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:46-58. [PMID: 26325022 DOI: 10.1016/j.bbagrm.2015.08.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/07/2015] [Accepted: 08/27/2015] [Indexed: 12/20/2022]
Abstract
The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Amanda J Blythe
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Archa H Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
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34
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Zelder F. Recent trends in the development of vitamin B12 derivatives for medicinal applications. Chem Commun (Camb) 2015; 51:14004-17. [PMID: 26287029 DOI: 10.1039/c5cc04843e] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Feature Article highlights recent developments in the field of vitamin B12 derivatives for medicinal applications. The following topics are emphasized: (1) the development of aquacorrinoids for cyanide detection and detoxification, (2) the use of vitamin B12 conjugates and (3) antivitamins B12 for therapy and diagnosis, and (4) the design of corrinoids as activators of soluble guanylyl cyclase (sGC).
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Affiliation(s)
- Felix Zelder
- Department of Chemistry, University of Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland.
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35
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Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL. Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA (NEW YORK, N.Y.) 2015; 21:1110-1121. [PMID: 25904133 PMCID: PMC4436664 DOI: 10.1261/rna.047522.114] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures.
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Affiliation(s)
| | - Christian Höner Zu Siederdissen
- Institute for Theoretical Chemistry, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science, Universität Leipzig, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Universität Leipzig, D-04107 Leipzig, Germany
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, University of Vienna, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, DK-1870 Frederiksberg, Denmark
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36
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Kielpinski LJ, Sidiropoulos N, Vinther J. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools. Methods Enzymol 2015; 558:153-180. [PMID: 26068741 DOI: 10.1016/bs.mie.2015.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
RNA structure-probing data can improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. In recent years, massive parallel sequencing has dramatically improved the throughput of RNA structure probing experiments, but at the same time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data, we have made a collection of tools, which allow raw sequencing reads to be converted to normalized probing values using different published strategies. In addition, we also provide tools for visualization of the probing data in the UCSC Genome Browser and for converting RNA coordinates to genomic coordinates and vice versa. The collection is implemented as functions in the R statistical environment and as tools in the Galaxy platform, making them easily accessible for the scientific community. We demonstrate the usefulness of the collection by applying it to the analysis of sequencing-based hydroxyl radical probing data and comparing different normalization strategies.
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Affiliation(s)
- Lukasz Jan Kielpinski
- Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nikolaos Sidiropoulos
- Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Vinther
- Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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37
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Ge P, Zhang S. Computational analysis of RNA structures with chemical probing data. Methods 2015; 79-80:60-6. [PMID: 25687190 DOI: 10.1016/j.ymeth.2015.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/16/2015] [Accepted: 02/09/2015] [Indexed: 11/28/2022] Open
Abstract
RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.
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Affiliation(s)
- Ping Ge
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA
| | - Shaojie Zhang
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.
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38
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Chen W, Zhang L. The pattern of DNA cleavage intensity around indels. Sci Rep 2015; 5:8333. [PMID: 25660536 PMCID: PMC4321175 DOI: 10.1038/srep08333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensities in the 200 base pair regions surrounding these indels. Our results show that DNA cleavage intensities close to the start and end points of indels are significantly lower than other regions, for both small human germline and somatic indels and also for mouse small indels. Compared to small indels, the patterns of DNA cleavage intensity around large indels are more complex, and there are two low intensity regions near each end of the indels that are approximately 13 bp apart from each other. Detailed analyses of a subset of indels show that there is slight difference in cleavage intensity distribution between insertion indels and deletion indels that could be contributed by their respective enrichment of different repetitive elements. These results will provide new insight into indel generation mechanisms.
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Affiliation(s)
- Wei Chen
- 1] Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China 063000 [2] Department of Computer Science, Virginia Tech, Blacksburg VA 24060
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg VA 24060
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39
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Mehta JV, Gajera SB, Patel MN. Antimalarial, antimicrobial, cytotoxic, DNA interaction and SOD like activities of tetrahedral copper(II) complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt C:1881-1892. [PMID: 25467683 DOI: 10.1016/j.saa.2014.10.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/01/2014] [Accepted: 10/23/2014] [Indexed: 06/04/2023]
Abstract
The mononuclear copper(II) complexes with P, O-donor ligand and different fluoroquinolones have been synthesized and characterized by elemental analysis, electronic spectra, TGA, EPR, FT-IR and LC-MS spectroscopy. An antimicrobial efficiency of the complexes has been tested against five different microorganisms in terms of minimum inhibitory concentration (MIC) and displays very good antimicrobial activity. The binding strength and binding mode of the complexes with Herring Sperm DNA (HS DNA) have been investigated by absorption titration and viscosity measurement studies. The studies suggest the classical intercalative mode of DNA binding. Gel electrophoresis assay determines the ability of the complexes to cleave the supercoiled form of pUC19 DNA. Synthesized complexes have been tested for their SOD mimic activity using nonenzymatic NBT/NADH/PMS system and found to have good antioxidant activity. All the complexes show good cytotoxic and in vitro antimalarial activities.
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Affiliation(s)
- Jugal V Mehta
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar 388 120, Gujarat, India
| | - Sanjay B Gajera
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar 388 120, Gujarat, India
| | - Mohan N Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar 388 120, Gujarat, India.
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40
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Chitrapriya N, Shin JH, Hwang IH, Kim Y, Kim C, Kim SK. Synthesis, DNA binding profile and DNA cleavage pathway of divalent metal complexes. RSC Adv 2015. [DOI: 10.1039/c5ra10695h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Divalent metal complexes of dipyridylamine ligand with an anthracene moiety induced considerable oxidative DNA cleavage in the presence hydrogen peroxide and dioxygen.
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Affiliation(s)
| | - Jong Heon Shin
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
| | - In Hong Hwang
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Youngmee Kim
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Republic of Korea
| | - Cheal Kim
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Seog K. Kim
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
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41
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Cantara WA, Olson ED, Musier-Forsyth K. Progress and outlook in structural biology of large viral RNAs. Virus Res 2014; 193:24-38. [PMID: 24956407 PMCID: PMC4252365 DOI: 10.1016/j.virusres.2014.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
Abstract
The field of viral molecular biology has reached a precipice for which pioneering studies on the structure of viral RNAs are beginning to bridge the gap. It has become clear that viral genomic RNAs are not simply carriers of hereditary information, but rather are active players in many critical stages during replication. Indeed, functions such as cap-independent translation initiation mechanisms are, in some cases, primarily driven by RNA structural determinants. Other stages including reverse transcription initiation in retroviruses, nuclear export and viral packaging are specifically dependent on the proper 3-dimensional folding of multiple RNA domains to recruit necessary viral and host factors required for activity. Furthermore, a large-scale conformational change within the 5'-untranslated region of HIV-1 has been proposed to regulate the temporal switch between viral protein synthesis and packaging. These RNA-dependent functions are necessary for replication of many human disease-causing viruses such as severe acute respiratory syndrome (SARS)-associated coronavirus, West Nile virus, and HIV-1. The potential for antiviral development is currently hindered by a poor understanding of RNA-driven molecular mechanisms, resulting from a lack of structural information on large RNAs and ribonucleoprotein complexes. Herein, we describe the recent progress that has been made on characterizing these large RNAs and provide brief descriptions of the techniques that will be at the forefront of future advances. Ongoing and future work will contribute to a more complete understanding of the lifecycles of retroviruses and RNA viruses and potentially lead to novel antiviral strategies.
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Affiliation(s)
| | | | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
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42
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Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res 2014; 42:12758-67. [PMID: 25313156 PMCID: PMC4227780 DOI: 10.1093/nar/gku934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 12/02/2022] Open
Abstract
While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5'-aldehyde. We conclude that hydroxyl radical abstracts a 5'-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5' deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2'-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple.
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Affiliation(s)
- Shakti Ingle
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Robert N Azad
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Swapan S Jain
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Thomas D Tullius
- Department of Chemistry, Boston University, Boston, MA 02215, USA Program in Bioinformatics, Boston University, Boston, MA 02215, USA
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43
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Abstract
The uridin-2'-yl radical (1) has been proposed as an intermediate during RNA oxidation. However, its reactivity has not been thoroughly studied due to the complex conditions under which it is typically generated. The uridin-2'-yl radical was independently generated from a benzyl ketone (2a) via Norrish type I photocleavage upon irradiation at λmax = 350 nm. Dioxygen and β-mercaptoethanol are unable to compete with loss of uracil from 1 in phosphate buffer. Thiol trapping competes with uracil fragmentation in less polar solvent conditions. This is ascribed mostly to a reduction in the rate constant for uracil elimination in the less polar solvent. Hydrogen atom transfer to 1 from β-mercaptoethanol occurs exclusively from the α-face to produce arabinouridine. Mass balances range from 72 to 95%. Furthermore, the synthesis of 2a is amenable to formation of the requisite phosphoramidite for solid-phase oligonucleotide synthesis. This and the fidelity with which the urdin-2'-yl radical is generated from 2a suggest that this precursor should be useful for studying the radical's reactivity in synthetic oligonucleotides.
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Affiliation(s)
- Rakesh Paul
- Department of Chemistry, Johns
Hopkins University 3400
North Charles Street, Baltimore, Maryland 21218, United
States
| | - Marc M. Greenberg
- Department of Chemistry, Johns
Hopkins University 3400
North Charles Street, Baltimore, Maryland 21218, United
States
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44
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Khan RA, Arjmand F, Tabassum S, Monari M, Marchetti F, Pettinari C. Organometallic ruthenium(II) scorpionate as topo IIα inhibitor; in vitro binding studies with DNA, HPLC analysis and its anticancer activity. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.05.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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45
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Homan PJ, Tandon A, Rice GM, Ding F, Dokholyan NV, Weeks KM. RNA tertiary structure analysis by 2'-hydroxyl molecular interference. Biochemistry 2014; 53:6825-33. [PMID: 25341083 DOI: 10.1021/bi501218g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a melded chemical and computational approach for probing and modeling higher-order intramolecular tertiary interactions in RNA. 2'-Hydroxyl molecular interference (HMX) identifies nucleotides in highly packed regions of an RNA by exploiting the ability of bulky adducts at the 2'-hydroxyl position to disrupt overall RNA structure. HMX was found to be exceptionally selective for quantitative detection of higher-order and tertiary interactions. When incorporated as experimental constraints in discrete molecular dynamics simulations, HMX information yielded accurate three-dimensional models, emphasizing the power of molecular interference to guide RNA tertiary structure analysis and fold refinement. In the case of a large, multidomain RNA, the Tetrahymena group I intron, HMX identified multiple distinct sets of tertiary structure interaction groups in a single, concise experiment.
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Affiliation(s)
- Philip J Homan
- Departments of Chemistry and ‡Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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46
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Sloane JL, Greenberg MM. Interstrand cross-link and bioconjugate formation in RNA from a modified nucleotide. J Org Chem 2014; 79:9792-8. [PMID: 25295850 PMCID: PMC4201359 DOI: 10.1021/jo501982r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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RNA
oligonucleotides containing a phenyl selenide derivative of
5-methyluridine were chemically synthesized by solid-phase synthesis.
The phenyl selenide is rapidly converted to an electrophilic, allylic
phenyl seleneate under mild oxidative conditions. The phenyl seleneate
yields interstrand cross-links when part of a duplex and is useful
for synthesizing oligonucleotide conjugates. Formation of the latter
is illustrated by reaction of an oligonucleotide containing the phenyl
selenide with amino acids in the presence of mild oxidant. The products
formed are analogous to those observed in tRNA that are believed to
be formed posttranslationally via a biosynthetic intermediate that
is chemically homologous to the phenyl seleneate.
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Affiliation(s)
- Jack L Sloane
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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47
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Cui F, Chen L, LoVerso PR, Zhurkin VB. Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy. BMC Bioinformatics 2014; 15:313. [PMID: 25244936 PMCID: PMC4261538 DOI: 10.1186/1471-2105-15-313] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/29/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND An organism's DNA sequence is one of the key factors guiding the positioning of nucleosomes within a cell's nucleus. Sequence-dependent bending anisotropy dictates how DNA is wrapped around a histone octamer. One of the best established sequence patterns consistent with this anisotropy is the periodic occurrence of AT-containing dinucleotides (WW) and GC-containing dinucleotides (SS) in the nucleosomal locations where DNA is bent in the minor and major grooves, respectively. Although this simple pattern has been observed in nucleosomes across eukaryotic genomes, its use for prediction of nucleosome positioning was not systematically tested. RESULTS We present a simple computational model, termed the W/S scheme, implementing this pattern, without using any training data. This model accurately predicts the rotational positioning of nucleosomes both in vitro and in vivo, in yeast and human genomes. About 65 - 75% of the experimentally observed nucleosome positions are predicted with the precision of one to two base pairs. The program is freely available at http://people.rit.edu/fxcsbi/WS_scheme/. We also introduce a simple and efficient way to compare the performance of different models predicting the rotational positioning of nucleosomes. CONCLUSIONS This paper presents the W/S scheme to achieve accurate prediction of rotational positioning of nucleosomes, solely based on the sequence-dependent anisotropic bending of nucleosomal DNA. This method successfully captures DNA features critical for the rotational positioning of nucleosomes, and can be further improved by incorporating additional terms related to the translational positioning of nucleosomes in a species-specific manner.
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Affiliation(s)
- Feng Cui
- Thomas H, Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
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48
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Li LJ, Fu B, Qiao Y, Wang C, Huang YY, Liu CC, Tian C, Du JL. Synthesis, characterization and cytotoxicity studies of platinum(II) complexes with reduced amino acid ester Schiff-bases as ligands. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.04.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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49
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Ranpura H, Bialonska D, Bolton PH. Finding and characterizing the complexes of drug like molecules with quadruplex DNA: combined use of an enhanced hydroxyl radical cleavage protocol and NMR. PLoS One 2014; 9:e96218. [PMID: 24763734 PMCID: PMC3999192 DOI: 10.1371/journal.pone.0096218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
Structural information on the complexes of drug like molecules with quadruplex DNAs can aid the development of therapeutics and research tools that selectively target specific quadruplex DNAs. Screening can identify candidate molecules that require additional evaluation. An enhanced hydroxyl radical cleavage protocol is demonstrated that can efficiently provide structural information on the complexes of the candidate molecules with quadruplex DNA. NMR methods have been used to offer additional structural information about the complexes as well as validate the results of the hydroxyl radical approach. This multi-step protocol has been demonstrated on complexes of the chair type quadruplex formed by the thrombin binding aptamer, d(GGTTGGTGTGGTTGG). The hydroxyl radical results indicate that NSC 176319, Cain’s quinolinium that was found by screening, exhibits selective binding to the two TT loops. The NMR results are consistent with selective disruption of the hydrogen bonding between T4 and T13 as well as unstacking of these residues from the bottom quartet. Thus, the combination of screening, hydroxyl radical footprinting and NMR can find new molecules that selectively bind to quadruplex DNAs as well as provide structural information about their complexes.
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Affiliation(s)
- Harikrushan Ranpura
- Chemistry Department, Wesleyan University, Middletown, Connecticut, United States of America
| | - Dobroslawa Bialonska
- Chemistry Department, Wesleyan University, Middletown, Connecticut, United States of America
| | - Philip H. Bolton
- Chemistry Department, Wesleyan University, Middletown, Connecticut, United States of America
- * E-mail:
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50
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Padlan CS, Malashkevich VN, Almo SC, Levy M, Brenowitz M, Girvin ME. An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates. RNA (NEW YORK, N.Y.) 2014; 20:447-461. [PMID: 24570482 PMCID: PMC3964907 DOI: 10.1261/rna.043034.113] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
RNA aptamers are being developed as inhibitors of macromolecular and cellular function, diagnostic tools, and potential therapeutics. Our understanding of the physical nature of this emerging class of nucleic acid-protein complexes is limited; few atomic resolution structures have been reported for aptamers bound to their protein target. Guided by chemical mapping, we systematically minimized an RNA aptamer (Lys1) selected against hen egg white lysozyme. The resultant 59-nucleotide compact aptamer (Lys1.2minE) retains nanomolar binding affinity and the ability to inhibit lysozyme's catalytic activity. Our 2.0-Å crystal structure of the aptamer-protein complex reveals a helical stem stabilizing two loops to form a protein binding platform that binds lysozyme distal to the catalytic cleft. This structure along with complementary solution analyses illuminate a novel protein-nucleic acid interface; (1) only 410 Å(2) of solvent accessible surface are buried by aptamer binding; (2) an unusually small fraction (∼18%) of the RNA-protein interaction is electrostatic, consistent with the limited protein phosphate backbone contacts observed in the structure; (3) a single Na(+) stabilizes the loops that constitute the protein-binding platform, and consistent with this observation, Lys1.2minE-lysozyme complex formation takes up rather than displaces cations at low ionic strength; (4) Lys1.2minE inhibits catalysis of large cell wall substrates but not catalysis of small model substrates; and (5) the helical stem of Lys1.2minE can be shortened to four base pairs (Lys1.2minF) without compromising binding affinity, yielding a 45-nucleotide aptamer whose structure may be an adaptable protein binding platform.
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