1
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Shaw A, Craig JM, Amiri H, Kim J, Upton HE, Pimentel SC, Huang JR, Marqusee S, Collins K, Gundlach JH, Bustamante CJ. Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535757. [PMID: 37066208 PMCID: PMC10104057 DOI: 10.1101/2023.04.05.535757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT from Bombyx mori with single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were able to quantify the RT's dwell time at every single nucleotide step along its RNA template. By challenging the enzyme with various RNA structures, we found that during cDNA synthesis the RT can sense and actively destabilize RNA structures 11-12 nt downstream of its front boundary. The ability to sequence single molecules of RNA with nanopores paves the way to investigate the single-nucleotide activity of other processive RNA translocases.
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Affiliation(s)
- Alan Shaw
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
| | | | - Hossein Amiri
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
| | - Jeonghoon Kim
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Bakar Fellows Program, University of California, Berkeley, CA, 94720
| | - Sydney C. Pimentel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Present address: NYU Grossman School of Medicine 550 First Avenue New York, NY 10016
| | - Jesse R. Huang
- Department of Physics, University of Washington, Seattle, WA, 98195
| | - Susan Marqusee
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kathleen Collins
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Bakar Fellows Program, University of California, Berkeley, CA, 94720
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195
| | - Carlos J. Bustamante
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Physics, University of California, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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2
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Mikkelsen AA, Gao F, Carino E, Bera S, Simon A. -1 Programmed ribosomal frameshifting in Class 2 umbravirus-like RNAs uses multiple long-distance interactions to shift between active and inactive structures and destabilize the frameshift stimulating element. Nucleic Acids Res 2023; 51:10700-10718. [PMID: 37742076 PMCID: PMC10602861 DOI: 10.1093/nar/gkad744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023] Open
Abstract
Plus-strand RNA viruses frequently employ -1 programmed ribosomal frameshifting (-1 PRF) to maximize their coding capacity. Ribosomes can frameshift at a slippery sequence if progression is impeded by a frameshift stimulating element (FSE), which is generally a stable, complex, dynamic structure with multiple conformations that contribute to the efficiency of -1 PRF. As FSE are usually analyzed separate from the viral genome, little is known about cis-acting long-distance interactions. Using full-length genomic RNA of umbravirus-like (ula)RNA citrus yellow vein associated virus (CY1) and translation in wheat germ extracts, six tertiary interactions were found associated with the CY1 FSE that span nearly three-quarters of the 2.7 kb genomic RNA. All six tertiary interactions are conserved in other Class 2 ulaRNAs and two are conserved in all ulaRNAs. Two sets of interactions comprise local and distal pseudoknots that involve overlapping FSE nucleotides and thus are structurally incompatible, suggesting that Class 2 FSEs assume multiple conformations. Importantly, two long-distance interactions connect with sequences on opposite sides of the critical FSE central stem, which would unzip the stem and destabilize the FSE. These latter interactions could allow a frameshifting ribosome to translate through a structurally disrupted upstream FSE that no longer blocks ribosome progression.
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Affiliation(s)
- Anna A Mikkelsen
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Elizabeth Carino
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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3
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Abstract
Protein synthesis by the ribosome is the final stage of biological information transfer and represents an irreversible commitment to gene expression. Accurate translation of messenger RNA is therefore essential to all life, and spontaneous errors by the translational machinery are highly infrequent (∼1/100,000 codons). Programmed -1 ribosomal frameshifting (-1PRF) is a mechanism in which the elongating ribosome is induced at high frequency to slip backward by one nucleotide at a defined position and to continue translation in the new reading frame. This is exploited as a translational regulation strategy by hundreds of RNA viruses, which rely on -1PRF during genome translation to control the stoichiometry of viral proteins. While early investigations of -1PRF focused on virological and biochemical aspects, the application of X-ray crystallography and cryo-electron microscopy (cryo-EM), and the advent of deep sequencing and single-molecule approaches have revealed unexpected structural diversity and mechanistic complexity. Molecular players from several model systems have now been characterized in detail, both in isolation and, more recently, in the context of the elongating ribosome. Here we provide a summary of recent advances and discuss to what extent a general model for -1PRF remains a useful way of thinking.
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Affiliation(s)
- Chris H Hill
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom;
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom;
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4
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Structures of tmRNA and SmpB as they transit through the ribosome. Nat Commun 2021; 12:4909. [PMID: 34389707 PMCID: PMC8363625 DOI: 10.1038/s41467-021-24881-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/13/2021] [Indexed: 01/01/2023] Open
Abstract
In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain. Here we present four cryo-EM structures of the ribosome during trans-translation at resolutions from 3.0 to 3.4 Å. These include the high-resolution structure of the whole pre-accommodated state, as well as structures of the accommodated state, the translocated state, and a translocation intermediate. Together, they shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its delivery by the elongation factor EF-Tu to its passage through the ribosomal A and P sites after the opening of the B1 bridges. Additionally, we describe the interactions between the tmRNA-SmpB complex and the ribosome. These explain why the process does not interfere with canonical translation.
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5
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Hsu CF, Chang KC, Chen YL, Hsieh PS, Lee AI, Tu JY, Chen YT, Wen JD. Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates. Nucleic Acids Res 2021; 49:6941-6957. [PMID: 34161580 PMCID: PMC8266650 DOI: 10.1093/nar/gkab512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Programmed –1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.
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Affiliation(s)
- Chiung-Fang Hsu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Lan Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Po-Szu Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - An-I Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jui-Yun Tu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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6
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Napthine S, Hill CH, Nugent HCM, Brierley I. Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless. Viruses 2021; 13:v13071230. [PMID: 34202160 PMCID: PMC8310280 DOI: 10.3390/v13071230] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 12/18/2022] Open
Abstract
The product of the interferon-stimulated gene C19orf66, Shiftless (SHFL), restricts human immunodeficiency virus replication through downregulation of the efficiency of the viral gag/pol frameshifting signal. In this study, we demonstrate that bacterially expressed, purified SHFL can decrease the efficiency of programmed ribosomal frameshifting in vitro at a variety of sites, including the RNA pseudoknot-dependent signals of the coronaviruses IBV, SARS-CoV and SARS-CoV-2, and the protein-dependent stimulators of the cardioviruses EMCV and TMEV. SHFL also reduced the efficiency of stop-codon readthrough at the murine leukemia virus gag/pol signal. Using size-exclusion chromatography, we confirm the binding of the purified protein to mammalian ribosomes in vitro. Finally, through electrophoretic mobility shift assays and mutational analysis, we show that expressed SHFL has strong RNA binding activity that is necessary for full activity in the inhibition of frameshifting, but shows no clear specificity for stimulatory RNA structures.
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Affiliation(s)
| | | | | | - Ian Brierley
- Correspondence: ; Tel.: +44-12-2333-6914; Fax: +44-12-2333-6926
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7
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Chang KC, Wen JD. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput Struct Biotechnol J 2021; 19:3580-3588. [PMID: 34257837 PMCID: PMC8246090 DOI: 10.1016/j.csbj.2021.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/01/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is a translation mechanism that regulates the relative expression level of two proteins encoded on the same messenger RNA (mRNA). This regulation is commonly used by viruses such as coronaviruses and retroviruses but rarely by host human cells, and for this reason, it has long been considered as a therapeutic target for antiviral drug development. Understanding the molecular mechanism of -1 PRF is one step toward this goal. Minus-one PRF occurs with a certain efficiency when translating ribosomes encounter the specialized mRNA signal consisting of the frameshifting site and a downstream stimulatory structure, which impedes translocation of the ribosome. The impeded ribosome can still undergo profound conformational changes to proceed with translocation; however, some of these changes may be unique and essential to frameshifting. In addition, most stimulatory structures exhibit conformational dynamics and sufficient mechanical strength, which, when under the action of ribosomes, may in turn further promote -1 PRF efficiency. In this review, we discuss how the dynamic features of ribosomes and mRNA stimulatory structures may influence the occurrence of -1 PRF and propose a hypothetical frameshifting model that recapitulates the role of conformational dynamics.
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Affiliation(s)
- Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, CA 94158, United States
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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8
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Yang L, Toh DFK, Krishna MS, Zhong Z, Liu Y, Wang S, Gong Y, Chen G. Tertiary Base Triple Formation in the SRV-1 Frameshifting Pseudoknot Stabilizes Secondary Structure Components. Biochemistry 2020; 59:4429-4438. [PMID: 33166472 DOI: 10.1021/acs.biochem.0c00611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Minor-groove base triples formed between stem 1 and loop 2 of the simian retrovirus type 1 (SRV-1) mRNA frameshifting pseudoknot are essential in stimulating -1 ribosomal frameshifting. How tertiary base triple formation affects the local stabilities of secondary structures (stem 1 and stem 2) and thus ribosomal frameshifting efficiency is not well understood. We made a short peptide nucleic acid (PNA) that is expected to invade stem 1 of the SRV-1 pseudoknot by PNA-RNA duplex formation to mimic the stem 1 unwinding process by a translating ribosome. In addition, we used a PNA for invading stem 2 in the SRV-1 pseudoknot. Our nondenaturing polyacrylamide gel electrophoresis data for the binding of PNA to the SRV-1 pseudoknot and mutants reveal that mutations in loop 2 disrupting base triple formation between loop 2 and stem 1 in the SRV-1 pseudoknot result in enhanced invasion by both PNAs. Our data suggest that tertiary stem 1-loop 2 base triple interactions in the SRV-1 pseudoknot can stabilize both of the secondary structural components, stem 1 and stem 2. Stem 2 stability is thus coupled to the structural stability of stem 1-loop 2 base triples, mediated through a long-range effect. The apparent dissociation constants of both PNAs are positively correlated with the pseudoknot mechanical stabilities and frameshifting efficiencies. The relatively simple PNA local invasion experiment may be used to characterize the energetic contribution of tertiary interactions and ligand binding in many other RNA and DNA structures.
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Affiliation(s)
- Lixia Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), No. 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P. R. China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhensheng Zhong
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Yiyao Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China
| | - Shaomeng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China
| | - Yubin Gong
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China
| | - Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), No. 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P. R. China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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9
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Choi J, O’Loughlin S, Atkins JF, Puglisi JD. The energy landscape of -1 ribosomal frameshifting. SCIENCE ADVANCES 2020; 6:eaax6969. [PMID: 31911945 PMCID: PMC6938710 DOI: 10.1126/sciadv.aax6969] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/04/2019] [Indexed: 05/02/2023]
Abstract
Maintenance of translational reading frame ensures the fidelity of information transfer during protein synthesis. Yet, programmed ribosomal frameshifting sequences within the coding region promote a high rate of reading frame change at predetermined sites thus enriching genomic information density. Frameshifting is typically stimulated by the presence of 3' messenger RNA (mRNA) structures, but how these mRNA structures enhance -1 frameshifting remains debatable. Here, we apply single-molecule and ensemble approaches to formulate a mechanistic model of ribosomal -1 frameshifting. Our model suggests that the ribosome is intrinsically susceptible to frameshift before its translocation and this transient state is prolonged by the presence of a precisely positioned downstream mRNA structure. We challenged this model using temperature variation in vivo, which followed the prediction made based on in vitro results. Our results provide a quantitative framework for analyzing other frameshifting enhancers and a potential approach to control gene expression dynamically using programmed frameshifting.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Sinéad O’Loughlin
- Schools of Biochemistry and Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland
| | - John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
- Corresponding author.
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