1
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Raguette LE, Gunasekera SS, Diaz Ventura RI, Aminov E, Linzer JT, Parwana D, Wu Q, Simmerling C, Nagan MC. Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations. J Phys Chem B 2024; 128:7921-7933. [PMID: 39110091 DOI: 10.1021/acs.jpcb.4c01910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.
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Affiliation(s)
- Lauren E Raguette
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sarah S Gunasekera
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Rebeca I Diaz Ventura
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Ethan Aminov
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jason T Linzer
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Diksha Parwana
- Biochemistry & Structural Biology Program, Stony Brook University, Stony Brook, New York 11794, United States
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Maria C Nagan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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2
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Linzer JT, Aminov E, Abdullah AS, Kirkup CE, Diaz Ventura RI, Bijoor VR, Jung J, Huang S, Tse CG, Álvarez Toucet E, Onghai HP, Ghosh AP, Grodzki AC, Haines ER, Iyer AS, Khalil MK, Leong AP, Neuhaus MA, Park J, Shahid A, Xie M, Ziembicki JM, Simmerling C, Nagan MC. Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. J Chem Inf Model 2024; 64:6092-6104. [PMID: 39002142 DOI: 10.1021/acs.jcim.4c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here, we present a systematic analysis of 15 RNA stem-loop sequences simulated with molecular dynamics simulations in an implicit solvent environment. Analysis of RNA cluster ensembles showed that the stem-loop structures can generally adopt the A-form RNA in the stem region. Loop structures are more sensitive, and experimental structures could only be reproduced with modification of CH···O interactions in the force field, combined with an implicit solvent nonpolar correction to better model base stacking interactions. Accurately modeling RNA with current atomistic physics-based models remains challenging, but the RNA systems studied herein may provide a useful benchmark set for testing other RNA modeling methods in the future.
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Affiliation(s)
- Jason T Linzer
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Ethan Aminov
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Aalim S Abdullah
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Colleen E Kirkup
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Rebeca I Diaz Ventura
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Vinay R Bijoor
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jiyun Jung
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sophie Huang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Chi Gee Tse
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Emily Álvarez Toucet
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Hugo P Onghai
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Arghya P Ghosh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Alex C Grodzki
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Emilee R Haines
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Aditya S Iyer
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Mark K Khalil
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Alexander P Leong
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Michael A Neuhaus
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Joseph Park
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Asir Shahid
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Matthew Xie
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jan M Ziembicki
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Maria C Nagan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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3
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Heel SV, Breuker K. Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top-Down Mass Spectrometry. Chempluschem 2024; 89:e202400178. [PMID: 38758051 DOI: 10.1002/cplu.202400178] [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: 03/06/2024] [Revised: 04/13/2024] [Indexed: 05/18/2024]
Abstract
The ongoing search for small molecule drugs that target ribonucleic acids (RNA) is complicated by a limited understanding of the principles that govern RNA-small molecule interactions. Here we have used stoichiometry-resolved native top-down mass spectrometry (MS) to study the binding of neomycin B to small model hairpin RNAs, an unstructured RNA, and a viral RNA construct. For 15-22 nt model RNAs with hairpin structure, we found that neomycin B binding to hairpin loops relies on interactions with both the nucleobases and the 2'-OH groups, and that a simple 5' or 3' overhang can introduce an additional binding motif. For a 47 nt RNA construct derived from stem IA of the human immunodeficiency virus 1 (HIV-1) rev response element (RRE) RNA, native top-down MS identified four different binding motifs, of which the purine-rich internal loop showed the highest affinity for neomycin B. Stoichiometry-resolved binding site mapping by native top-down MS allows for a new perspective on binding specificity, and has the potential to reveal unexpected principles of small molecule binding to RNA.
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Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
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4
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Jang SS, Ray KK, Lynall DG, Shepard KL, Nuckolls C, Gonzalez RL. RNA adapts its flexibility to efficiently fold and resist unfolding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.595525. [PMID: 38853856 PMCID: PMC11160689 DOI: 10.1101/2024.05.27.595525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Recent studies have demonstrated that the mechanisms through which biopolymers like RNA interconvert between multiple folded structures are critical for their cellular functions. A major obstacle to elucidating these mechanisms is the lack of experimental approaches that can resolve these interconversions between functionally relevant biomolecular structures. Here, using a nano-electronic device with microsecond time resolution, we dissect the complete set of structural rearrangements executed by an ultra-stable RNA, the UUCG stem-loop, at the single-molecule level. We show that the stem-loop samples at least four conformations along two folding pathways leading to two distinct folded structures, only one of which has been previously observed. By modulating its flexibility, the stem-loop can adaptively select between these pathways, enabling it to both fold rapidly and resist unfolding. This paradigm of stabilization through compensatory changes in flexibility broadens our understanding of stable RNA structures and is expected to serve as a general strategy employed by all biopolymers.
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Affiliation(s)
- Sukjin S. Jang
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| | - Korak Kumar Ray
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| | - David G. Lynall
- Department of Electrical Engineering, Columbia University, New York, NY 10027 USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027 USA
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027 USA
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5
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Li J, Song Y. Plant thermosensors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112025. [PMID: 38354752 DOI: 10.1016/j.plantsci.2024.112025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Plants dynamically regulate their genes expression and physiological outputs to adapt to changing temperatures. The underlying molecular mechanisms have been extensively studied in diverse plants and in multiple dimensions. However, the question of exactly how temperature is detected at molecular level to transform the physical information into recognizable intracellular signals remains continues to be one of the undetermined occurrences in plant science. Recent studies have provided the physical and biochemical mechanistic breakthrough of how temperature changes can influence molecular thermodynamically stability, thus changing molecular structures, activities, interaction and signaling transduction. In this review, we focus on the thermosensing mechanisms of recognized and potential plant thermosensors, to describe the multi-level thermal input system in plants. We also consider the attributes of a thermosensor on the basis of thermal-triggered changes in function, structure, and physical parameters. This study thus provides a reference for discovering more plant thermosensors and elucidating plant thermal adaptive mechanisms.
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Affiliation(s)
- Jihong Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuan Song
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China; Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China.
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6
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Gupta S, Padmashali N, Pal D. INTERPIN: A repository for intrinsic transcription termination hairpins in bacteria. Biochimie 2023; 214:228-236. [PMID: 37499897 DOI: 10.1016/j.biochi.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work in tandem to cause intrinsic transcription termination (ITT), while the single hairpin can do the same alone. Therefore, exploring these ITT sites and the hairpins across bacterial genomes becomes highly desirable. INTERPIN is the largest archived collection of in silico inferred ITT hairpins in bacteria, covering 12745 bacterial genomes and encompassing ten bacterial phyla for ∼25 million hairpins. Users can obtain details on operons, individual cluster, and single ITT hairpins that were screened therein. Integrated Genome Viewer (IGV) software interactively visualizes hairpin secondary and tertiary structures in the genomic context. We also discuss statistics for the occurrence of cluster or single hairpins and other termination alternatives while showing the validation of predicted hairpins against in vivo detected hairpins. The database is freely available at http://pallab.cds.iisc.ac.in/INTERPIN/. INTERPIN (database and software) can make predictions for both AT and GC-rich genomes, which has not been achieved by any other program so far. It can also be used to improve genome annotation as well as to get predictions to improve the understanding of the ITT pathway by further analysis.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Namrata Padmashali
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India.
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7
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Yang C, Song X, Feng Y, Zhao G, Liu Y. Stability of DNA and RNA hairpins: a comparative study based on ox-DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:265101. [PMID: 36972608 DOI: 10.1088/1361-648x/acc7eb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
Advances in single-molecule experiments on macromolecular crowding urgently need an efficient simulation method to resolve their discrepancies quantitatively. Ox-DNA model has been since reworked to treat the thermodynamics and mechanical properties of DNA/RNA hairpin at a stretching force. In hopping experiments, the critical forces of RNA hairpins at different temperatures are greater than those of DNA hairpins, in addition, the Gibbs free energy at a fixed temperature required to convert an RNA hairpin into a single-stranded molecule at zero force is obviously greater than that of DNA hairpin and gradually decreases by increasing the temperature. As far as force-ramping experiments are concerned, the first-rupture forces of RNA/DNA hairpins corresponding to the maximum probability density linearly pertain to the force-loading rate, with those of RNA hairpins being greater. The extended ox-DNA model could potentially identify the interaction between biologically inert polymer and RNA/DNA hairpins in crowded environments.
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Affiliation(s)
- Chao Yang
- College of Physics, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Xiaoya Song
- College of Physics, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Yuyu Feng
- College of Physics, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Guangju Zhao
- College of Physics, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Yanhui Liu
- College of Physics, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
- Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education (Guizhou University), Guiyang, Guizhou 550025, People's Republic of China
- State Key Laboratory of Public Big Data, Guizhou University, Guiyang 550025, People's Republic of China
- Kechuang Industrial Development Company Limited,Gui'an New Area, Guiyang 550025, People's Republic of China
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8
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Forstmeier PC, Meyer MO, Bevilacqua PC. The Functional RNA Identification (FRID) Pipeline: Identification of Potential Pseudoknot-Containing RNA Elements as Therapeutic Targets for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535424. [PMID: 37066195 PMCID: PMC10103974 DOI: 10.1101/2023.04.03.535424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The COVID-19 pandemic persists despite the development of effective vaccines. As such, it remains crucial to identify new targets for antiviral therapies. The causative virus of COVID-19, SARS-CoV-2, is a positive-sense RNA virus with RNA structures that could serve as therapeutic targets. One such RNA with established function is the frameshift stimulatory element (FSE), which promotes programmed ribosomal frameshifting. To accelerate identification of additional functional RNA elements, we introduce a novel computational approach termed the Functional RNA Identification (FRID) pipeline. The guiding principle of our pipeline, which uses established component programs as well as customized component programs, is that functional RNA elements have conserved secondary and pseudoknot structures that facilitate function. To assess the presence and conservation of putative functional RNA elements in SARS-CoV-2, we compared over 6,000 SARS-CoV-2 genomic isolates. We identified 22 functional RNA elements from the SARS-CoV-2 genome, 14 of which have conserved pseudoknots and serve as potential targets for small molecule or antisense oligonucleotide therapeutics. The FRID pipeline is general and can be applied to identify pseudoknotted RNAs for targeted therapeutics in genomes or transcriptomes from any virus or organism.
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9
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Yu T, Liu T, Wang Y, Zhang S, Zhang W. Thermodynamics and kinetics of an A-U RNA base pair under force studied by molecular dynamics simulations. Phys Rev E 2023; 107:024404. [PMID: 36932572 DOI: 10.1103/physreve.107.024404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Mechanical force has been widely used to study RNA folding and unfolding. Understanding how the force affects the opening and closing of a single base pair, which is a basic step for RNA folding and unfolding and a fundamental behavior in some important biological activities, is crucial to understanding the mechanism of RNA folding and unfolding under mechanical force. In this work, we investigated the opening and closing process of an RNA base pair under mechanical force with constant-force stretching molecular dynamics simulations. It was found that high mechanical force results in overstretching, and the open state is a high-energy state. The enthalpy and entropy change of the base-pair opening-closing transition were obtained and the results at low forces were in good agreement with the nearest-neighbor model. The temperature and force dependence of the opening and closing rates were also obtained. The position of the transition state for the base-pair opening-closing transition under mechanical force was determined. The free energy barrier of opening a base pair without force is the enthalpy increase, and the work done by the force from the closed state to the transition state decreases the barrier and increases the opening rate. The free energy barrier of closing the base pair without force results from the entropy loss, and the work done by the force from the open state to the transition state increases the barrier and decreases the closing rate. The transition rates are strongly dependent on the temperature and force, while the transition path times are weakly dependent on force and temperature.
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Affiliation(s)
- Ting Yu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Taigang Liu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, People's Republic of China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou, Henan 466000, People's Republic of China
| | - Shuhao Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
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10
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Jang SS, Dubnik S, Hon J, Hellenkamp B, Lynall DG, Shepard KL, Nuckolls C, Gonzalez RL. Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors. J Am Chem Soc 2023; 145:402-412. [PMID: 36547391 PMCID: PMC10025942 DOI: 10.1021/jacs.2c10218] [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] [Indexed: 12/24/2022]
Abstract
We have developed and used single-molecule field-effect transistors (smFETs) to characterize the conformational free-energy landscape of RNA stem-loops. Stem-loops are one of the most common RNA structural motifs and serve as building blocks for the formation of complex RNA structures. Given their prevalence and integral role in RNA folding, the kinetics of stem-loop (un)folding has been extensively characterized using both experimental and computational approaches. Interestingly, these studies have reported vastly disparate timescales of (un)folding, which has been interpreted as evidence that (un)folding of even simple stem-loops occurs on a highly rugged conformational energy landscape. Because smFETs do not rely on fluorophore reporters of conformation or mechanical (un)folding forces, they provide a unique approach that has allowed us to directly monitor tens of thousands of (un)folding events of individual stem-loops at a 200 μs time resolution. Our results show that under our experimental conditions, stem-loops (un)fold over a 1-200 ms timescale during which they transition between ensembles of unfolded and folded conformations, the latter of which is composed of at least two sub-populations. The 1-200 ms timescale of (un)folding we observe here indicates that smFETs report on complete (un)folding trajectories in which unfolded conformations of the RNA spend long periods of time wandering the free-energy landscape before sampling one of several misfolded conformations or the natively folded conformation. Our findings highlight the extremely rugged landscape on which even the simplest RNA structural elements fold and demonstrate that smFETs are a unique and powerful approach for characterizing the conformational free-energy of RNA.
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Affiliation(s)
- Sukjin S. Jang
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Sarah Dubnik
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Jason Hon
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Björn Hellenkamp
- Department of Electrical Engineering, Columbia University, 3000 Broadway, New York, 10027, USA
| | - David G. Lynall
- Department of Electrical Engineering, Columbia University, 3000 Broadway, New York, 10027, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, 3000 Broadway, New York, 10027, USA
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
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11
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Wu LF, Liu Z, Roberts SJ, Su M, Szostak JW, Sutherland JD. Template-Free Assembly of Functional RNAs by Loop-Closing Ligation. J Am Chem Soc 2022; 144:13920-13927. [PMID: 35880790 PMCID: PMC9354263 DOI: 10.1021/jacs.2c05601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first ribozymes are thought to have emerged at a time when RNA replication proceeded via nonenzymatic template copying processes. However, functional RNAs have stable folded structures, and such structures are much more difficult to copy than short unstructured RNAs. How can these conflicting requirements be reconciled? Also, how can the inhibition of ribozyme function by complementary template strands be avoided or minimized? Here, we show that short RNA duplexes with single-stranded overhangs can be converted into RNA stem loops by nonenzymatic cross-strand ligation. We then show that loop-closing ligation reactions enable the assembly of full-length functional ribozymes without any external template. Thus, one can envisage a potential pathway whereby structurally complex functional RNAs could have formed at an early stage of evolution when protocell genomes might have consisted only of collections of short replicating oligonucleotides.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Samuel J Roberts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Meng Su
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Jack W Szostak
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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12
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Rundell S, Munyaradzi O, Bong D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs. Biochemistry 2021; 61:85-91. [PMID: 34955016 DOI: 10.1021/acs.biochem.1c00693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
General design principles for recognition at noncanonical interfaces of DNA and RNA remain elusive. Triplex hybridization of bifacial peptide nucleic acids (bPNAs) with oligo-T/U DNAs and RNAs is a robust recognition platform that can be used to define structure-function relationships in synthetic triplex formation. To this end, a set of minimal (mw < 1 kD) bPNA variants was synthesized to probe the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on hybridization with short, unstructured T-rich DNA and U-rich RNAs. Thermodynamic parameters extracted from optical melting analyses of bPNA variant hybrids indicated that there are two bPNA backbone modifications that significantly improve hybridization: alternating (d, l) configuration in open-chain dipeptides and homochiral dipeptide cyclization to diketopiperazine. Further, binding to DNA is preferred over RNA for all bPNA variants. Thymine-uracil substitutions in DNA substrates revealed that the methyl group of thymine accounts for 71% of ΔΔGDNA-RNA for open-chain bPNAs but only 40% of ΔΔGDNA-RNA for diketopiperazine bPNA, suggesting a greater sensitivity to RNA conformation and more optimized stacking in the cyclic bPNA. Together, these data reveal pressure points for tuning triplex hybridization at the chiral centers of bPNA, backbone conformation, stacking effects at the base triple, and the nucleic acid substrate itself. A structural blueprint for enhancing bPNA targeting of both DNA and RNA substrates includes syndiotactic base presentation (as found in homochiral diketopiperazines and d, l peptides), expansion of base stacking, and further investigation of bPNA backbone preorganization.
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Affiliation(s)
- Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
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13
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Zerze GH, Piaggi PM, Debenedetti PG. A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States. J Phys Chem B 2021; 125:13685-13695. [PMID: 34890201 DOI: 10.1021/acs.jpcb.1c08038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important characteristic of RNA folding is the adoption of alternative configurations of similar stability, often referred to as misfolded configurations. These configurations are considered to compete with correctly folded configurations, although their rigorous thermodynamic and structural characterization remains elusive. Tetraloop motifs found in large ribozymes are ideal systems for an atomistically detailed computational quantification of folding free energy landscapes and the structural characterization of their constituent free energy basins, including nonnative states. In this work, we studied a group of closely related 10-mer tetraloops using a combined parallel tempering and metadynamics technique that allows a reliable sampling of the free energy landscapes, requiring only knowledge that the stem folds into a canonical A-RNA configuration. We isolated and analyzed unfolded, folded, and misfolded populations that correspond to different free energy basins. We identified a distinct misfolded state that has a stability very close to that of the correctly folded state. This misfolded state contains a predominant population that shares the same structural features across all tetraloops studied here and lacks the noncanonical A-G base pair in its loop portion. Further analysis performed with biased trajectories showed that although this competitive misfolded state is not an essential intermediate, it is visited in most of the transitions from unfolded to correctly folded states. Moreover, the tetraloops can transition from this misfolded state to the correctly folded state without requiring extensive unfolding.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo M Piaggi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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14
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Esmaeeli R, Piña MDLN, Frontera A, Pérez A, Bauzá A. Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study. J Chem Theory Comput 2021; 17:6624-6633. [PMID: 34586810 PMCID: PMC8515804 DOI: 10.1021/acs.jctc.1c00756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
In this study, we
demonstrate that anion−π interactions
(an attractive noncovalent force between electron deficient π-systems
and anions) are involved in the stabilization of GAAA and GGAG RNA
tetraloops. Using the single recognition particle (SRP)–RNA
complexes as a case of study, we combined molecular dynamics (MD)
and quantum mechanics (QM) calculations to shed light on the structural
influence of phosphate–G anion−π interactions
and hydrogen bonds (HBs) involving K+/Mg2+ water
clusters. In addition, the RNA assemblies herein were further characterized
by means of the “atoms in molecules” (AIM) and noncovalent
interactions plot (NCIplot) methodologies. We believe the results
derived from this study might be important in the fields of chemical
biology (RNA folding and engineering) and supramolecular chemistry
(anion−π interactions) as well as to further expand the
current knowledge regarding RNA structural motifs.
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Affiliation(s)
- Reza Esmaeeli
- Chemistry Department, University of Florida, Gainesville, Florida 32611, United States
| | - María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Alberto Pérez
- Chemistry Department, University of Florida, Gainesville, Florida 32611, United States
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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15
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Yu CH, Kabza AM, Sczepanski JT. Assembly of long L-RNA by native RNA ligation. Chem Commun (Camb) 2021; 57:10508-10511. [PMID: 34550128 DOI: 10.1039/d1cc04296c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to their intrinsic nuclease resistance, L-oligonucleotides are being increasingly utilized in the development of molecular tools and sensors. Yet, it remains challenging to synthesize long L-oligonucleotides, potential limiting future applications. Herein, we report straightforward and versitile approach to assemble long L-RNAs from two or more shorter fragments using T4 RNA ligase 1. We show that this approach is compatible with the assembly of several classes of functional L-RNA, which we highlight by generating a 124 nt L-RNA biosensor that functions in serum.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| | - Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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16
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Conservation in the Iron Responsive Element Family. Genes (Basel) 2021; 12:genes12091365. [PMID: 34573347 PMCID: PMC8466369 DOI: 10.3390/genes12091365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Iron responsive elements (IREs) are mRNA stem-loop targets for translational control by the two iron regulatory proteins IRP1 and IRP2. They are found in the untranslated regions (UTRs) of genes that code for proteins involved in iron metabolism. There are ten “classic” IRE types that define the conserved secondary and tertiary structure elements necessary for proper IRP binding, and there are 83 published “IRE-like” sequences, most of which depart from the established IRE model. Here are structurally-guided discussions regarding the essential features of an IRE and what is important for IRE family membership.
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17
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Günzel C, Kühnl F, Arnold K, Findeiß S, Weinberg CE, Stadler PF, Mörl M. Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches. RNA Biol 2021; 18:457-467. [PMID: 32882151 PMCID: PMC7971258 DOI: 10.1080/15476286.2020.1816336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5' untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modelling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviour in vivo critically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developed in silico methods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyse the influence of 5' hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free licence on GitHub (https://github.com/xileF1337/riboswitch_design).
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Affiliation(s)
- Christian Günzel
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Felix Kühnl
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16–18, D-04107 Leipzig, Germany
| | - Katharina Arnold
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16–18, D-04107 Leipzig, Germany
| | - Christina E. Weinberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16–18, D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße Leipzig, D-04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Facultad De Ciencias, Universidad National De Colombia, Sede Bogotá, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
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18
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Cheng CH, Ishii K, Tahara T. Microsecond Equilibrium Dynamics of Hairpin-Forming Oligonucleotides Quantified by Two-Color Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem B 2020; 124:10673-10681. [PMID: 33200606 DOI: 10.1021/acs.jpcb.0c07600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA and DNA play distinct roles in biological systems. However, the underlying physicochemical difference has been poorly understood, in particular, that in dynamical aspects. In this paper, we report on a comparative study of the formation-dissociation dynamics of a hairpin structure of RNA and DNA with development of two-color two-dimensional fluorescence lifetime correlation spectroscopy (two-color 2D FLCS). In this extension of 2D FLCS, we newly introduce the two-color detection scheme to analyze not only donor fluorescence photons but also acceptor fluorescence photons from a doubly labeled Förster resonance energy transfer (FRET) pair. This new 2D FLCS is utilized to resolve multiple species present in an equilibrated condition with a microsecond time resolution and enhanced sensitivity, and the combined use with the filtered fluorescence correlation spectroscopy (FCS) method enables a quantitative discussion on microsecond structural dynamics occurring in the equilibrium. This integrated approach is applied to FRET-labeled RNA/DNA oligonucleotides having analogous hairpin-forming sequences, and it was revealed that the hairpin dissociation rate of RNA is an order of magnitude slower than that of DNA while their hairpin-forming rates are comparable. This marked difference is attributable to the distinct duplex structure of RNA and DNA. The present study demonstrates that the integrated approach combining two-color 2D FLCS and filtered FCS has a high potential for quantifying microsecond kinetics at the single-molecule level, which allows us to experimentally construct a free energy landscape.
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Affiliation(s)
- Chao-Han Cheng
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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19
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Zhao C, Zhang D, Jiang Y, Chen SJ. Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability. Biophys J 2020; 119:1439-1455. [PMID: 32949490 PMCID: PMC7568001 DOI: 10.1016/j.bpj.2020.07.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
The ability to accurately predict RNA hairpin structure and stability for different loop sequences and salt conditions is important for understanding, modeling, and designing larger RNA folds. However, traditional RNA secondary structure models cannot treat loop-sequence and ionic effects on RNA hairpin folding. Here, we describe a general, three-dimensional (3D) conformation-based computational method for modeling salt concentration-dependent conformational distributions and the detailed 3D structures for a set of three RNA hairpins that contain a variable, 15-nucleotide loop sequence. For a given RNA sequence, the new, to our knowledge, method integrates a Vfold2D two-dimensional structure folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations and Monte Carlo tightly bound ion estimations of ion-mediated electrostatic interactions. The model predicts free-energy landscapes for the different RNA hairpin-forming sequences with variable salt conditions. The theoretically predicted results agree with the experimental fluorescence measurements, validating the strategy. Furthermore, the theoretical model goes beyond the experimental results by enabling in-depth 3D structural analysis, revealing energetic mechanisms for the sequence- and salt-dependent folding stability. Although the computational framework presented here is developed for RNA hairpin systems, the general method may be applied to investigate other RNA systems, such as multiway junctions or pseudoknots in mixed metal ion solutions.
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Affiliation(s)
- Chenhan Zhao
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri
| | - Yangwei Jiang
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri.
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20
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Wang Y, Liu T, Yu T, Tan ZJ, Zhang W. Salt effect on thermodynamics and kinetics of a single RNA base pair. RNA (NEW YORK, N.Y.) 2020; 26:470-480. [PMID: 31988191 PMCID: PMC7075264 DOI: 10.1261/rna.073882.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/11/2020] [Indexed: 05/09/2023]
Abstract
Due to the polyanionic nature of RNAs, the structural folding of RNAs are sensitive to solution salt conditions, while there is still lack of a deep understanding of the salt effect on the thermodynamics and kinetics of RNAs at a single base-pair level. In this work, the thermodynamic and the kinetic parameters for the base-pair AU closing/opening at different salt concentrations were calculated by 3-µsec all-atom molecular dynamics (MD) simulations at different temperatures. It was found that for the base-pair formation, the enthalpy change [Formula: see text] is nearly independent of salt concentration, while the entropy change [Formula: see text] exhibits a linear dependence on the logarithm of salt concentration, verifying the empirical assumption based on thermodynamic experiments. Our analyses revealed that such salt concentration dependence of the entropy change mainly results from the dependence of ion translational entropy change for the base pair closing/opening on salt concentration. Furthermore, the closing rate increases with the increasing of salt concentration, while the opening rate is nearly independent of salt concentration. Additionally, our analyses revealed that the free energy surface for describing the base-pair opening and closing dynamics becomes more rugged with the decrease of salt concentration.
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Affiliation(s)
- Yujie Wang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou, Henan, 466001, P.R. China
| | - Taigang Liu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan, 453003, P.R. China
| | - Ting Yu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
| | - Wenbing Zhang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
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21
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Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies. Methods Mol Biol 2020. [PMID: 32006317 DOI: 10.1007/978-1-0716-0278-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Many RNA architectures were discovered to be involved in essential biological pathways acting as catalysts and/or regulators of gene expression, transcription, translation, splicing, or viral infection. The key to understand their diverse biological functions is to investigate their structure and dynamic. Nuclear Magnetic Resonance (NMR) is a powerful method to gain insight into these properties. However, the study of high-molecular-weight RNAs by NMR remains challenging. Advances in biochemical and NMR methods over the recent years allow to overcome the limitation of NMR. In particular, the incorporation of paramagnetic probes, coupled to the measurement of the induced effects on nuclear spins, has become an efficient tool providing long-range distance restraints and information on dynamic in solution. At the same time, the use of spin label enabled the application of Electron Paramagnetic Resonance (EPR) to study biological macromolecules. Combining NMR and EPR is emerging as a new approach to investigate the architecture of biological systems.Here, we describe an efficient protocol to introduce a paramagnetic probe into a RNA at a specific position. This method enables various combinations of isotopic labeling for NMR and is also of interest for EPR studies.
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22
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Ursu A, Vézina-Dawod S, Disney MD. Methods to identify and optimize small molecules interacting with RNA (SMIRNAs). Drug Discov Today 2019; 24:2002-2016. [PMID: 31356880 PMCID: PMC6842402 DOI: 10.1016/j.drudis.2019.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/11/2019] [Accepted: 06/27/2019] [Indexed: 01/14/2023]
Abstract
RNAs, particularly noncoding RNAs (ncRNAs), are becoming increasingly important therapeutic targets, because they are causative and antagonists of human disease. Indeed, aberrant RNA structural elements and expression deregulate biological processes. In this review, we describe methodologies to discover and optimize small molecules interacting with RNA (SMIRNAs), including the evaluation of direct target engagement and the rescue of RNA-mediated phenotypes in vitro and in vivo. Such studies are essential to fully characterize the mode of action of SMIRNAs and advance our understanding of rationally and efficiently drugging RNAs for therapeutic benefit.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Simon Vézina-Dawod
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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23
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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24
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D'Ascenzo L, Vicens Q, Auffinger P. Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA. Nucleic Acids Res 2019; 46:7989-7997. [PMID: 29986118 PMCID: PMC6125677 DOI: 10.1093/nar/gky578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/01/2018] [Indexed: 12/17/2022] Open
Abstract
In contrast to GNRA tetraloop receptors that are common in RNA, receptors for the more thermostable UNCG loops have remained elusive for almost three decades. An analysis of all RNA structures with resolution ≤3.0 Å from the PDB allowed us to identify three previously unnoticed receptors for UNCG and GNRA tetraloops that adopt a common UNCG fold, named ‘Z-turn’ in agreement with our previously published nomenclature. These receptors recognize the solvent accessible second Z-turn nucleotide in different but specific ways. Two receptors participating in a complex network of tertiary interactions are associated with the rRNA UUCG and GAAA Z-turns capping helices H62 and H35a in rRNA large subunits. Structural comparison of fully assembled ribosomes and comparative sequence analysis of >6500 rRNA sequences helped us recognize that these motifs are almost universally conserved in rRNA, where they may contribute to organize the large subunit around the subdomain-IV four-way junction. The third UCCG receptor was identified in a rRNA/protein construct crystallized at acidic pH. These three non-redundant Z-turn receptors are relevant for our understanding of the assembly of rRNA and other long-non-coding RNAs, as well as for the design of novel folding motifs for synthetic biology.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Quentin Vicens
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France.,Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado, Denver School of Medicine, Aurora, CO 80045, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
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25
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Kocak DD, Josephs EA, Bhandarkar V, Adkar SS, Kwon JB, Gersbach CA. Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol 2019; 37:657-666. [PMID: 30988504 PMCID: PMC6626619 DOI: 10.1038/s41587-019-0095-1] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 03/11/2019] [Indexed: 12/26/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeat) systems have been broadly adopted for basic science, biotechnology, and gene and cell therapy. In some cases, these bacterial nucleases have demonstrated off-target activity. This creates a potential hazard for therapeutic applications and could confound results in biological research. Therefore, improving the precision of these nucleases is of broad interest. Here we show that engineering a hairpin secondary structure onto the spacer region of single guide RNAs (hp-sgRNAs) can increase specificity by several orders of magnitude when combined with various CRISPR effectors. We first demonstrate that designed hp-sgRNAs can tune the activity of a transactivator based on Cas9 from Streptococcus pyogenes (SpCas9). We then show that hp-sgRNAs increase the specificity of gene editing using five different Cas9 or Cas12a variants. Our results demonstrate that RNA secondary structure is a fundamental parameter that can tune the activity of diverse CRISPR systems.
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Affiliation(s)
- D Dewran Kocak
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Eric A Josephs
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
- Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Vidit Bhandarkar
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Shaunak S Adkar
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Jennifer B Kwon
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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26
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Kiening M, Ochsenreiter R, Hellinger HJ, Rattei T, Hofacker I, Frishman D. Conserved Secondary Structures in Viral mRNAs. Viruses 2019; 11:E401. [PMID: 31035717 PMCID: PMC6563262 DOI: 10.3390/v11050401] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 12/29/2022] Open
Abstract
RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, such as long mRNAs remains a challenging task, as the contingent of structures a sequence can theoretically fold into grows exponentially with sequence length. We applied a structure prediction pipeline to Viral Orthologous Groups that first identifies the local boundaries of potentially structured regions and subsequently predicts their functional importance. Using this procedure, the orthologous groups were split into structurally homogenous subgroups, which we call subVOGs. This is the first compilation of potentially functional conserved RNA structures in viral coding regions, covering the complete RefSeq viral database. We were able to recover structural elements from previous studies and discovered a variety of novel structured regions. The subVOGs are available through our web resource RNASIV (RNA structure in viruses; http://rnasiv.bio.wzw.tum.de).
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Affiliation(s)
- Michael Kiening
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.
| | - Roman Ochsenreiter
- University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
| | - Hans-Jörg Hellinger
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Ivo Hofacker
- University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.
- St Petersburg State Polytechnic University, St Petersburg 195251, Russia.
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27
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Bergonzo C, Grishaev A. Maximizing accuracy of RNA structure in refinement against residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2019; 73:117-139. [PMID: 31049778 DOI: 10.1007/s10858-019-00236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Structural information about ribonucleic acid (RNA) is lagging behind that of proteins, in part due to its high charge and conformational variability. Molecular dynamics (MD) has played an important role in describing RNA structure, complementing information from both nuclear magnetic resonance (NMR), or X-ray crystallography. We examine the impact of the choice of the empirical force field for RNA structure refinement using cross-validation against residual dipolar couplings (RDCs) as structural accuracy reporter. Four force fields, representing both the state-of-the art in RNA simulation and the most popular selections in NMR structure determination, are compared for a prototypical A-RNA helix. RNA structural accuracy is also evaluated as a function of both density and nature of input NMR data including RDCs, anisotropic chemical shifts, and distance restraints. Our results show a complex interplay between the experimental restraints and the force fields indicating two best-performing choices: high-fidelity refinement in explicit solvent, and the conformational database-derived potentials. Accuracy of RNA models closely tracks the density of 1-bond C-H RDCs, with other data types having beneficial, but smaller effects. At lower RDC density, or when refining against NOEs only, the two selected force fields are capable of accurately describing RNA helices with little or no experimental RDC data, making them available for the higher order structure assembly or better quantification of the intramolecular dynamics. Unrestrained simulations of simple RNA motifs with state-of-the art MD force fields appear to capture the flexibility inherent in nucleic acids while also maintaining a good agreement with the experimental observables.
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Affiliation(s)
- Christina Bergonzo
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Alexander Grishaev
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
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28
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Nicholson DA, Sengupta A, Sung HL, Nesbitt DJ. Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies. J Phys Chem B 2018; 122:9869-9876. [PMID: 30289262 DOI: 10.1021/acs.jpcb.8b06872] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Amino acid and nucleic acid interactions are central in biology and may have played a role in the evolutionary development of protein-based life from an early "RNA Universe." To explore the possible role of single amino acids in promoting nucleic acid folding, single-molecule Förster resonance energy transfer experiments have been implemented with a DNA hairpin construct (7 nucleotide double strand with a 40A loop) as a simple model for secondary structure formation. Exposure to positively charged amino acids (arginine and lysine) is found to clearly stabilize the secondary structure. Kinetically, each amino acid promotes folding by generating a large increase in the folding rate with little change in the unfolding rate. From analysis as a function of temperature, arginine and lysine are found to significantly increase the overall exothermicity of folding while imposing only a small entropic penalty on the folding process. Detailed investigations into the kinetics and thermodynamics of this amino acid-induced folding stability reveal arginine and lysine to interact with nucleic acids in a manner reminiscent of monovalent cations. Specifically, these observations are interpreted in the context of an ion atmosphere surrounding the nucleic acid, in which amino acid salts stabilize folding qualitatively like small monovalent cations but also exhibit differences because of the composition of their side chains.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - Abhigyan Sengupta
- Department of Bioengineering , University of California at Merced , Merced , California 95340 , United States
| | - Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
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29
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Sun TT, Zhao C, Chen SJ. Predicting Cotranscriptional Folding Kinetics For Riboswitch. J Phys Chem B 2018; 122:7484-7496. [PMID: 29985608 DOI: 10.1021/acs.jpcb.8b04249] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
On the basis of a helix-based transition rate model, we developed a new method for sampling cotranscriptional RNA conformational ensemble and the prediction of cotranscriptional folding kinetics. Applications to E. coli. SRP RNA and pbuE riboswitch indicate that the model may provide reliable predictions for the cotranscriptional folding pathways and population kinetics. For E. coli. SRP RNA, the predicted population kinetics and the folding pathway are consistent with the SHAPE profiles in the recent cotranscriptional SHAPE-seq experiments. For the pbuE riboswitch, the model predicts the transcriptional termination efficiency as a function of the force. The theoretical results show (a) a force-induced transition from the aptamer (antiterminator) to the terminator structure and (b) the different folding pathways for the riboswitch with and without the ligand (adenine). More specifically, without adenine, the aptamer structure emerges as a short-lived kinetic transient state instead of a thermodynamically stable intermediate state. Furthermore, from the predicted extension-time curves, the model identifies a series of conformational switches in the pulling process, where the predicted relative residence times for the different structures are in accordance with the experimental data. The model may provide a new tool for quantitative predictions of cotranscriptional folding kinetics, and results can offer useful insights into cotranscriptional folding-related RNA functions such as regulation of gene expression with riboswitches.
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Affiliation(s)
- Ting-Ting Sun
- Department of Physics , Zhejiang University of Science and Technology , Hangzhou 310023 , P. R. China.,Department of Physics, Department of Biochemistry, and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Chenhan Zhao
- Department of Physics, Department of Biochemistry, and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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30
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Wang Y, Wang Z, Wang Y, Liu T, Zhang W. The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair. J Chem Phys 2018; 148:045101. [PMID: 29390847 DOI: 10.1063/1.5013282] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.
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Affiliation(s)
- Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yanli Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Taigang Liu
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
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31
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Yang L, Zhong Z, Tong C, Jia H, Liu Y, Chen G. Single-Molecule Mechanical Folding and Unfolding of RNA Hairpins: Effects of Single A-U to A·C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting. J Am Chem Soc 2018; 140:8172-8184. [PMID: 29884019 DOI: 10.1021/jacs.8b02970] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A wobble A·C pair can be protonated at near physiological pH to form a more stable wobble A+·C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A·C mismatch on the top (near the loop, U22C), middle (U25C), and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A·C pair substitution and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of an apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (∼2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (∼1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.
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Affiliation(s)
- Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,School of Physics, and State Key Laboratory of Optoelectronic Materials and Technologies , Sun Yat-sen University , Guangzhou 510275 , People's Republic of China
| | - Cailing Tong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yiran Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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32
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Lubbe AS, Liu Q, Smith SJ, de Vries JW, Kistemaker JCM, de Vries AH, Faustino I, Meng Z, Szymanski W, Herrmann A, Feringa BL. Photoswitching of DNA Hybridization Using a Molecular Motor. J Am Chem Soc 2018; 140:5069-5076. [PMID: 29551069 PMCID: PMC5909178 DOI: 10.1021/jacs.7b09476] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Reversible control
over the functionality of biological systems
via external triggers may be used in future medicine to reduce the
need for invasive procedures. Additionally, externally regulated biomacromolecules
are now considered as particularly attractive tools in nanoscience
and the design of smart materials, due to their highly programmable
nature and complex functionality. Incorporation of photoswitches into
biomolecules, such as peptides, antibiotics, and nucleic acids, has
generated exciting results in the past few years. Molecular motors
offer the potential for new and more precise methods of photoregulation,
due to their multistate switching cycle, unidirectionality of rotation,
and helicity inversion during the rotational steps. Aided by computational
studies, we designed and synthesized a photoswitchable DNA hairpin,
in which a molecular motor serves as the bridgehead unit. After it
was determined that motor function was not affected by the rigid arms
of the linker, solid-phase synthesis was employed to incorporate the
motor into an 8-base-pair self-complementary DNA strand. With the
photoswitchable bridgehead in place, hairpin formation was unimpaired,
while the motor part of this advanced biohybrid system retains excellent
photochemical properties. Rotation of the motor generates large changes
in structure, and as a consequence the duplex stability of the oligonucleotide
could be regulated by UV light irradiation. Additionally, Molecular
Dynamics computations were employed to rationalize the observed behavior
of the motor–DNA hybrid. The results presented herein establish
molecular motors as powerful multistate switches for application in
biological environments.
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Affiliation(s)
- Anouk S Lubbe
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands
| | - Qing Liu
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands
| | - Sanne J Smith
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands
| | - Jan Willem de Vries
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands
| | - Jos C M Kistemaker
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands
| | - Alex H de Vries
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands.,Groningen Biomolecular Sciences and Biotechnology (GBB) Institute , University of Groningen , Nijenborgh 7 , 9747AG Groningen , The Netherlands
| | - Ignacio Faustino
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute , University of Groningen , Nijenborgh 7 , 9747AG Groningen , The Netherlands
| | - Zhuojun Meng
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute , University of Groningen , Nijenborgh 7 , 9747AG Groningen , The Netherlands
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands.,Department of Radiology, University Medical Center Groningen , University of Groningen , Hanzeplein 1 , 9713GZ Groningen , The Netherlands
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands.,DWI-Leibniz Institute for Interactive Materials , Forckenbeckstr. 50 , 52056 Aachen , Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University , Worringerweg 2 , 52074 Aachen , Germany
| | - Ben L Feringa
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands
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33
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Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH. Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops. Biochemistry 2018; 57:2121-2131. [PMID: 29570276 PMCID: PMC5963885 DOI: 10.1021/acs.biochem.7b01306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
GU base pairs are important RNA structural motifs and often close loops. Accurate prediction of RNA structures relies upon understanding the interactions determining structure. The thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs are not well understood. Here, several self-complementary oligonucleotide sequences expected to form duplexes with 2 × 2 nucleotide internal loops closed by GU pairs were investigated. Surprisingly, nuclear magnetic resonance revealed that many of the sequences exist in equilibrium between hairpin and duplex conformations. This equilibrium is not observed with loops closed by Watson-Crick pairs. To measure the thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs, non-self-complementary sequences that preclude formation of hairpins were designed. The measured thermodynamics indicate that some internal loops closed by GU pairs are unusually unstable. This instability accounts for the observed equilibria between duplex and hairpin conformations. Moreover, it suggests that future three-dimensional structures of loops closed by GU pairs may reveal interactions that unexpectedly destabilize folding.
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Affiliation(s)
- Kyle D. Berger
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | | | - Brent M. Znosko
- Department of Chemistry, Saint Louis University, St. Louis MO 63103
| | - Hongying Sun
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - David H. Mathews
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - Douglas H. Turner
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
- Department of Chemistry, University of Rochester, Rochester, NY 14627
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34
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Leonard KN, Blose JM. Effects of osmolytes and macromolecular crowders on stable GAAA tetraloops and their preference for a CG closing base pair. PeerJ 2018; 6:e4236. [PMID: 29456882 PMCID: PMC5815330 DOI: 10.7717/peerj.4236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/15/2017] [Indexed: 11/20/2022] Open
Abstract
Osmolytes and macromolecular crowders have the potential to influence the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in vivo. To further understand the cellular function of RNA we observed the effects of a model osmolyte, polyethylene glycol (PEG) 200, and a model macromolecular crowding agent, PEG 8000, on the GAAA tetraloop motif. GAAA tetraloops are conserved, stable tetraloops, and are critical participants in RNA tertiary structure. They also have a thermodynamic preference for a CG closing base pair. The thermal denaturation of model hairpins containing GAAA loops was monitored using UV-Vis spectroscopy in the presence and absence of PEG 200 or PEG 8000. Both of the cosolutes tested influenced the thermodynamic preference for a CG base pair by destabilizing the loop with a CG closing base pair relative to the loop with a GC closing base pair. This result also extended to a related DNA triloop, which provides further evidence that the interactions between the loop and closing base pair are identical for the d(GCA) triloop and the GAAA tetraloop. Our results suggest that in the presence of model PEG molecules, loops with a GC closing base pair may retain some preferential interactions with the cosolutes that are lost in the presence of the CG closing base pair. These results reveal that relatively small structural changes could influence how neutral cosolutes tune the stability and function of secondary structure motifs in vivo.
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Affiliation(s)
- Kaethe N. Leonard
- Department of Chemistry and Biochemistry, State University of New York, The College at Brockport, Brockport, NY, United States of America
| | - Joshua M. Blose
- Department of Chemistry and Biochemistry, State University of New York, The College at Brockport, Brockport, NY, United States of America
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35
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Smith LG, Zhao J, Mathews DH, Turner DH. Physics-based all-atom modeling of RNA energetics and structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 8. [PMID: 28815951 DOI: 10.1002/wrna.1422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/03/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
Abstract
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422.
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Affiliation(s)
- Louis G Smith
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Jianbo Zhao
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA
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36
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Schuabb C, Pataraia S, Berghaus M, Winter R. Exploring the effects of temperature and pressure on the structure and stability of a small RNA hairpin. Biophys Chem 2017; 231:161-166. [DOI: 10.1016/j.bpc.2016.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 11/30/2022]
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37
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Whittum ME, Blose JM. Effects of osmolytes on stable UUCG tetraloops and their preference for a CG closing base pair. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:583-597. [PMID: 29035162 DOI: 10.1080/15257770.2017.1375518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Osmolytes have the potential to affect the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in the cell. To contribute to the understanding of the in vivo function of RNA we observed the effects of different classes of osmolytes on the UNCG tetraloop motif. UNCG tetraloops are the most common and stable of the RNA tetraloops and are nucleation sites for RNA folding. They also have a significant thermodynamic preference for a CG closing base pair. The thermal denaturation of model hairpins containing UUCG loops was monitored using UV-Vis spectroscopy in the presence of osmolytes with different chemical properties. Interestingly, all of the osmolytes tested destabilized the hairpins, but all had little effect on the thermodynamic preference for a CG base pair, except for polyethylene glycol (PEG) 200. PEG 200 destabilized the loop with the CG closing base pair relative to the loop with a GC closing base pair. The destabilization was linear with increasing concentrations of PEG 200, and the slope of this relationship was not perturbed by changes in the hairpin stem outside of the closing pair. This result suggests that in the presence of PEG 200, the UUCG loop with a GC closing base pair may retain some preferential interactions with the cosolute that are lost in the presence of the CG closing base pair. These results reveal that relatively small structural changes may influence how osmolytes tune the stability, and thus the function of a secondary structure motif in vivo.
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Affiliation(s)
- Michelle E Whittum
- a Department of Chemistry and Biochemistry, The College at Brockport , State University of New York , Brockport , New York , USA
| | - Joshua M Blose
- a Department of Chemistry and Biochemistry, The College at Brockport , State University of New York , Brockport , New York , USA
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38
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Qi F, Frishman D. Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions. Nucleic Acids Res 2017; 45:6109-6118. [PMID: 28335026 PMCID: PMC5449622 DOI: 10.1093/nar/gkx161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Secondary structure elements in the coding regions of mRNAs play an important role in gene expression and regulation, but distinguishing functional from non-functional structures remains challenging. Here we investigate the dependence of sequence–structure relationships in the coding regions on temperature based on the recent PARTE data by Wan et al. Our main finding is that the regions with high and low thermostability (high Tm and low Tm regions) are under evolutionary pressure to preserve RNA secondary structure and primary sequence, respectively. Sequences of low Tm regions display a higher degree of evolutionary conservation compared to high Tm regions. Low Tm regions are under strong synonymous constraint, while high Tm regions are not. These findings imply that high Tm regions contain thermo-stable functionally important RNA structures, which impose relaxed evolutionary constraint on sequence as long as the base-pairing patterns remain intact. By contrast, low thermostability regions contain single-stranded functionally important conserved RNA sequence elements accessible for binding by other molecules. We also find that theoretically predicted structures of paralogous mRNA pairs become more similar with growing temperature, while experimentally measured structures tend to diverge, which implies that the melting pathways of RNA structures cannot be fully captured by current computational approaches.
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Affiliation(s)
- Fei Qi
- Department of Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.,St Petersburg State Polytechnic University, St Petersburg 195251, Russia
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39
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Mukherjee D, Bhattacharyya D. Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. J Mol Model 2017; 23:300. [DOI: 10.1007/s00894-017-3470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
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40
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Kiliszek A, Blaszczyk L, Kierzek R, Rypniewski W. Stabilization of RNA hairpins using non-nucleotide linkers and circularization. Nucleic Acids Res 2017; 45:e92. [PMID: 28334744 PMCID: PMC5449636 DOI: 10.1093/nar/gkx122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/09/2017] [Indexed: 12/21/2022] Open
Abstract
An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem. One method involves stilbene diether or hexaethylene glycol linkers and circularization by T4 RNA ligase. Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Leszek Blaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Núñez-Villanueva D, Iadevaia G, Stross AE, Jinks MA, Swain JA, Hunter CA. H-Bond Self-Assembly: Folding versus Duplex Formation. J Am Chem Soc 2017; 139:6654-6662. [PMID: 28470070 PMCID: PMC5469522 DOI: 10.1021/jacs.7b01357] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 01/05/2023]
Abstract
Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Alexander E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Michael A. Jinks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Jonathan A. Swain
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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Xu H, Plaut B, Zhu X, Chen M, Mavinkurve U, Maiti A, Song G, Murari K, Mandal M. Direct Observation of Folding Energy Landscape of RNA Hairpin at Mechanical Loading Rates. J Phys Chem B 2017; 121:2220-2229. [PMID: 28248503 DOI: 10.1021/acs.jpcb.6b10362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long P5ab RNA hairpin. We find that in the free-energy landscape the barrier height (G‡) and transition distance (x‡) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas ΔG‡ reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (ΔG) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates. Previously, helix formation and denaturation have been described as two-state (F ↔ U) transitions for P5ab. Herein, we report three intermediate states I1, I, and I2 located at 4, 11, and 16 nm respectively, from the folded conformation. The intermediates were observed only when the hairpin was subjected to an optimal r, 7.6 pN/s. The results indicate that the complementary strands in P5ab can zip and unzip through complex routes, whereby mismatches act as checkpoints and often impose barriers. The study highlights the significance of loading rates in force-spectroscopy experiments that are increasingly being used to measure the folding properties of biomolecules.
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Affiliation(s)
- Huizhong Xu
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Benjamin Plaut
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Xiran Zhu
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Maverick Chen
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Udit Mavinkurve
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Anindita Maiti
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Guangtao Song
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Krishna Murari
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Maumita Mandal
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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43
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Wang Y, Gong S, Wang Z, Zhang W. The thermodynamics and kinetics of a nucleotide base pair. J Chem Phys 2017; 144:115101. [PMID: 27004898 DOI: 10.1063/1.4944067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.
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Affiliation(s)
- Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
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44
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Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures. Oncogene 2016; 36:1123-1133. [PMID: 27524419 PMCID: PMC5311031 DOI: 10.1038/onc.2016.279] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 02/08/2023]
Abstract
Recurrent mutations in core splicing factors have been reported in several clonal disorders, including cancers. Mutations in SF3B1, a component of the U2 splicing complex, are the most common. SF3B1 mutations are associated with aberrant pre-mRNA splicing using cryptic 3’ splice sites (3’SS) but the mechanism of their selection is not clear. To understand how cryptic 3’SS are selected, we performed comprehensive analysis of transcriptome-wide changes to splicing and gene expression associated with SF3B1 mutations in patient samples as well as an experimental model of inducible expression. Hundreds of cryptic 3’SS were detectable across the genome in cells expressing mutant SF3B1. These 3’SS are typically sequestered within RNA secondary structures and poorly accessible compared to their corresponding canonical 3’SS. We hypothesized that these cryptic 3’SS are inaccessible during normal splicing catalysis and that this constraint is overcome in spliceosomes containing mutant SF3B1. This model of secondary structure-dependent selection of cryptic 3’SS was found across multiple clonal processes associated with SF3B1 mutations (myelodysplastic syndrome and chronic lymphocytic leukemia). We validated our model predictions in mini-gene splicing assays. Additionally, we found deregulated expression of proteins with relevant functions in splicing factor-related diseases both in association with aberrant splicing and without corresponding splicing changes. Our results show that SF3B1 mutations are associated with a distinct splicing program shared across multiple clonal processes and define a biochemical mechanism for altered 3’SS choice.
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45
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Gervasi NM, Scott SS, Aschrafi A, Gale J, Vohra SN, MacGibeny MA, Kar AN, Gioio AE, Kaplan BB. The local expression and trafficking of tyrosine hydroxylase mRNA in the axons of sympathetic neurons. RNA (NEW YORK, N.Y.) 2016; 22:883-95. [PMID: 27095027 PMCID: PMC4878614 DOI: 10.1261/rna.053272.115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/01/2016] [Indexed: 05/06/2023]
Abstract
Synthesis and regulation of catecholamine neurotransmitters in the central nervous system are implicated in the pathogenesis of a number of neuropsychiatric disorders. To identify factors that regulate the presynaptic synthesis of catecholamines, we tested the hypothesis that the rate-limiting enzyme of the catecholamine biosynthetic pathway, tyrosine hydroxylase (TH), is locally synthesized in axons and presynaptic nerve terminals of noradrenergic neurons. To isolate pure axonal mRNA and protein, rat superior cervical ganglion sympathetic neurons were cultured in compartmentalized Campenot chambers. qRT-PCR and RNA in situ hybridization analyses showed that TH mRNA is present in distal axons. Colocalization experiments with nerve terminal marker proteins suggested that both TH mRNA and protein localize in regions of the axon that resemble nerve terminals (i.e., synaptic boutons). Analysis of polysome-bound RNA showed that TH mRNA is present in polysomes isolated from distal axons. Metabolic labeling of axonally synthesized proteins labeled with the methionine analog, L-azidohomoalanine, showed that TH is locally synthesized in axons. Moreover, the local transfection and translation of exogenous TH mRNA into distal axons facilitated axonal dopamine synthesis. Finally, using chimeric td-Tomato-tagged constructs, we identified a sequence element within the TH 3'UTR that is required for the axonal localization of the reporter mRNA. Taken together, our results provide the first direct evidence that TH mRNA is trafficked to the axon and that the mRNA is locally translated. These findings raise the interesting possibility that the biosynthesis of the catecholamine neurotransmitters is locally regulated in the axon and/or presynaptic nerve terminal.
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Affiliation(s)
- Noreen M Gervasi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shane S Scott
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jenna Gale
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sanah N Vohra
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Margaret A MacGibeny
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Amar N Kar
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Anthony E Gioio
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Barry B Kaplan
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.
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47
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Toribio R, Díaz-López I, Boskovic J, Ventoso I. An RNA trapping mechanism in Alphavirus mRNA promotes ribosome stalling and translation initiation. Nucleic Acids Res 2016; 44:4368-80. [PMID: 26984530 PMCID: PMC4872096 DOI: 10.1093/nar/gkw172] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 02/29/2016] [Indexed: 02/05/2023] Open
Abstract
During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pathway in mammals. However, some viral mRNAs can initiate translation in the presence of phosphorylated eIF2 via stable RNA stem-loop structures (DLP; Downstream LooP) located in their coding sequence (CDS), which promote 43S preinitiation complex stalling on the initiation codon. We show here that during the scanning process, DLPs of Alphavirus mRNA become trapped in ES6S region (680–914 nt) of 18S rRNA that are projected from the solvent side of 40S subunit. This trapping can lock the progress of the 40S subunit on the mRNA in a way that places the upstream initiator AUGi on the P site of 40S subunit, obviating the participation of eIF2. Notably, the DLP structure is released from 18S rRNA upon 60S ribosomal subunit joining, suggesting conformational changes in ES6Ss during the initiation process. These novel findings illustrate how viral mRNA is threaded into the 40S subunit during the scanning process, exploiting the topology of the 40S subunit solvent side to enhance its translation in vertebrate hosts.
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Affiliation(s)
- René Toribio
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Irene Díaz-López
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology and Biocomputing Programme, Electron Microscopy Unit, Spanish Nacional Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Iván Ventoso
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
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48
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Abstract
G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.
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Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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49
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Xu X, Yu T, Chen SJ. Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A 2016; 113:116-21. [PMID: 26699466 PMCID: PMC4711849 DOI: 10.1073/pnas.1517511113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.
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Affiliation(s)
- Xiaojun Xu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Tao Yu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211; Department of Physics, Jianghan University, Wuhan, Hubei 430056, China
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211;
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50
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Schrodt MV, Andrews CT, Elcock AH. Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:5906-17. [PMID: 26580891 PMCID: PMC4806854 DOI: 10.1021/acs.jctc.5b00899] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An understanding of how the conformational behavior of single-stranded DNAs and RNAs depend on sequence is likely to be important for attempts to rationalize the thermodynamics of nucleic acid folding. In an attempt to further our understanding of such sequence dependences, we report here the results of 192 (1 μs) explicit-solvent molecular dynamics (MD) simulations of 48 DNA and 48 RNA tetranucleotide sequences performed using recently reported modifications to the AMBER force field. Each tetranucleotide was simulated starting from two different conformations, a fully natively stacked and a completely unstacked conformation, and populations of the various possible base stacking arrangements were analyzed. The simulations indicate that, for both DNA and RNA, the populations of fully natively stacked conformations increase linearly with increasing numbers of purines in the sequence, while the conformational entropies, computed by two complementary methods, decrease. Despite the comparatively short simulation times, the computed free energies of stacking of the 16 possible combinations of bases in the middle of the sequences are found to be in good correspondence with values reported recently from simulations of dinucleoside monophosphates using the same force field. Finally, consistent with recent reports from other groups, non-native stacking interactions, i.e., between bases that are not adjacent in sequence, are shown to be a recurring feature of the simulations; in particular, stacking interactions of bases in a i:i+2 relationship are shown to occur significantly more frequently when the intervening base is a pyrimidine. Given that the high prevalence of non-native stacking interactions is thought to be unrealistic, it appears that further parametrization work will be required before accurate conformational descriptions of single-stranded nucleic acids can be obtained with current force fields.
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Affiliation(s)
| | - Casey T. Andrews
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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