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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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Haque F, Zhang H, Wang S, Chang CL, Savran C, Guo P. Methods for Single-Molecule Sensing and Detection Using Bacteriophage Phi29 DNA Packaging Motor. Methods Mol Biol 2018; 1805:423-450. [PMID: 29971730 DOI: 10.1007/978-1-4939-8556-2_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacteriophage phi29 DNA packaging motor consists of a dodecameric portal channel protein complex termed connector that allows transportation of genomic dsDNA and a hexameric packaging RNA (pRNA) ring to gear the motor. The elegant design of the portal protein has facilitated its applications for real-time single-molecule detection of biopolymers and chemicals with high sensitivity and selectivity. The robust self-assembly property of the pRNA has enabled biophysical studies of the motor complex to determine the stoichiometry and structure/folding of the pRNA at single-molecule level. This chapter focuses on biophysical and analytical methods for studying the phi29 motor components at the single-molecule level, such as single channel conductance assays of membrane-embedded connectors; single molecule photobleaching (SMPB) assay for determining the stoichiometry of phi29 motor components; fluorescence resonance energy transfer (FRET) assay for determining the structure and folding of pRNA; atomic force microscopy (AFM) for imaging pRNA nanoparticles of various size, shape, and stoichiometry; and bright-field microscopy with magnetomechanical system for direct visualization of viral DNA packaging process. The phi29 system with explicit engineering capability has incredible potentials for diverse applications in nanotechnology and nanomedicine including, but not limited to, DNA sequencing, drug delivery to diseased cells, environmental surveillance, and early disease diagnosis.
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Affiliation(s)
- Farzin Haque
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Chun-Li Chang
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.,School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Cagri Savran
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.,School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA. .,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA. .,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA. .,Markey Cancer Center, University of Kentucky, Lexington, KY, USA. .,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA. .,Sylvan G. Frank Endowed Chair in Pharmaceutics and Drug Delivery, The Ohio State University, Columbus, OH, USA.
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Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism. J Virol 2016; 90:8036-46. [PMID: 27356896 DOI: 10.1128/jvi.00508-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
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Hao Y, Kieft JS. Three-way junction conformation dictates self-association of phage packaging RNAs. RNA Biol 2016; 13:635-45. [PMID: 27217219 DOI: 10.1080/15476286.2016.1190075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The packaging RNA (pRNA) found in the phi29 family of bacteriophage is an essential component of a powerful molecular motor used to package the phage's DNA genome into the capsid. The pRNA forms homomultimers mediated by intermolecular "kissing-loop" interactions, thus it is an example of the unusual phenomenon of a self-associating RNA that can form symmetric higher-order multimers. Previous research showed the pRNAs from phi29 family phages have diverse self-association properties and the kissing-loop interaction is not the sole structural element dictating multimerization. We found that a 3-way junction (3wj) within each pRNA, despite not making direct intermolecular contacts, plays important roles in stabilizing the intermolecular interactions and dictating the size of the multimer formed (dimer, trimer, etc.). Specifically, the 3wj in the pRNA from phage M2 appears to favor a different conformation compared to the 3wj in the phi29 pRNA, and the M2 junction facilitates formation of a higher-order multimer that is more thermostable. This behavior provides insights into the fundamental principles of RNA self-association, and additionally may be useful to engineer fine-tuned properties into pRNAs for nanotechnology.
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Affiliation(s)
- Yumeng Hao
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver School of Medicine , Aurora , CO , USA
| | - Jeffrey S Kieft
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver School of Medicine , Aurora , CO , USA
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Shu D, Pi F, Wang C, Zhang P, Guo P. New approach to develop ultra-high inhibitory drug using the power function of the stoichiometry of the targeted nanomachine or biocomplex. Nanomedicine (Lond) 2016; 10:1881-97. [PMID: 26139124 DOI: 10.2217/nnm.15.37] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIMS To find methods for potent drug development by targeting to biocomplex with high copy number. METHODS Phi29 DNA packaging motor components with different stoichiometries were used as model to assay virion assembly with Yang Hui's Triangle [Formula: see text], where Z = stoichiometry, M = drugged subunits per biocomplex, p and q are the fraction of drugged and undrugged subunits in the population. RESULTS Inhibition efficiency follows a power function. When number of drugged subunits to block the function of the complex K = 1, the uninhibited biocomplex equals q(z), demonstrating the multiplicative effect of stoichiometry on inhibition with stoichiometry 1000 > 6 > 1. Complete inhibition of virus replication was found when Z = 6. CONCLUSION Drug inhibition potency depends on the stoichiometry of the targeted components of the biocomplex or nanomachine. The inhibition effect follows a power function of the stoichiometry of the target biocomplex.
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Affiliation(s)
- Dan Shu
- Department of Pharmaceutical Sciences, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Fengmei Pi
- Department of Pharmaceutical Sciences, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Department of Biostatistics & Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA
| | - Peng Zhang
- Department of Surgery, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Peixuan Guo
- Department of Pharmaceutical Sciences, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
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Durand G, Dausse E, Goux E, Fiore E, Peyrin E, Ravelet C, Toulmé JJ. A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers. Nucleic Acids Res 2016; 44:4450-9. [PMID: 27067541 PMCID: PMC4872101 DOI: 10.1093/nar/gkw206] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 01/22/2023] Open
Abstract
Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 106 RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with KDs in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy.
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Affiliation(s)
- Guillaume Durand
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Emma Goux
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Eric Peyrin
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Corinne Ravelet
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
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Bindewald E, Afonin KA, Viard M, Zakrevsky P, Kim T, Shapiro BA. Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches. NANO LETTERS 2016; 16:1726-35. [PMID: 26926528 PMCID: PMC6319913 DOI: 10.1021/acs.nanolett.5b04651] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
RNA is an attractive material for the creation of molecular logic gates that release programmed functionalities only in the presence of specific molecular interaction partners. Here we present HyperFold, a multistrand RNA/DNA structure prediction approach for predicting nucleic acid complexes that can contain pseudoknots. We show that HyperFold also performs competitively compared to other published folding algorithms. We performed a large variety of RNA/DNA hybrid reassociation experiments for different concentrations, DNA toehold lengths, and G+C content and find that the observed tendencies for reassociation correspond well to computational predictions. Importantly, we apply this method to the design and experimental verification of a two-stranded RNA molecular switch that upon binding to a single-stranded RNA toehold disease-marker trigger mRNA changes its conformation releasing an shRNA-like Dicer substrate structure. To demonstrate the concept, connective tissue growth factor (CTGF) mRNA and enhanced green fluorescent protein (eGFP) mRNA were chosen as trigger and target sequences, respectively. In vitro experiments confirm the formation of an RNA switch and demonstrate that the functional unit is being released when the trigger RNA interacts with the switch toehold. The designed RNA switch is shown to be functional in MDA-MB-231 breast cancer cells. Several other switches were also designed and tested. We conclude that this approach has considerable potential because, in principle, it allows the release of an siRNA designed against a gene that differs from the gene that is utilized as a biomarker for a disease state.
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Affiliation(s)
- Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Kirill A. Afonin
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Paul Zakrevsky
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Taejin Kim
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism. Microbiol Mol Biol Rev 2016; 80:161-86. [PMID: 26819321 DOI: 10.1128/mmbr.00056-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1 ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.
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Evadé L, Dausse E, Taouji S, Daguerre E, Chevet E, Toulmé JJ. Aptamer-mediated nanoparticle interactions: from oligonucleotide-protein complexes to SELEX screens. Methods Mol Biol 2016; 1297:153-67. [PMID: 25896002 DOI: 10.1007/978-1-4939-2562-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Aptamers are oligonucleotides displaying specific binding properties for a predetermined target. They can be easily immobilized on various surfaces such as nanoparticles. Functionalized particles can then be used to various aims. We took advantage of the AlphaScreen(®) technology for monitoring aptamer-mediated interactions. A particle bearing an aptamer contains a photosensitizer whereas another type of particle contains a chemiluminescer. Irradiation causes the formation of singlet oxygen species in the photosensitizer-containing bead that in turn activates the chemiluminescer. Luminescence emission can be observed if the two types of beads are in close proximity (<200 nm). This is achieved when the cognate ligand of the aptamer is grafted onto the chemiluminescer-containing bead. Using this technology we have screened oligonucleotide libraries and monitored aptamer-protein interactions. This constitutes the basis for aptamer-based analytical assays.
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Affiliation(s)
- Laetitia Evadé
- Novaptech, European Institute of Chemistry and Biology, Pessac, France
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10
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Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation. Biotechnol Adv 2015; 32:853-72. [PMID: 24913057 DOI: 10.1016/j.biotechadv.2014.01.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 01/24/2014] [Accepted: 01/25/2014] [Indexed: 12/15/2022]
Abstract
Biomotors were once described into two categories: linear motor and rotation motor. Recently, a third type of biomotor with revolution mechanism without rotation has been discovered. By analogy, rotation resembles the Earth rotating on its axis in a complete cycle every 24h, while revolution resembles the Earth revolving around the Sun one circle per 365 days (see animations http://nanobio.uky.edu/movie.html). The action of revolution that enables a motor free of coiling and torque has solved many puzzles and debates that have occurred throughout the history of viral DNA packaging motor studies. It also settles the discrepancies concerning the structure, stoichiometry, and functioning of DNA translocation motors. This review uses bacteriophages Phi29, HK97, SPP1, P22, T4, and T7 as well as bacterial DNA translocase FtsK and SpoIIIE or the large eukaryotic dsDNA viruses such as mimivirus and vaccinia virus as examples to elucidate the puzzles. These motors use ATPase, some of which have been confirmed to be a hexamer, to revolve around the dsDNA sequentially. ATP binding induces conformational change and possibly an entropy alteration in ATPase to a high affinity toward dsDNA; but ATP hydrolysis triggers another entropic and conformational change in ATPase to a low affinity for DNA, by which dsDNA is pushed toward an adjacent ATPase subunit. The rotation and revolution mechanisms can be distinguished by the size of channel: the channels of rotation motors are equal to or smaller than 2 nm, that is the size of dsDNA, whereas channels of revolution motors are larger than 3 nm. Rotation motors use parallel threads to operate with a right-handed channel, while revolution motors use a left-handed channel to drive the right-handed DNA in an anti-chiral arrangement. Coordination of several vector factors in the same direction makes viral DNA-packaging motors unusually powerful and effective. Revolution mechanism that avoids DNA coiling in translocating the lengthy genomic dsDNA helix could be advantageous for cell replication such as bacterial binary fission and cell mitosis without the need for topoisomerase or helicase to consume additional energy.
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11
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De-Donatis GM, Zhao Z, Wang S, Huang LP, Schwartz C, Tsodikov OV, Zhang H, Haque F, Guo P. Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size. Cell Biosci 2014; 4:30. [PMID: 24940480 PMCID: PMC4060578 DOI: 10.1186/2045-3701-4-30] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/16/2014] [Indexed: 12/03/2022] Open
Abstract
Background Double-stranded DNA translocation is ubiquitous in living systems. Cell mitosis, bacterial binary fission, DNA replication or repair, homologous recombination, Holliday junction resolution, viral genome packaging and cell entry all involve biomotor-driven dsDNA translocation. Previously, biomotors have been primarily classified into linear and rotational motors. We recently discovered a third class of dsDNA translocation motors in Phi29 utilizing revolution mechanism without rotation. Analogically, the Earth rotates around its own axis every 24 hours, but revolves around the Sun every 365 days. Results Single-channel DNA translocation conductance assay combined with structure inspections of motor channels on bacteriophages P22, SPP1, HK97, T7, T4, Phi29, and other dsDNA translocation motors such as bacterial FtsK and eukaryotic mimiviruses or vaccinia viruses showed that revolution motor is widespread. The force generation mechanism for revolution motors is elucidated. Revolution motors can be differentiated from rotation motors by their channel size and chirality. Crystal structure inspection revealed that revolution motors commonly exhibit channel diameters larger than 3 nm, while rotation motors that rotate around one of the two separated DNA strands feature a diameter smaller than 2 nm. Phi29 revolution motor translocated double- and tetra-stranded DNA that occupied 32% and 64% of the narrowest channel cross-section, respectively, evidencing that revolution motors exhibit channel diameters significantly wider than the dsDNA. Left-handed oriented channels found in revolution motors drive the right-handed dsDNA via anti-chiral interaction, while right-handed channels observed in rotation motors drive the right-handed dsDNA via parallel threads. Tethering both the motor and the dsDNA distal-end of the revolution motor does not block DNA packaging, indicating that no rotation is required for motors of dsDNA phages, while a small-angle left-handed twist of dsDNA that is aligned with the channel could occur due to the conformational change of the phage motor channels from a left-handed configuration for DNA entry to a right-handed configuration for DNA ejection for host cell infection. Conclusions The revolution motor is widespread among biological systems, and can be distinguished from rotation motors by channel size and chirality. The revolution mechanism renders dsDNA void of coiling and torque during translocation of the lengthy helical chromosome, thus resulting in more efficient motor energy conversion.
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Affiliation(s)
- Gian Marco De-Donatis
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zhengyi Zhao
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Lisa P Huang
- Current address: Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., Hamilton, NJ 08690, USA
| | - Chad Schwartz
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Farzin Haque
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,William Farish Endowed Chair in Nanobiotechnology, School of Pharmacy, University of Kentucky, 565 Biopharmaceutical Complex, 789 S. Limestone Street, Lexington, KY 40536, USA
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12
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Shu Y, Pi F, Sharma A, Rajabi M, Haque F, Shu D, Leggas M, Evers BM, Guo P. Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 2014; 66:74-89. [PMID: 24270010 DOI: 10.1016/j.addr.2013.11.006] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 10/11/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
Abstract
Human genome sequencing revealed that only ~1.5% of the DNA sequence coded for proteins. More and more evidence has uncovered that a substantial part of the 98.5% so-called "junk" DNAs actually code for noncoding RNAs. Two milestones, chemical drugs and protein drugs, have already appeared in the history of drug development, and it is expected that the third milestone in drug development will be RNA drugs or drugs that target RNA. This review focuses on the development of RNA therapeutics for potential cancer treatment by applying RNA nanotechnology. A therapeutic RNA nanoparticle is unique in that its scaffold, ligand, and therapeutic component can all be composed of RNA. The special physicochemical properties lend to the delivery of siRNA, miRNA, ribozymes, or riboswitches; imaging using fluogenenic RNA; and targeting using RNA aptamers. With recent advances in solving the chemical, enzymatic, and thermodynamic stability issues, RNA nanoparticles have been found to be advantageous for in vivo applications due to their uniform nano-scale size, precise stoichiometry, polyvalent nature, low immunogenicity, low toxicity, and target specificity. In vivo animal studies have revealed that RNA nanoparticles can specifically target tumors with favorable pharmacokinetic and pharmacodynamic parameters without unwanted accumulation in normal organs. This review summarizes the key studies that have led to the detailed understanding of RNA nanoparticle formation as well as chemical and thermodynamic stability issue. The methods for RNA nanoparticle construction, and the current challenges in the clinical application of RNA nanotechnology, such as endosome trapping and production costs, are also discussed.
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Affiliation(s)
- Yi Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Fengmei Pi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ashwani Sharma
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Mehdi Rajabi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Farzin Haque
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Dan Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Markos Leggas
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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13
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Zhang H, Guo P. Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation. Methods 2014; 67:169-76. [PMID: 24440482 DOI: 10.1016/j.ymeth.2014.01.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/28/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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14
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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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15
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Guo P, Schwartz C, Haak J, Zhao Z. Discovery of a new motion mechanism of biomotors similar to the earth revolving around the sun without rotation. Virology 2013; 446:133-43. [PMID: 24074575 PMCID: PMC3941703 DOI: 10.1016/j.virol.2013.07.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/27/2013] [Accepted: 07/21/2013] [Indexed: 12/14/2022]
Abstract
Biomotors have been classified into linear and rotational motors. For 35 years, it has been popularly believed that viral dsDNA-packaging apparatuses are pentameric rotation motors. Recently, a third class of hexameric motor has been found in bacteriophage phi29 that utilizes a mechanism of revolution without rotation, friction, coiling, or torque. This review addresses how packaging motors control dsDNA one-way traffic; how four electropositive layers in the channel interact with the electronegative phosphate backbone to generate four steps in translocating one dsDNA helix; how motors resolve the mismatch between 10.5 bases and 12 connector subunits per cycle of revolution; and how ATP regulates sequential action of motor ATPase. Since motors with all number of subunits can utilize the revolution mechanism, this finding helps resolve puzzles and debates concerning the oligomeric nature of packaging motors in many phage systems. This revolution mechanism helps to solve the undesirable dsDNA supercoiling issue involved in rotation.
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Affiliation(s)
- Peixuan Guo
- Nanobiotechnology Center, and Markey Cancer Center, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
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16
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Schwartz C, De Donatis GM, Fang H, Guo P. The ATPase of the phi29 DNA packaging motor is a member of the hexameric AAA+ superfamily. Virology 2013; 443:20-7. [PMID: 23706809 PMCID: PMC3700617 DOI: 10.1016/j.virol.2013.04.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/01/2013] [Accepted: 04/07/2013] [Indexed: 12/21/2022]
Abstract
The AAA+ superfamily of proteins is a class of motor ATPases performing a wide range of functions that typically exist as hexamers. The ATPase of phi29 DNA packaging motor has long been a subject of debate in terms of stoichiometry and mechanism of action. Here, we confirmed the stoichiometry of phi29 motor ATPase to be a hexamer and provide data suggesting that the phi29 motor ATPase is a member of the classical hexameric AAA+ superfamily. Native PAGE, EMSA, capillary electrophoresis, ATP titration, and binomial distribution assay show that the ATPase is a hexamer. Mutations in the known Walker motifs of the ATPase validated our previous assumptions that the protein exists as another member of this AAA+ superfamily. Our data also supports the finding that the phi29 DNA packaging motor uses a revolution mechanism without rotation or coiling (Schwartz et al., this issue).
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Affiliation(s)
| | | | | | - Peixuan Guo
- Nanobiotechnology Center, College of Pharmacy and Markey Cancer Center,
University of Kentucky, Lexington, KY, USA
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17
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Yokota H, Chujo YA, Harada Y. Single-molecule imaging of the oligomer formation of the nonhexameric Escherichia coli UvrD helicase. Biophys J 2013; 104:924-33. [PMID: 23442971 DOI: 10.1016/j.bpj.2013.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/06/2012] [Accepted: 01/08/2013] [Indexed: 11/18/2022] Open
Abstract
Superfamily I helicases are nonhexameric helicases responsible for the unwinding of nucleic acids. However, whether they unwind DNA in the form of monomers or oligomers remains a controversy. In this study, we addressed this question using direct single-molecule fluorescence visualization of Escherichia coli UvrD, a superfamily I DNA helicase. We performed a photobleaching-step analysis of dye-labeled helicases and determined that the helicase is bound to 18-basepair (bp) double-stranded DNA (dsDNA) with a 3' single-stranded DNA (ssDNA) tail (12, 20, or 40 nt) in a dimeric or trimeric form in the absence of ATP. We also discovered through simultaneous visualization of association/dissociation of the helicase with/from DNA and the DNA unwinding dynamics of the helicase in the presence of ATP that these dimeric and trimeric forms are responsible for the unwinding of DNA. We can therefore propose a new kinetic scheme for the helicase-DNA interaction in which not only a dimeric helicase but also a trimeric helicase can unwind DNA. This is, to our knowledge, the first direct single-molecule nonhexameric helicase quantification study, and it strongly supports a model in which an oligomer is the active form of the helicase, which carries important implications for the DNA unwinding mechanism of all superfamily I helicases.
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Affiliation(s)
- Hiroaki Yokota
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Kyoto, Japan.
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18
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Revolution rather than rotation of AAA+ hexameric phi29 nanomotor for viral dsDNA packaging without coiling. Virology 2013; 443:28-39. [PMID: 23763768 PMCID: PMC3850062 DOI: 10.1016/j.virol.2013.04.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/16/2013] [Accepted: 04/20/2013] [Indexed: 01/28/2023]
Abstract
It has long been believed that the DNA-packaging motor of dsDNA viruses
utilizes a rotation mechanism. Here we report a revolution rather than rotation
mechanism for the bacteriophage phi29 DNA packaging motor. The phi29 motor
contains six copies of the ATPase (Schwartz et al., this issue); ATP binding to
one ATPase subunit stimulates the ATPase to adopt a conformation with a high
affinity for dsDNA. ATP hydrolysis induces a new conformation with a lower
affinity, thus transferring the dsDNA to an adjacent subunit by a power stroke.
DNA revolves unidirectionally along the hexameric channel wall of the ATPase,
but neither the dsDNA nor the ATPase itself rotates along its own axis. One ATP
is hydrolyzed in each transitional step, and six ATPs are consumed for one
helical turn of 360°. Transition of the same dsDNA chain along the
channel wall, but at a location 60° different from the last contact,
urges dsDNA to move forward 1.75 base pairs each step (10.5 bp per
turn/6ATP=1.75 bp per ATP). Each connector subunit tilts with a
left-handed orientation at a 30° angle in relation to its vertical axis
that runs anti-parallel to the right-handed dsDNA helix, facilitating the
one-way traffic of dsDNA. The connector channel has been shown to cause four
steps of transition due to four positively charged lysine rings that make direct
contact with the negatively charged DNA phosphate backbone. Translocation of
dsDNA into the procapsid by revolution avoids the difficulties during rotation
that are associated with DNA supercoiling. Since the revolution mechanism can
apply to any stoichiometry, this motor mechanism might reconcile the
stoichiometry discrepancy in many phage systems where the ATPase has been found
as a tetramer, hexamer, or nonamer.
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19
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Zhao Z, Khisamutdinov E, Schwartz C, Guo P. Mechanism of one-way traffic of hexameric phi29 DNA packaging motor with four electropositive relaying layers facilitating antiparallel revolution. ACS NANO 2013; 7:4082-92. [PMID: 23510192 PMCID: PMC3667633 DOI: 10.1021/nn4002775] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/20/2013] [Indexed: 05/21/2023]
Abstract
The importance of nanomotors in nanotechnology is akin to that of mechanical engines to daily life. The AAA+ superfamily is a class of nanomotors performing various functions. Their hexagonal arrangement facilitates bottom-up assembly for stable structures. The bacteriophage phi29 DNA translocation motor contains three coaxial rings: a dodecamer channel, a hexameric ATPase ring, and a hexameric pRNA ring. The viral DNA packaging motor has been believed to be a rotational machine. However, we discovered a revolution mechanism without rotation. By analogy, the earth revolves around the sun while rotating on its own axis. One-way traffic of dsDNA translocation is facilitated by five factors: (1) ATPase changes its conformation to revolve dsDNA within a hexameric channel in one direction; (2) the 30° tilt of the channel subunits causes an antiparallel arrangement between two helices of dsDNA and channel wall to advance one-way translocation; (3) unidirectional flow property of the internal channel loops serves as a ratchet valve to prevent reversal; (4) 5'-3' single-direction movement of one DNA strand along the channel wall ensures single direction; and (5) four electropositive layers interact with one strand of the electronegative dsDNA phosphate backbone, resulting in four relaying transitional pauses during translocation. The discovery of a riding system along one strand provides a motion nanosystem for cargo transportation and a tool for studying force generation without coiling, friction, and torque. The revolution of dsDNA among 12 subunits offers a series of recognition sites on the DNA backbone to provide additional spatial variables for nucleotide discrimination for sensing applications.
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Ultrastable pRNA hexameric ring gearing hexameric phi29 DNA-packaging motor by revolving without rotating and coiling. Curr Opin Biotechnol 2013; 24:581-90. [PMID: 23683853 DOI: 10.1016/j.copbio.2013.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/11/2013] [Accepted: 03/21/2013] [Indexed: 11/20/2022]
Abstract
Biomotors have previously been classified into two categories: linear and rotational motors. It has long been popularly believed that viral DNA packaging motors are rotation motors. We have recently found that the DNA-packaging motor of bacteriophage phi29 uses a third mechanism: revolution without rotation. phi29 motor consists of three-coaxial rings of hexameric RNA, a hexameric ATPase, and a dodecameric channel. The motor uses six ATP to revolve one helical turn of dsDNA around the hexameric ring of ATPase gp16. Each dodecameric segment tilts at a 30°-angle and runs anti-parallel to the dsDNA helix to facilitate translation in one direction. The negatively charged phosphate backbone interacts with four positively charged lysine rings, resulting in four steps of transition. This review will discuss how the novel pRNA meets motor requirements for translocation concerning structure, stoichiometry, and thermostability; how pRNA studies have led to the generation of the concept of RNA nanotechnology; and how pRNA is fabricated into nanoparticles to deliver siRNA, miRNA, and ribozymes to cancer and virus-infected cells.
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21
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Incorporation of a viral DNA-packaging motor channel in lipid bilayers for real-time, single-molecule sensing of chemicals and double-stranded DNA. Nat Protoc 2013; 8:373-92. [PMID: 23348364 DOI: 10.1038/nprot.2013.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Over the past decade, nanopores have rapidly emerged as stochastic biosensors. This protocol describes the cloning, expression and purification of the channel of the bacteriophage phi29 DNA-packaging nanomotor and its subsequent incorporation into lipid membranes for single-pore sensing of double-stranded DNA (dsDNA) and chemicals. The membrane-embedded phi29 nanochannel remains functional and structurally intact under a range of conditions. When ions and macromolecules translocate through this nanochannel, reliable fingerprint changes in conductance are observed. Compared with other well-studied biological pores, the phi29 nanochannel has a larger cross-sectional area, which enables the translocation of dsDNA. Furthermore, specific amino acids can be introduced by site-directed mutagenesis within the large cavity of the channel to conjugate receptors that are able to bind specific ligands or analytes for desired applications. The lipid membrane-embedded nanochannel system has immense potential nanotechnological and biomedical applications in bioreactors, environmental sensing, drug monitoring, controlled drug delivery, early disease diagnosis and high-throughput DNA sequencing. The total time required for completing one round of this protocol is around 1 month.
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Zhang H, Schwartz C, De Donatis GM, Guo P. "Push through one-way valve" mechanism of viral DNA packaging. Adv Virus Res 2012; 83:415-65. [PMID: 22748815 DOI: 10.1016/b978-0-12-394438-2.00009-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Double-stranded (ds)DNA viruses package their genomic DNA into a procapsid using a force-generating nanomotor powered by ATP hydrolysis. Viral DNA packaging motors are mainly composed of the connector channel and two DNA packaging enzymes. In 1998, it was proposed that viral DNA packaging motors exercise a mechanism similar to the action of AAA+ ATPases that assemble into ring-shaped oligomers, often hexamers, with a central channel (Guo et al. Molecular Cell, 2:149). This chapter focuses on the most recent findings in the bacteriophage ϕ29 DNA packaging nanomotor to address this intriguing notion. Almost all dsDNA viruses are composed entirely of protein, but in the unique case of ϕ29, packaging RNA (pRNA) plays an intermediate role in the packaging process. Evidence revealed that DNA packaging is accomplished via a "push through one-way valve" mechanism. The ATPase gp16 pushes dsDNA through the connector channel section by section into the procapsid. The dodecameric connector channel functions as a one-way valve that only allows dsDNA to enter but not exit the procapsid during DNA packaging. Although the roles of the ATPase gp16 and the motor connector channel are separate and independent, pRNA bridges these two components to ensure the coordination of an integrated motor. ATP induces a conformational change in gp16, leading to its stronger binding to dsDNA. Furthermore, ATP hydrolysis led to the departure of dsDNA from the ATPase/dsDNA complex, an action used to push dsDNA through the connector channel. It was found unexpectedly that by mutating the basic lysine rings of the connector channel or by changing the pH did not measurably impair DNA translocation or affect the one-way traffic property of the channel, suggesting that the positive charges in the lysine ring are not essential in gearing the dsDNA. The motor channel exercises three discrete, reversible, and controllable steps of gating, with each step altering the channel size by 31% to control the direction of translocation of dsDNA. Many DNA packaging models have been contingent upon the number of base pairs packaged per ATP relative to helical turns for B-type DNA. Both 2 and 2.5 bp per ATP have been used to argue for four, five, or six discrete steps of DNA translocation. The "push through one-way valve" mechanism renews the perception of dsDNA packaging energy calculations and provides insight into the discrepancy between 2 and 2.5 bp per ATP. Application of the DNA packaging motor in nanotechnology and nanomedicine is also addressed. Comparison with nine other DNA packaging models revealed that the "push through one-way valve" is the most agreeable mechanism to interpret most of the findings that led to historical models. The application of viral DNA packaging motors is also discussed.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY, USA
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23
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Haque F, Shu D, Shu Y, Shlyakhtenko LS, Rychahou PG, Evers BM, Guo P. Ultrastable synergistic tetravalent RNA nanoparticles for targeting to cancers. NANO TODAY 2012; 7:245-257. [PMID: 23024702 PMCID: PMC3458310 DOI: 10.1016/j.nantod.2012.06.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One of the advantages of nanotechnology is the feasibility to construct therapeutic particles carrying multiple therapeutics with defined structure and stoichiometry. The field of RNA nanotechnology is emerging. However, controlled assembly of stable RNA nanoparticles with multiple functionalities which retain their original role is challenging due to refolding after fusion. Herein, we report the construction of thermodynamically stable X-shaped RNA nanoparticles to carry four therapeutic RNA motifs by self-assembly of reengineered small RNA fragments. We proved that each arm of the four helices in the X-motif can harbor one siRNA, ribozyme, or aptamer without affecting the folding of the central pRNA-X core, and each daughter RNA molecule within the nanoparticle folds into their respective authentic structures and retains their biological and structural function independently. Gene silencing effects were progressively enhanced as the number of the siRNA in each pRNA-X nanoparticles gradually increased from one to two, three, and four. More importantly, systemic injection of ligand-containing nanoparticles into the tail-vein of mice revealed that the RNA nanoparticles remained intact and strongly bound to cancers without entering the liver, lung or any other organs or tissues, while remaining in cancer tissue for more than 8 h.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Dan Shu
- Nanobiotechnology Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Yi Shu
- Nanobiotechnology Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Piotr G. Rychahou
- Markey Cancer Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - B. Mark Evers
- Markey Cancer Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Peixuan Guo
- Nanobiotechnology Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
- Markey Cancer Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
- Corresponding author at: Department of Pharmaceutical Sciences, 789 S. Limestone Avenue, Room # 565, Lexington, KY 40536-0596, United States. Tel.: +1 859 218 0128; fax: +1 859 257 1307. , (P. Guo)
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Lease RA, Arluison V, Lavelle C. Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly in vivo.. FRONTIERS IN LIFE SCIENCE 2012; 6:19-32. [PMID: 23914307 PMCID: PMC3725660 DOI: 10.1080/21553769.2012.761163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/18/2012] [Indexed: 11/23/2022]
Abstract
The primacy and power of RNA in governing many processes of life has begun to be more fully appreciated in both the discovery and inventive sciences. A variety of RNA interactions regulate gene expression, and structural self-assembly underlies many of these processes. The understanding sparked by these discoveries has inspired and informed the engineering of novel RNA structures, control elements, and genetic circuits in cells. Many of these engineered systems are built up fundamentally from RNA–RNA interactions, often combining modular, rational design with functional selection and screening. It is therefore useful to review the particular class of RNA-based regulatory mechanisms that rely on RNA self-assembly either through homomeric (self–self) or heteromeric (self–nonself) RNA–RNA interactions. Structures and sequence elements within individual RNAs create a basis for the pairing interactions, and in some instances can even lead to the formation of RNA polymers. Example systems of dimers, multimers, and polymers are reviewed in this article in the context of natural systems, wherein the function and impact of self-assemblies are understood. Following this, a brief overview is presented of specific engineered RNA self-assembly systems implemented in vivo, with lessons learned from both discovery and engineering approaches to RNA–RNA self-assembly.
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Affiliation(s)
- Richard A Lease
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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25
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Ye X, Hemida M, Zhang HM, Hanson P, Ye Q, Yang D. Current advances in Phi29 pRNA biology and its application in drug delivery. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:469-81. [PMID: 22362726 DOI: 10.1002/wrna.1111] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Bacteriophage 29 (Phi29) packaging RNA (pRNA) is one of the key components in the viral DNA-packaging motor. It contains two functional domains facilitating the translocation of DNA into the viral capsid by interacting with other elements in the motor and promoting adenosine triphosphates hydrolysis. Through the connection between interlocking loops in adjacent pRNA monomers, pRNA functions in the form of multimer ring in the motor. Previous studies have addressed the unique structure and conformation of pRNA. However, there are different DNA-packaging models proposed for the viral genome transportation mechanism. The DNA-packaging ability and the unique features of pRNA have been attracting efforts to study its potential applications in nanotechnology. The pRNA has been proved to be a promising tool for delivering nucleic acid-based therapeutic molecules by covalent linkage with ribozymes, small interfering RNAs, aptamers, and artificial microRNAs. The flexibility in constructing dimers, trimers, and hexamers enables the assembly of polyvalent nanoparticles to carry drug molecules for therapeutic purposes, cell ligands for target delivery, image detector for drug entry monitoring, and endosome disrupter for drug release. Besides these fascinating pharmacological advantages, pRNA-based drug delivery has also been demonstrated to prolong the drug half life with minimal induction of immune response and toxicity.
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Affiliation(s)
- Xin Ye
- The Institute for Heart and Lung Health, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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26
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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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27
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Schwartz C, Fang H, Huang L, Guo P. Sequential action of ATPase, ATP, ADP, Pi and dsDNA in procapsid-free system to enlighten mechanism in viral dsDNA packaging. Nucleic Acids Res 2011; 40:2577-86. [PMID: 22110031 PMCID: PMC3315319 DOI: 10.1093/nar/gkr841] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Many cells and double-stranded DNA (dsDNA) viruses contain an AAA(+) ATPase that assembles into oligomers, often hexamers, with a central channel. The dsDNA packaging motor of bacteriophage phi29 also contains an ATPase to translocate dsDNA through a dodecameric channel. The motor ATPase has been investigated substantially in the context of the entire procapsid. Here, we report the sequential action between the ATPase and additional motor components. It is suggested that the contact of ATPase to ATP resulted in its conformational change to a higher binding affinity toward dsDNA. It was found that ATP hydrolysis led to the departure of dsDNA from the ATPase/dsDNA complex, an action that is speculated to push dsDNA to pass the connector channel. Our results suggest that dsDNA packaging goes through a combined effort of both the gp16 ATPase for pushing and the channel as a one-way valve to control the dsDNA translocation direction. Many packaging models have previously been proposed, and the packaging mechanism has been contingent upon the number of nucleotides packaged per ATP relative to the 10.5 bp per helical turn for B-type dsDNA. Both 2 and 2.5 bp per ATP have been used to argue for four, five or six discrete steps of dsDNA translocation. Combination of the two distinct roles of gp16 and connector renews the perception of previous dsDNA packaging energy calculations and provides insight into the discrepancy between 2 and 2.5 bp per ATP.
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Affiliation(s)
- Chad Schwartz
- The School of Environmental, Energy, Biological, and Medical Engineering (SEEBME), Nanobiomedical Center, University of Cincinnati, Cincinnati, OH 45267, USA
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28
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Geng J, Fang H, Haque F, Zhang L, Guo P. Three reversible and controllable discrete steps of channel gating of a viral DNA packaging motor. Biomaterials 2011; 32:8234-42. [PMID: 21807410 DOI: 10.1016/j.biomaterials.2011.07.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/11/2011] [Indexed: 01/06/2023]
Abstract
The channel of the viral DNA packaging motor allows dsDNA to enter the protein procapsid shell during maturation and to exit during infection. We recently showed that the bacteriophage phi29 DNA packaging motor exercises a one-way traffic property using a channel as a valve for dsDNA translocation. This raises a question of how dsDNA is ejected during infection if the channel only allows the dsDNA to travel inward. We proposed that DNA forward or reverse travel is controlled by conformational changes of the channel. Here we reported our direct observation that the channel indeed exercises conformational changes by single channel recording at a single-molecule level. The changes were induced by high electrical voltage, or by affinity binding to the C-terminal wider end located within the capsid. Novel enough, the conformational change of the purified connector channel exhibited three discrete gating steps, with a size reduction of 32% for each step. We investigated the role of the terminal and internal loop of the channel in gating by different mutants. The step-wise conformational change of the channel was also reversible and controllable, making it an ideal nano-valve for constructing a nanomachine with potential applications in nanobiotechnology and nanomedicine.
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Affiliation(s)
- Jia Geng
- Nanobiomedical Center, SEEBME, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45267, USA
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29
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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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Abdelmawla S, Guo S, Zhang L, Pulukuri SM, Patankar P, Conley P, Trebley J, Guo P, Li QX. Pharmacological characterization of chemically synthesized monomeric phi29 pRNA nanoparticles for systemic delivery. Mol Ther 2011; 19:1312-22. [PMID: 21468004 DOI: 10.1038/mt.2011.35] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Previous studies have shown that the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor folds into a compact structure, constituting a RNA nanoparticle that can be modularized with functional groups as a nanodelivery system. pRNA nanoparticles can also be self-assembled by the bipartite approach without altering folding property. The present study demonstrated that 2'-F-modified pRNA nanoparticles were readily manufactured through this scalable bipartite strategy, featuring total chemical synthesis and permitting diverse functional modularizations. The RNA nanoparticles were chemically and metabolically stable and demonstrated a favorable pharmacokinetic (PK) profile in mice (half-life (T(1/2)): 5-10 hours, clearance (Cl): <0.13 l/kg/hour, volume of distribution (V(d)): 1.2 l/kg). It did not induce an interferon (IFN) response nor did it induce cytokine production in mice. Repeat intravenous administrations in mice up to 30 mg/kg did not result in any toxicity. Fluorescent folate-pRNA nanoparticles efficiently and specifically bound and internalized to folate receptor (FR)-bearing cancer cells in vitro. It also specifically and dose-dependently targeted to FR(+) xenograft tumor in mice with minimal accumulation in normal tissues. This first comprehensive pharmacological study suggests that the pRNA nanoparticle had all the preferred pharmacological features to serve as an efficient nanodelivery platform for broad medical applications.
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31
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Gu X, Schroeder SJ. Different sequences show similar quaternary interaction stabilities in prohead viral RNA self-assembly. J Biol Chem 2011; 286:14419-26. [PMID: 21349846 DOI: 10.1074/jbc.m110.191064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prohead RNA (pRNA) is an essential component of the self-assembling ϕ29 bacteriophage DNA packaging motor. Different related species of bacteriophage share only 12% similarity in pRNA sequences. The secondary structure for pRNA is conserved, however. In this study, we present evidence for self-assembly in different pRNA sequences and new measurements of the energetics for the quaternary interactions in pRNA dimers and trimers. The energetics for self-assembly in different pRNA sequences are similar despite very different sequences in the loop-loop interactions. The architecture surrounding the interlocking loops contributes to the stability of the pRNA quaternary interactions, and sequence variation outside the interlocking loops may counterbalance the changes in the loop sequences. Thus, the evolutionary divergence of pRNA sequences maintains not only conservation of function and secondary structure but also stabilities of quaternary interactions. The self-assembly of pRNA can be fine-tuned with variations in magnesium chloride, sodium chloride, temperature, and concentration. The ability to control pRNA self-assembly holds promise for the development of nanoparticle therapeutic applications for this biological molecule. The pRNA system is well suited for future studies to further understand the energetics of RNA tertiary and quaternary interactions, which can provide insight into larger biological assemblies such as viruses and biomolecular motors.
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Affiliation(s)
- Xiaobo Gu
- Department of Chemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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32
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Shu Y, Cinier M, Shu D, Guo P. Assembly of multifunctional phi29 pRNA nanoparticles for specific delivery of siRNA and other therapeutics to targeted cells. Methods 2011; 54:204-14. [PMID: 21320601 DOI: 10.1016/j.ymeth.2011.01.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/06/2011] [Accepted: 01/20/2011] [Indexed: 01/31/2023] Open
Abstract
Recent advances in RNA nanotechnology have led to the emergence of a new field and brought vitality to the area of therapeutics [P. Guo, The emerging field of RNA nanotechnology, Nat. Nanotechnol., 2010]. Due to the complementary nature of the four nucleotides and its special catalytic activity, RNA can be manipulated with simplicity characteristic of DNA, while possessing versatile structure and diverse function similar to proteins. Loops and tertiary architecture serve as mounting dovetails or wedges to eliminate external linking dowels. Unique features in transcription, termination, self-assembly, self-processing, and acid-resistance enable in vivo production of nanoparticles harboring aptamer, siRNA, ribozyme, riboswitch, or other regulators for therapy, detection, regulation, and intracellular computation. The unique property of noncanonical base-pairing and stacking enables RNA to fold into well-defined structures for constructing nanoparticles with special functionalities. Bacteriophage phi29 DNA packaging motor is geared by a ring consisting of six packaging RNA (pRNA) molecules. pRNA is able to form a multimeric complex via the interaction of two reengineered interlocking loops. This unique feature makes it an ideal polyvalent vehicle for nanomachine fabrication, pathogen detection, and delivery of siRNA or other therapeutics. This review describes methods in using pRNA as a building block for the construction of RNA dimers, trimers, and hexamers as nanoparticles in medical applications. Methods for industrial-scale production of large and stable RNA nanoparticles will be introduced. The unique favorable PK (pharmacokinetics) profile with a half life (T(1/2)) of 5-10h comparing to 0.25 of conventional 2'-F siRNA, and advantageous in vivo features such as non-toxicity, non-induction of interferons or non-stimulating of cytokine response in animals will also be reviewed.
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Affiliation(s)
- Yi Shu
- Nanobiomedical Center, University of Cincinnati, Cincinnati, OH 45267, USA
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33
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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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34
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Jing P, Haque F, Shu D, Montemagno C, Guo P. One-way traffic of a viral motor channel for double-stranded DNA translocation. NANO LETTERS 2010; 10:3620-7. [PMID: 20722407 PMCID: PMC2935672 DOI: 10.1021/nl101939e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/23/2010] [Indexed: 05/20/2023]
Abstract
Linear double-stranded DNA (dsDNA) viruses package their genome into a procapsid using an ATP-driven nanomotor. Here we report that bacteriophage phi29 DNA packaging motor exercises a one-way traffic property for dsDNA translocation from N-terminal entrance to C-terminal exit with a valve mechanism in DNA packaging, as demonstrated by voltage ramping, electrode polarity switching, and sedimentation force assessment. Without the use of gating control as found in other biological channels, the observed single direction dsDNA transportation provides a novel system with a natural valve to control dsDNA loading and gene delivery in bioreactors, liposomes, or high throughput DNA sequencing apparatus.
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Affiliation(s)
| | | | | | | | - Peixuan Guo
- Address correspondence to: Peixuan Guo Vontz Center for Molecular Studies, ML#0508, 3125 Eden Avenue, Room 2308, University of Cincinnati Cincinnati, OH 45267. Phone: (513)558-0041. Fax: (513)558-0024. E-mail: ,
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35
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Xiao F, Demeler B, Guo P. Assembly mechanism of the sixty-subunit nanoparticles via interaction of RNA with the reengineered protein connector of phi29 DNA-packaging motor. ACS NANO 2010; 4:3293-301. [PMID: 20509670 PMCID: PMC2889630 DOI: 10.1021/nn100158k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 05/19/2010] [Indexed: 05/19/2023]
Abstract
Bacterial virus phi29 genomic DNA is packaged into a procapsid shell with the aid of a motor containing a 12-subunit connector channel and a hexameric pRNA (packaging RNA) ring. The wide end, or the C-terminus, of the cone-shaped connector is embedded within the procapsid shell, whereas the narrow end, or N-terminus, extends outside of the procapsid, providing a binding location for pRNA. Recently, we have reported the mechanism of in vivo assembly of an ellipsoid nanoparticle with seven connectors through an interaction among a peptide tag. Here we report the formation of a similar nanoparticle in vitro via the addition of DNA or RNA oligos to connector proteins. Free connectors guided by one or two copies of oligonucleotides were assembled into a rosette structure containing 60 subunits of reengineered proteins. The number of oligonucleotides within the particle is length-dependent but sequence-independent. Reversible shifting between the 12- and 60-subunit nanoparticles (between individual connectors and rosette structures, respectively) was demonstrated by the alternative addition of oligonucleotides and the treatment of ribonuclease, suggesting a potential application as a switch or regulator in nanobiotechnology. This advancement allows for a simple method to produce multivalent nanoparticles that contain five 12-unit nanoparticles with defined structure and stoichiometry. That is, it will be possible to assemble nanoparticles in vitro with the combination of 60 assortments of ligands, tags, therapeutic drugs, and diagnostic moieties for multivalent delivery or enhancement of signal detection in nanotechnological and nanomedicinal applications.
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Affiliation(s)
- Feng Xiao
- Department of Biomedical Engineering, College of Engineering/College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229
| | - Peixuan Guo
- Department of Biomedical Engineering, College of Engineering/College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267
- Address correspondence to
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36
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Zhang H, Shu D, Wang W, Guo P. Design and application of single fluorophore dual-view imaging system containing both the objective- and prism-type TIRF. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2010; 7571:757107-757108. [PMID: 20436791 DOI: 10.1117/12.847457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Simultaneous detection of two fluorescent markers is important in determination of distance, relative motion and conformational change of nanoparticles or nanodevices. We constructed an imaging system which combines deep-cooled sensitive EMCCD camera with both the objective- and prism-type TIRF. A laser combiner was introduced to facilitate laser controls for simultaneous dual-channel imaging by deliver lasers with different wavelength synchronically via an optic fiber to the sample. The system produces stable signal with extremely low background fluorescence for single-fluorophore detection. It has been applied to study the structure, stoichiometry, and function of the phi29 DNA packaging motor. Single-molecule photobleaching combined with binomial distribution analysis clarified the stoichiometry of pRNA on the motor and elucidated the mechanism of pRNA hexamer assembly. The feasibility of single-molecule FRET with this system was demonstrated. Distance rulers of dual-labeled molecule standards were used to evaluate the system. We have also re-engineered the energy conversion protein, gp16, of phi29 motor for single fluorophore labeling to facilitate the single-molecule studies of motor mechanism. The potential applications of single-molecule high-resolution imaging with photobleaching (SHRImP) and single molecule high resolution with co-localization (SHREC) approaches to the study of the phi29 nanomotor are under investigation.
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Affiliation(s)
- Hui Zhang
- Department of Biomedical Engineering, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA
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37
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Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy. Ann Biomed Eng 2009; 37:2064-81. [PMID: 19495981 DOI: 10.1007/s10439-009-9723-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 05/20/2009] [Indexed: 01/16/2023]
Abstract
Nanobiotechnology involves the creation, characterization, and modification of organized nanomaterials to serve as building blocks for constructing nanoscale devices in technology and medicine. Living systems contain a wide variety of nanomachines and highly ordered structures of macromolecules. The novelty and ingenious design of the bacterial virus phi29 DNA packaging motor and its parts inspired the synthesis of this motor and its components as biomimetics. This 30-nm nanomotor uses six copies of an ATP-binding pRNA to gear the motor. The structural versatility of pRNA has been utilized to construct dimers, trimers, hexamers, and patterned superstructures via the interaction of two interlocking loops. The approach, based on bottom-up assembly, has also been applied to nanomachine fabrication, pathogen detection and the delivery of drugs, siRNA, ribozymes, and genes to specific cells in vitro and in vivo. Another essential component of the motor is the connector, which contains 12 copies of a protein gp10 to form a 3.6-nm central channel as a path for DNA. This article will review current studies of the structure and function of the phi29 DNA packaging motor, as well as the mechanism of motion, the principle of in vitro construction, and its potential nanotechnological and medical applications.
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38
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Zhang H, Shu D, Browne M, Guo P. Approaches for stoichiometry and distance determination of nanometer bio-complex by dual-channel single molecule imaging. IEEE/NIH LIFE SCIENCE SYSTEMS AND APPLICATIONS WORKSHOP. IEEE/NIH LIFE SCIENCE SYSTEMS AND APPLICATIONS WORKSHOP 2009; 2009:124-127. [PMID: 20485472 DOI: 10.1109/lissa.2009.4906725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A dual-channel imaging system with single fluorophore sensitivity was assembled in this lab. Inclusion of an integrated laser combiner was introduced to facilitate simultaneous dual-channel imaging. The imaging system has been applied to study the structure, stoichiometry, distance and function of the phi29 DNA packaging motor. Approaches including single molecule photobleaching, single molecule FRET and binomial distribution quantification were carried out to clarify the stoichiometry and distance of pRNA on the biologically active packaging motor. The results were statistically analyzed to access the copy number of pRNA, and the distance constraint was used to verify the 3D structure of the computer model of phi29 DNA packaging motor.
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Affiliation(s)
- Hui Zhang
- Department of Biomedical Engineering, College of Medicine/College of Engineering, University of Cincinnati, 3125 Eden Ave., Cincinnati, OH, 45267, USA
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39
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Xiao F, Sun J, Coban O, Schoen P, Wang JCY, Cheng RH, Guo P. Fabrication of massive sheets of single layer patterned arrays using lipid directed reengineered phi29 motor dodecamer. ACS NANO 2009; 3:100-107. [PMID: 19206255 PMCID: PMC2651733 DOI: 10.1021/nn800409a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2008] [Accepted: 11/24/2008] [Indexed: 05/27/2023]
Abstract
The bottom-up assembly of patterned arrays is an exciting and important area in current nanotechnology. Arrays can be engineered to serve as components in chips for a virtually inexhaustible list of applications ranging from disease diagnosis to ultra-high-density data storage. Phi29 motor dodecamer has been reported to form elegant multilayer tetragonal arrays. However, multilayer protein arrays are of limited use for nanotechnological applications which demand nanoreplica or coating technologies. The ability to produce a single layer array of biological structures with high replication fidelity represents a significant advance in the area of nanomimetics. In this paper, we report on the assembly of single layer sheets of reengineered phi29 motor dodecamer. A thin lipid monolayer was used to direct the assembly of massive sheets of single layer patterned arrays of the reengineered motor dodecamer. Uniform, clean and highly ordered arrays were constructed as shown by both transmission electron microscopy and atomic force microscopy imaging.
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Affiliation(s)
- Feng Xiao
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio 45221
| | - Jinchuan Sun
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Oana Coban
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio 45221
| | - Peter Schoen
- Department of Scanning Probe Microscopy and Biophysical Chemistry, Radboud University, Nijmegen, The Netherlands
| | - Joseph Che-Yen Wang
- Department of Molecular & Cellular Biology, University of California, Davis, California 95616
| | - R. Holland Cheng
- Department of Molecular & Cellular Biology, University of California, Davis, California 95616
| | - Peixuan Guo
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio 45221
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