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Hill AC, Bartley LE, Schroeder SJ. Prohead RNA: a noncoding viral RNA of novel structure and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:428-37. [PMID: 26810250 PMCID: PMC5066667 DOI: 10.1002/wrna.1330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/23/2015] [Accepted: 12/02/2015] [Indexed: 12/12/2022]
Abstract
Prohead RNA (pRNA) is an essential component of the powerful Φ29-like bacteriophage DNA packaging motor. However, the specific role of this unique RNA in the Φ29 packaging motor remains unknown. This review examines pRNA as a noncoding RNA of novel structure and function. In order to highlight the reasons for exploring the structure and function of pRNA, we (1) provide an overview of Φ29-like bacteriophage and the Φ29 DNA packaging motor, including putative motor mechanisms and structures of its component parts; (2) discuss pRNA structure and possible roles for pRNA in the Φ29 packaging motor; (3) summarize pRNA self-assembly; and (4) describe the prospective therapeutic applications of pRNA. Many questions remain to be answered in order to connect what is currently known about pRNA structure to its novel function in the Φ29 packaging motor. The knowledge gained from studying the structure, function, and sequence variation in pRNA will help develop tools to better navigate the conformational landscapes of RNA. WIREs RNA 2016, 7:428-437. doi: 10.1002/wrna.1330 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alyssa C Hill
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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2
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RNAComposer and RNA 3D structure prediction for nanotechnology. Methods 2016; 103:120-7. [PMID: 27016145 DOI: 10.1016/j.ymeth.2016.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/04/2016] [Accepted: 03/21/2016] [Indexed: 11/21/2022] Open
Abstract
RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented.
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3
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Insights into the structure and assembly of the bacteriophage 29 double-stranded DNA packaging motor. J Virol 2014; 88:3986-96. [PMID: 24403593 DOI: 10.1128/jvi.03203-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The tailed double-stranded DNA (dsDNA) bacteriophage 29 packages its 19.3-kbp genome into a preassembled procapsid structure by using a transiently assembled phage-encoded molecular motor. This process is remarkable considering that compaction of DNA to near-crystalline densities within the confined space of the capsid requires that the packaging motor work against significant entropic, enthalpic, and DNA-bending energies. The motor consists of three phage-encoded components: the dodecameric connector protein gp10, an oligomeric RNA molecule known as the prohead RNA (pRNA), and the homomeric ring ATPase gp16. Although atomic resolution structures of the connector and different pRNA subdomains have been determined, the mechanism of self-assembly and the resulting stoichiometry of the various motor components on the phage capsid have been the subject of considerable controversy. Here a subnanometer asymmetric cryoelectron microscopy (cryo-EM) reconstruction of a connector-pRNA complex at a unique vertex of the procapsid conclusively demonstrates the pentameric symmetry of the pRNA and illuminates the relative arrangement of the connector and the pRNA. Additionally, a combination of biochemical and cryo-EM analyses of motor assembly intermediates suggests a sequence of molecular events that constitute the pathway by which the motor assembles on the head, thereby reconciling conflicting data regarding pRNA assembly and stoichiometry. Taken together, these data provide new insight into the assembly, structure, and mechanism of a complex molecular machine. IMPORTANCE Viruses consist of a protein shell, or capsid, that protects and surrounds their genetic material. Thus, genome encapsidation is a fundamental and essential step in the life cycle of any virus. In dsDNA viruses, powerful molecular motors essentially pump the viral DNA into a preformed protein shell. This article describes how a viral dsDNA packaging motor self-assembles on the viral capsid and provides insight into its mechanism of action.
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4
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Bouchard P, Legault P. Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction. Biochemistry 2013; 53:258-69. [PMID: 24325625 PMCID: PMC3893828 DOI: 10.1021/bi401491g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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Substrate
recognition by the Neurospora Varkud
satellite ribozyme depends on the formation of a magnesium-dependent
kissing-loop interaction between the stem-loop I (SLI) substrate and
stem-loop V (SLV) of the catalytic domain. From mutagenesis studies,
it has been established that this I/V kissing-loop interaction involves
three Watson–Crick base pairs and is associated with a structural
rearrangement of the SLI substrate that facilitates catalysis. Here,
we report the NMR structural characterization of this I/V kissing-loop
using isolated stem-loops. NMR studies were performed on different
SLI/SLV complexes containing a common SLV and shiftable, preshifted,
or double-stranded SLI variants. These studies confirm the presence
of three Watson–Crick base pairs at the kissing-loop junction
and provide evidence for the structural rearrangement of shiftable
SLI variants upon SLV binding. NMR structure determination of an SLI/SLV
complex demonstrates that both the SLI and SLV loops adopt U-turn
structures, which facilitates intermolecular Watson–Crick base
pairing. Several other interactions at the I/V interface, including
base triples and base stacking, help create a continuously stacked
structure. These NMR studies provide a structural basis to understand
the stability of the I/V kissing-loop interaction and lead us to propose
a kinetic model for substrate activation in the VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Quebec H3C 3J7, Canada
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5
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Zhang H, Endrizzi JA, Shu Y, Haque F, Sauter C, Shlyakhtenko LS, Lyubchenko Y, Guo P, Chi YI. Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA. RNA (NEW YORK, N.Y.) 2013; 19:1226-37. [PMID: 23884902 PMCID: PMC3753930 DOI: 10.1261/rna.037077.112] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 06/06/2013] [Indexed: 05/22/2023]
Abstract
The bacteriophage phi29 DNA packaging motor, one of the strongest biological motors characterized to date, is geared by a packaging RNA (pRNA) ring. When assembled from three RNA fragments, its three-way junction (3WJ) motif is highly thermostable, is resistant to 8 M urea, and remains associated at extremely low concentrations in vitro and in vivo. To elucidate the structural basis for its unusual stability, we solved the crystal structure of this pRNA 3WJ motif at 3.05 Å. The structure revealed two divalent metal ions that coordinate 4 nt of the RNA fragments. Single-molecule fluorescence resonance energy transfer (smFRET) analysis confirmed a structural change of 3WJ upon addition of Mg²⁺. The reported pRNA 3WJ conformation is different from a previously published construct that lacks the metal coordination sites. The phi29 DNA packaging motor contains a dodecameric connector at the vertex of the procapsid, with a central pore for DNA translocation. This portal connector serves as the foothold for pRNA binding to procapsid. Subsequent modeling of a connector/pRNA complex suggests that the pRNA of the phi29 DNA packaging motor exists as a hexameric complex serving as a sheath over the connector. The model of hexameric pRNA on the connector agrees with AFM images of the phi29 pRNA hexamer acquired in air and matches all distance parameters obtained from cross-linking, complementary modification, and chemical modification interference.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
| | - James A. Endrizzi
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
| | - Yi Shu
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Cristallogenèse & Biologie Structurale, F-67084 Strasbourg, France
| | - Lyudmila S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Yuri Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
- Corresponding authorsE-mail E-mail
| | - Young-In Chi
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
- Corresponding authorsE-mail E-mail
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6
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Harjes E, Kitamura A, Zhao W, Morais MC, Jardine PJ, Grimes S, Matsuo H. Structure of the RNA claw of the DNA packaging motor of bacteriophage Φ29. Nucleic Acids Res 2012; 40:9953-63. [PMID: 22879380 PMCID: PMC3479190 DOI: 10.1093/nar/gks724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage ϕ29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33–35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.
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Affiliation(s)
- Elena Harjes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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7
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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8
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Zhang X, Tung CS, Sowa GZ, Hatmal MM, Haworth IS, Qin PZ. Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. J Am Chem Soc 2012; 134:2644-52. [PMID: 22229766 DOI: 10.1021/ja2093647] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (H(T) and H(L)) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which H(T) and H(L) stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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9
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Morais MC. The dsDNA Packaging Motor in Bacteriophage ø29. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:511-47. [DOI: 10.1007/978-1-4614-0980-9_23] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proc Natl Acad Sci U S A 2011; 108:20573-8. [PMID: 22143768 DOI: 10.1073/pnas.1106516108] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic-accuracy structure prediction of macromolecules should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete sampling of a biopolymer's many degrees of freedom. We present herein a working hypothesis, called the "stepwise ansatz," for recursively constructing well-packed atomic-detail models in small steps, enumerating several million conformations for each monomer, and covering all build-up paths. By making use of high-performance computing and the Rosetta framework, we provide first tests of this hypothesis on a benchmark of 15 RNA loop-modeling problems drawn from riboswitches, ribozymes, and the ribosome, including 10 cases that are not solvable by current knowledge-based modeling approaches. For each loop problem, this deterministic stepwise assembly method either reaches atomic accuracy or exposes flaws in Rosetta's all-atom energy function, indicating the resolution of the conformational sampling bottleneck. As a further rigorous test, we have carried out a blind all-atom prediction for a noncanonical RNA motif, the C7.2 tetraloop/receptor, and validated this model through nucleotide-resolution chemical mapping experiments. Stepwise assembly is an enumerative, ab initio build-up method that systematically outperforms existing Monte Carlo and knowledge-based methods for 3D structure prediction.
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11
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Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA. A boost for the emerging field of RNA nanotechnology. ACS NANO 2011; 5:3405-18. [PMID: 21604810 PMCID: PMC3102291 DOI: 10.1021/nn200989r] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This Nano Focus article highlights recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, which took place in Cleveland, OH, USA (October 23-25, 2010) ( http://www.eng.uc.edu/nanomedicine/RNA2010/ ), chaired by Peixuan Guo and co-chaired by David Rueda and Scott Tenenbaum. The conference was the first of its kind to bring together more than 30 invited speakers in the frontier of RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics. A special invited talk on the well-established principles of DNA nanotechnology was arranged to provide models for RNA nanotechnology. An Administrator from National Institutes of Health (NIH) National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer discussed the current nanocancer research directions and future funding opportunities at NCI. As indicated by the feedback received from the invited speakers and the meeting participants, this meeting was extremely successful, exciting, and informative, covering many groundbreaking findings, pioneering ideas, and novel discoveries.
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Affiliation(s)
- Girish C. Shukla
- Center for Gene Regulation in Health and Disease, Department of Biological Sciences, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Farzin Haque
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Yitzhak Tor
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Jean-Jacques Toulmé
- Université Bordeaux Segalen, INSERM U869, Bâtiment 3A 1er étage, 33076 Bordeaux Cedex, France
| | - Hervé Isambert
- Institut Curie, Research Division, CNRS UMR 168, 11 rue P. & M. Curie, 75005 Paris, France
| | - Peixuan Guo
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Scott A. Tenenbaum
- College of Nanoscale Science & Engineering, University at Albany-SUNY, Albany, New York 12203, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
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Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. Proc Natl Acad Sci U S A 2011; 108:7357-62. [PMID: 21471452 DOI: 10.1073/pnas.1016690108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Prohead RNA (pRNA) is an essential component in the assembly and operation of the powerful bacteriophage 29 DNA packaging motor. The pRNA forms a multimeric ring via intermolecular base-pairing interactions between protomers that serves to guide the assembly of the ring ATPase that drives DNA packaging. Here we report the quaternary structure of this rare multimeric RNA at 3.5 Å resolution, crystallized as tetrameric rings. Strong quaternary interactions and the inherent flexibility helped rationalize how free pRNA is able to adopt multiple oligomerization states in solution. These characteristics also allowed excellent fitting of the crystallographic pRNA protomers into previous prohead/pRNA cryo-EM reconstructions, supporting the presence of a pentameric, but not hexameric, pRNA ring in the context of the DNA packaging motor. The pentameric pRNA ring anchors itself directly to the phage prohead by interacting specifically with the fivefold symmetric capsid structures that surround the head-tail connector portal. From these contacts, five RNA superhelices project from the pRNA ring, where they serve as scaffolds for binding and assembly of the ring ATPase, and possibly mediate communication between motor components. Construction of structure-based designer pRNAs with little sequence similarity to the wild-type pRNA were shown to fully support the packaging of 29 DNA.
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Shu D, Zhang H, Petrenko R, Meller J, Guo P. Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters for RNA nanoparticles. ACS NANO 2010; 4:6843-53. [PMID: 20954698 PMCID: PMC2990273 DOI: 10.1021/nn1014853] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/04/2010] [Indexed: 05/19/2023]
Abstract
The increasing interest in RNA nanotechnology and the demonstrated feasibility of using RNA nanoparticles as therapeutics have prompted the need for imaging systems with nanometer-scale resolution for RNA studies. Phi29 dimeric pRNAs can serve as building blocks in assembly into the hexameric ring of the nanomotors, as modules of RNA nanoparciles, and as vehicles for specific delivery of therapeutics to cancers or viral infected cells. The understanding of the 3D structure of this novel RNA dimeric particle is fundamentally and practically important. Although a 3D model of pRNA dimer has been proposed based on biochemical analysis, no distance measurements or X-ray diffraction data have been reported. Here we evaluated the application of our customized single-molecule dual-viewing system for distance measurement within pRNA dimers using single-molecule Fluorescence Resonance Energy Transfer (smFRET). Ten pRNA monomers labeled with single donor or acceptor fluorophores at various locations were constructed and eight dimers were assembled. smFRET signals were detected for six dimers. The tethered arm sizes of the fluorophores were estimated empirically from dual-labeled RNA/DNA standards. The distances between donor and acceptor were calculated and used as distance parameters to assess and refine the previously reported 3D model of the pRNA dimer. Distances between nucleotides in pRNA dimers were found to be different from those of the dimers bound to procapsid, suggesting a conformational change of the pRNA dimer upon binding to the procapsid.
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Affiliation(s)
- Dan Shu
- Nanobiomedical Center, College of Engineering and Applied Science/College of Medicine, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Hui Zhang
- Nanobiomedical Center, College of Engineering and Applied Science/College of Medicine, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | | | - Jarek Meller
- Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Peixuan Guo
- Nanobiomedical Center, College of Engineering and Applied Science/College of Medicine, University of Cincinnati, Cincinnati, Ohio 45221, United States
- Address correspondence to
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