1
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Li S, Palo MZ, Zhang X, Pintilie G, Zhang K. Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Nat Commun 2023; 14:1294. [PMID: 36928031 PMCID: PMC10020454 DOI: 10.1038/s41467-023-36724-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5'-splice site analog product and a 3'-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2'-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing.
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Affiliation(s)
- Shanshan Li
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
| | - Michael Z Palo
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Xiaojing Zhang
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Grigore Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Kaiming Zhang
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
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2
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Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z. Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Nat Catal 2023. [DOI: 10.1038/s41929-023-00934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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3
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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4
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Zakrevsky P, Calkins E, Kao YL, Singh G, Keleshian VL, Baudrey S, Jaeger L. In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules. Nucleic Acids Res 2021; 49:2289-2305. [PMID: 33524109 PMCID: PMC7913685 DOI: 10.1093/nar/gkab021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/05/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022] Open
Abstract
GNRA tetraloop-binding receptor interactions are key components in the macromolecular assembly of a variety of functional RNAs. In nature, there is an apparent bias for GAAA/11nt receptor and GYRA/helix interactions, with the former interaction being thermodynamically more stable than the latter. While past in vitro selections allowed isolation of novel GGAA and GUGA receptors, we report herein an in vitro selection that revealed several novel classes of specific GUAA receptors with binding affinities comparable to those from natural GAAA/11nt interactions. These GUAA receptors have structural homology with double-locked bulge RNA modules naturally occurring in ribosomal RNAs. They display mutational robustness that enables exploration of the sequence/phenotypic space associated to GNRA/receptor interactions through epistasis. Their thermodynamic self-assembly fitness landscape is characterized by a rugged neutral network with possible evolutionary trajectories toward natural GNRA/receptor interactions. High throughput sequencing analysis revealed synergetic mutations located away from the tertiary interactions that positively contribute to assembly fitness. Our study suggests that the repertoire of GNRA/receptor interactions is much larger than initially thought from the analysis of natural stable RNA molecules and also provides clues for their evolution towards natural GNRA/receptors.
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Affiliation(s)
- Paul Zakrevsky
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Erin Calkins
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Yi-Ling Kao
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Gurkeerat Singh
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Vasken L Keleshian
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Stephanie Baudrey
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
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5
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Mitchell C, Polanco JA, DeWald L, Kress D, Jaeger L, Grabow WW. Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch. Nucleic Acids Res 2020; 47:6439-6451. [PMID: 31045210 PMCID: PMC6614920 DOI: 10.1093/nar/gkz304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/22/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled synthetic contexts in order to gain new and critical insights into their particular structural features and overall performance. Here, we characterized the binding affinity of a unique loop–receptor interaction found in the tetrahydrofolate (THF) riboswitch using rationally designed self-assembling tectoRNAs. Our work suggests that the THF loop–receptor interaction has been fine-tuned for its particular role as a riboswitch component. We also demonstrate that the thermodynamic stability of this interaction can be modulated by the presence of folinic acid, which induces a local structural change at the level of the loop–receptor. This corroborates the existence of a THF binding site within this tertiary module and paves the way for its potential use as a THF responsive module for RNA nanotechnology and synthetic biology.
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Affiliation(s)
- Charles Mitchell
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Julio A Polanco
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Laura DeWald
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Dustin Kress
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
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6
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Cai X, Arias DS, Velazquez LR, Vexler S, Bevier AL, Fygenson DK. DNA Nunchucks: Nanoinstrumentation for Single-Molecule Measurement of Stiffness and Bending. NANO LETTERS 2020; 20:1388-1395. [PMID: 31872766 DOI: 10.1021/acs.nanolett.9b04980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bending of double-stranded DNA (dsDNA) has important applications in biology and engineering, but measurement of DNA bend angles is notoriously difficult and rarely dynamic. Here we introduce a nanoscale instrument that makes dynamic measurement of the bend in short dsDNAs easy enough to be routine. The instrument works by embedding the ends of a dsDNA in stiff, fluorescently labeled DNA nanotubes, thereby mechanically magnifying their orientations. The DNA nanotubes are readily confined to a plane and imaged while freely diffusing. Single-molecule bend angles are rapidly and reliably extracted from the images by a neural network. We find that angular variance across a population increases with dsDNA length, as predicted by the worm-like chain model, although individual distributions can differ significantly from one another. For dsDNAs with phased A6-tracts, we measure an intrinsic bend of 17 ± 1° per A6-tract, consistent with other methods, and a length-dependent angular variance that indicates A6-tracts are (80 ± 30)% stiffer than generic dsDNA.
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Affiliation(s)
- Xinyue Cai
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - D Sebastian Arias
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Lourdes R Velazquez
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Shelby Vexler
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Alexander L Bevier
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - D Kuchnir Fygenson
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
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7
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Modulating Immune Response with Nucleic Acid Nanoparticles. Molecules 2019; 24:molecules24203740. [PMID: 31627288 PMCID: PMC6832290 DOI: 10.3390/molecules24203740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
Nano-objects made of nucleic acids are becoming promising materials in the biomedical field. This is, in part, due to DNA and RNA self-assembly properties that can be accurately computed to fabricate various complex nanoarchitectures of 2D and 3D shapes. The nanoparticles can be assembled from DNA, RNA, and chemically modified oligonucleotide mixtures which, in turn, influence their chemical and biophysical properties. Solid-phase synthesis allows large-scale production of individual oligonucleotide strands with batch-to-batch consistency and exceptional purity. All of these advantageous characteristics of nucleic-acid-based nanoparticles were known to be exceptionally useful as a nanoplatform for drug delivery purposes. Recently, several important discoveries have been achieved, demonstrating that nucleic acid nanoparticles (NANPs) can also be used to modulate the immune response of host cells. The purpose of this review is to briefly overview studies demonstrating architectural design principles of NANPs, as well as the ability of NANPs to control immune responses.
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8
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Grabow WW, Andrews GE. On the nature and origin of biological information: The curious case of RNA. Biosystems 2019; 185:104031. [PMID: 31525398 DOI: 10.1016/j.biosystems.2019.104031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/18/2022]
Abstract
Biological information is most commonly thought of in terms of biology's Central Dogma where DNA is viewed as a linearized code used to synthesize proteins. Using DNA's chemical cousin, RNA, as a case study we consider how biological information operates outside the linear arrangement of its polymeric subunits. Much like individual pieces of a jigsaw puzzle, particular structures enable biomolecules to undergo precise molecular interactions with one another based on their respective shapes. By exploring the relationship between sequence and structure in RNA we argue that biological information finds its ultimate functional fulfillment in the three-dimensional structural arrangement of its atoms. We show how recurrent structural RNA motifs-operating at the tertiary level of a molecule-provide robust building blocks for the formation of new structural configurations and thereby convey the information required for emergent biological functions. We posit that these same RNA structures, guided by their respective thermodynamic stabilities, experience selective pressure to maintain particular three-dimensional architectures over and above pressures to maintain a particular sequence of nucleotides. Ultimately, this framework for understanding the nature of biological information provides a useful paradigm for understanding its origins and how biological information can result from chaotic prebiotic conditions.
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Affiliation(s)
- Wade W Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA, 918119-1997, USA.
| | - Grace E Andrews
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA, 918119-1997, USA
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9
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Calkins ER, Zakrevsky P, Keleshian VL, Aguilar EG, Geary C, Jaeger L. Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome. Nucleic Acids Res 2019; 47:480-494. [PMID: 30418638 PMCID: PMC6326782 DOI: 10.1093/nar/gky1111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/22/2018] [Indexed: 01/02/2023] Open
Abstract
Stable RNAs rely on a vast repertoire of long-range interactions to assist in the folding of complex cellular machineries such as the ribosome. The universally conserved L39/H89 interaction is a long-range GNRA-like/receptor interaction localized in proximity to the peptidyl transferase center of the large subunit of the ribosome. Because of its central location, L39/H89 likely originated at an early evolutionary stage of the ribosome and played a significant role in its early function. However, L39/H89 self-assembly is impaired outside the ribosomal context. Herein, we demonstrate that structural modularity principles can be used to re-engineer L39/H89 to self-assemble in vitro. The new versions of L39/H89 improve affinity and loop selectivity by several orders of magnitude and retain the structural and functional features of their natural counterparts. These versions of L39/H89 are proposed to be ancestral forms of L39/H89 that were capable of assembling and folding independently from proteins and post-transcriptional modifications. This work demonstrates that novel RNA modules can be rationally designed by taking advantage of the modular syntax of RNA. It offers the prospect of creating new biochemical models of the ancestral ribosome and increases the tool kit for RNA nanotechnology and synthetic biology.
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Affiliation(s)
- Erin R Calkins
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Paul Zakrevsky
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Vasken L Keleshian
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Eduardo G Aguilar
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Cody Geary
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
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10
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Sharma IM, Rappé MC, Addepalli B, Grabow WW, Zhuang Z, Abeysirigunawardena SC, Limbach PA, Jaeger L, Woodson SA. A metastable rRNA junction essential for bacterial 30S biogenesis. Nucleic Acids Res 2019; 46:5182-5194. [PMID: 29850893 PMCID: PMC6007441 DOI: 10.1093/nar/gky120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/13/2018] [Indexed: 12/26/2022] Open
Abstract
Tertiary sequence motifs encode interactions between RNA helices that create the three-dimensional structures of ribosomal subunits. A Right Angle motif at the junction between 16S helices 5 and 6 (J5/6) is universally conserved amongst small subunit rRNAs and forms a stable right angle in minimal RNAs. J5/6 does not form a right angle in the mature ribosome, suggesting that this motif encodes a metastable structure needed for ribosome biogenesis. In this study, J5/6 mutations block 30S ribosome assembly and 16S maturation in Escherichia coli. Folding assays and in-cell X-ray footprinting showed that J5/6 mutations favor an assembly intermediate of the 16S 5' domain and prevent formation of the central pseudoknot. Quantitative mass spectrometry revealed that mutant pre-30S ribosomes lack protein uS12 and are depleted in proteins uS5 and uS2. Together, these results show that impaired folding of the J5/6 right angle prevents the establishment of inter-domain interactions, resulting in global collapse of the 30S structure observed in electron micrographs of mutant pre-30S ribosomes. We propose that the J5/6 motif is part of a spine of RNA helices that switch conformation at distinct stages of assembly, linking peripheral domains with the 30S active site to ensure the integrity of 30S biogenesis.
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Affiliation(s)
- Indra Mani Sharma
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Mollie C Rappé
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | | | - Patrick A Limbach
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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11
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Geary C, Chworos A, Verzemnieks E, Voss NR, Jaeger L. Composing RNA Nanostructures from a Syntax of RNA Structural Modules. NANO LETTERS 2017; 17:7095-7101. [PMID: 29039189 PMCID: PMC6363482 DOI: 10.1021/acs.nanolett.7b03842] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Natural stable RNAs fold and assemble into complex three-dimensional architectures by relying on the hierarchical formation of intricate, recurrent networks of noncovalent tertiary interactions. These sequence-dependent networks specify RNA structural modules enabling orientational and topological control of helical struts to form larger self-folding domains. Borrowing concepts from linguistics, we defined an extended structural syntax of RNA modules for programming RNA strands to assemble into complex, responsive nanostructures under both thermodynamic and kinetic control. Based on this syntax, various RNA building blocks promote the multimolecular assembly of objects with well-defined three-dimensional shapes as well as the isothermal folding of long RNAs into complex single-stranded nanostructures during transcription. This work offers a glimpse of the limitless potential of RNA as an informational medium for designing programmable and functional nanomaterials useful for synthetic biology, nanomedicine, and nanotechnology.
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Affiliation(s)
- Cody Geary
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Arkadiusz Chworos
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Erik Verzemnieks
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Neil R. Voss
- Biological, Chemical, and Physical Sciences Department, Roosevelt University, 1400 North Roosevelt Blvd., Schaumburg, Illinois 60173, United States
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
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12
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Bui MN, Brittany Johnson M, Viard M, Satterwhite E, Martins AN, Li Z, Marriott I, Afonin KA, Khisamutdinov EF. Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2017; 13:1137-1146. [PMID: 28064006 PMCID: PMC6637421 DOI: 10.1016/j.nano.2016.12.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 12/21/2022]
Abstract
RNA nanotechnology employs synthetically modified ribonucleic acid (RNA) to engineer highly stable nanostructures in one, two, and three dimensions for medical applications. Despite the tremendous advantages in RNA nanotechnology, unmodified RNA itself is fragile and prone to enzymatic degradation. In contrast to use traditionally modified RNA strands e.g. 2'-fluorine, 2'-amine, 2'-methyl, we studied the effect of RNA/DNA hybrid approach utilizing a computer-assisted RNA tetra-uracil (tetra-U) motif as a toolkit to address questions related to assembly efficiency, versatility, stability, and the production costs of hybrid RNA/DNA nanoparticles. The tetra-U RNA motif was implemented to construct four functional triangles using RNA, DNA and RNA/DNA mixtures, resulting in fine-tunable enzymatic and thermodynamic stabilities, immunostimulatory activity and RNAi capability. Moreover, the tetra-U toolkit has great potential in the fabrication of rectangular, pentagonal, and hexagonal NPs, representing the power of simplicity of RNA/DNA approach for RNA nanotechnology and nanomedicine community.
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Affiliation(s)
- My N Bui
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mathias Viard
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Emily Satterwhite
- Nanoscale Science Program, University of North Carolina at Charlotte, The Center for Biomedical Engineering and Science, Charlotte, NC 28223, USA
| | - Angelica N Martins
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - Ian Marriott
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, University of North Carolina at Charlotte, The Center for Biomedical Engineering and Science, Charlotte, NC 28223, USA
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13
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Jones CP, Ferré-D'Amaré AR. RNA quaternary structure and global symmetry. Trends Biochem Sci 2015; 40:211-20. [PMID: 25778613 PMCID: PMC4380790 DOI: 10.1016/j.tibs.2015.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/16/2022]
Abstract
Many proteins associate into symmetric multisubunit complexes. Structural analyses suggested that, by contrast, virtually all RNAs with complex 3D structures function as asymmetric monomers. Recent crystal structures revealed that several biological RNAs exhibit global symmetry at the level of their tertiary and quaternary structures. Here we survey known examples of global RNA symmetry, including the true quaternary symmetry of the bacteriophage ϕ29 prohead RNA (pRNA) and the internal pseudosymmetry of the single-chain flavin mononucleotide (FMN), glycine, and cyclic di-AMP (c-di-AMP) riboswitches. For these RNAs, global symmetry stabilizes the RNA fold, coordinates ligand-RNA interactions, and facilitates association with symmetric binding partners.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
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14
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Rogers TA, Andrews GE, Jaeger L, Grabow WW. Fluorescent monitoring of RNA assembly and processing using the split-spinach aptamer. ACS Synth Biol 2015; 4:162-6. [PMID: 24932527 DOI: 10.1021/sb5000725] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
As insights into RNA's many diverse cellular roles continue to be gained, interest and applications in RNA self-assembly and dynamics remain at the forefront of structural biology. The bifurcation of functional molecules into nonfunctional fragments provides a useful strategy for controlling and monitoring cellular RNA processes and functionalities. Herein we present the bifurcation of the preexisting Spinach aptamer and demonstrate its utility as a novel split aptamer system for monitoring RNA self-assembly as well as the processing of pre-short interfering substrates. We show for the first time that the Spinach aptamer can be divided into two nonfunctional halves that, once assembled, restore the original fluorescent signal characteristic of the unabridged aptamer. In this regard, the split-Spinach aptamer is represented as a potential tool for monitoring the self-assembly of artificial and/or natural RNAs.
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Affiliation(s)
- Tucker A. Rogers
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Grant E. Andrews
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Bio-Molecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Wade W. Grabow
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
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15
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Gardner PP, Eldai H. Annotating RNA motifs in sequences and alignments. Nucleic Acids Res 2015; 43:691-8. [PMID: 25520192 PMCID: PMC4333381 DOI: 10.1093/nar/gku1327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 11/30/2014] [Accepted: 12/05/2014] [Indexed: 11/21/2022] Open
Abstract
RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam.
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Affiliation(s)
- Paul P Gardner
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Hisham Eldai
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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16
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Abstract
CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such as the ribosome, large ribozymes, and riboswitches. Thus, the next step in synthetic RNA design will involve new ways to implement these same types of dynamic and responsive architectures into nanostructures functioning as real nanomachines in and outside the cell. RNA nanotechnology will likely garner broader utility and influence with a greater focus on the interplay between thermodynamic and kinetic influences on RNA self-assembly and using natural RNAs as guiding principles.
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Affiliation(s)
- Wade W. Grabow
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Bio-Molecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
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17
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Protein-guided RNA dynamics during early ribosome assembly. Nature 2014; 506:334-8. [PMID: 24522531 PMCID: PMC3968076 DOI: 10.1038/nature13039] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/20/2014] [Indexed: 01/30/2023]
Abstract
The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the rRNA structure so that later proteins may join the complex is poorly understood. Here we use single molecule fluorescence resonance energy transfer (smFRET) to observe real-time encounters between ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4-RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free energy path to protein-RNA recognition. Three-color FRET and molecular dynamics (MD) simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. This protein-guided dynamics offers an alternative explanation for induced fit in RNA-protein complexes.
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18
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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19
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Kim N, Petingi L, Schlick T. Network Theory Tools for RNA Modeling. WSEAS TRANSACTIONS ON MATHEMATICS 2013; 9:941-955. [PMID: 25414570 PMCID: PMC4235620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An introduction into the usage of graph or network theory tools for the study of RNA molecules is presented. By using vertices and edges to define RNA secondary structures as tree and dual graphs, we can enumerate, predict, and design RNA topologies. Graph connectivity and associated Laplacian eigenvalues relate to biological properties of RNA and help understand RNA motifs as well as build, by computational design, various RNA target structures. Importantly, graph theoretical representations of RNAs reduce drastically the conformational space size and therefore simplify modeling and prediction tasks. Ongoing challenges remain regarding general RNA design, representation of RNA pseudoknots, and tertiary structure prediction. Thus, developments in network theory may help advance RNA biology.
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Affiliation(s)
- Namhee Kim
- New York University Department of Chemistry Courant Institute of Mathematical Sciences 251 Mercer Street New York, NY 10012, USA
| | - Louis Petingi
- College of Staten Island City University of New York Department of Computer Science 2800 Victory Boulevard Staten Island, NY 10314, USA
| | - Tamar Schlick
- New York University Department of Chemistry Courant Institute of Mathematical Sciences 251 Mercer Street New York, NY 10012, USA
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20
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Ishikawa J, Furuta H, Ikawa Y. RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:651-64. [PMID: 23836522 DOI: 10.1002/wrna.1185] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/30/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Abstract
RNA molecules are versatile biomaterials that act not only as DNA-like genetic materials but also have diverse functions in regulation of cellular biosystems. RNA is capable of regulating gene expression by sequence-specific hybridization. This feature allows the design of RNA-based artificial gene regulators (riboregulators). RNA can also build complex two-dimensional (2D) and 3D nanostructures, which afford protein-like functions and make RNA an attractive material for nanobiotechnology. RNA tectonics is a methodology in RNA nanobiotechnology for the design and construction of RNA nanostructures/nanoobjects through controlled self-assembly of modular RNA units (tectoRNAs). RNA nanostructures designed according to the concept of RNA tectonics are also attractive as tools in synthetic biology, but in vivo RNA tectonics is still in the early stages. This review presents a summary of the achievements of RNA tectonics and its related researches in vitro, and also introduces recent developments that facilitated the use of RNA nanostructures in bacterial cells.
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Affiliation(s)
- Junya Ishikawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
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21
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Grabow WW, Zhuang Z, Shea JE, Jaeger L. The GA-minor submotif as a case study of RNA modularity, prediction, and design. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:181-203. [PMID: 23378290 DOI: 10.1002/wrna.1153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Complex natural RNAs such as the ribosome, group I and group II introns, and RNase P exemplify the fact that three-dimensional (3D) RNA structures are highly modular and hierarchical in nature. Tertiary RNA folding typically takes advantage of a rather limited set of recurrent structural motifs that are responsible for controlling bends or stacks between adjacent helices. Herein, the GA minor and related structural motifs are presented as a case study to highlight several structural and folding principles, to gain further insight into the structural evolution of naturally occurring RNAs, as well as to assist the rational design of artificial RNAs.
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Affiliation(s)
- Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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