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Cryo-EM Structures of Two Bacteriophage Portal Proteins Provide Insights for Antimicrobial Phage Engineering. Viruses 2021; 13:v13122532. [PMID: 34960800 PMCID: PMC8703570 DOI: 10.3390/v13122532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Widespread antibiotic resistance has returned attention to bacteriophages as a means of managing bacterial pathogenesis. Synthetic biology approaches to engineer phages have demonstrated genomic editing to broaden natural host ranges, or to optimise microbicidal action. Gram positive pathogens cause serious pastoral animal and human infections that are especially lethal in newborns. Such pathogens are targeted by the obligate lytic phages of the Salasmaviridae and Guelinviridae families. These phages have relatively small ~20 kb linear protein-capped genomes and their compact organisation, relatively few structural elements, and broad host range, are appealing from a phage-engineering standpoint. In this study, we focus on portal proteins, which are core elements for the assembly of such tailed phages. The structures of dodecameric portal complexes from Salasmaviridae phage GA1, which targets Bacillus pumilus, and Guelinviridae phage phiCPV4 that infects Clostridium perfringens, were determined at resolutions of 3.3 Å and 2.9 Å, respectively. Both are found to closely resemble the related phi29 portal protein fold. However, the portal protein of phiCPV4 exhibits interesting differences in the clip domain. These structures provide new insights on structural diversity in Caudovirales portal proteins and will be essential for considerations in phage structural engineering.
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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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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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Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P. RNA nanotechnology for computer design and in vivo computation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120310. [PMID: 24000362 PMCID: PMC3758167 DOI: 10.1098/rsta.2012.0310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.
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Affiliation(s)
- Meikang Qiu
- Department of Computer Engineering, San Jose State University, San Jose, CA 95192, USA
| | - Emil Khisamutdinov
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Zhengyi Zhao
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Cheryl Pan
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742, Korea
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Peixuan Guo
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
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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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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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Shu Y, Haque F, Shu D, Li W, Zhu Z, Kotb M, Lyubchenko Y, Guo P. Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs. RNA (NEW YORK, N.Y.) 2013; 19:767-77. [PMID: 23604636 PMCID: PMC3683911 DOI: 10.1261/rna.037002.112] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/05/2013] [Indexed: 05/19/2023]
Abstract
Due to structural flexibility, RNase sensitivity, and serum instability, RNA nanoparticles with concrete shapes for in vivo application remain challenging to construct. Here we report the construction of 14 RNA nanoparticles with solid shapes for targeting cancers specifically. These RNA nanoparticles were resistant to RNase degradation, stable in serum for >36 h, and stable in vivo after systemic injection. By applying RNA nanotechnology and exemplifying with these 14 RNA nanoparticles, we have established the technology and developed "toolkits" utilizing a variety of principles to construct RNA architectures with diverse shapes and angles. The structure elements of phi29 motor pRNA were utilized for fabrication of dimers, twins, trimers, triplets, tetramers, quadruplets, pentamers, hexamers, heptamers, and other higher-order oligomers, as well as branched diverse architectures via hand-in-hand, foot-to-foot, and arm-on-arm interactions. These novel RNA nanostructures harbor resourceful functionalities for numerous applications in nanotechnology and medicine. It was found that all incorporated functional modules, such as siRNA, ribozymes, aptamers, and other functionalities, folded correctly and functioned independently within the nanoparticles. The incorporation of all functionalities was achieved prior, but not subsequent, to the assembly of the RNA nanoparticles, thus ensuring the production of homogeneous therapeutic nanoparticles. More importantly, upon systemic injection, these RNA nanoparticles targeted cancer exclusively in vivo without accumulation in normal organs and tissues. These findings open a new territory for cancer targeting and treatment. The versatility and diversity in structure and function derived from one biological RNA molecule implies immense potential concealed within the RNA nanotechnology field.
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Affiliation(s)
- Yi Shu
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Dan Shu
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Wei Li
- Nanobiotechnology Center, SEEBME, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Zhenqi Zhu
- Department of Molecular Genetics, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Malak Kotb
- Department of Molecular Genetics, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, 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, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
- Corresponding authorE-mail
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8
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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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Geng J, Wang S, Fang H, Guo P. Channel size conversion of Phi29 DNA-packaging nanomotor for discrimination of single- and double-stranded nucleic acids. ACS NANO 2013; 7:3315-23. [PMID: 23488809 PMCID: PMC3663147 DOI: 10.1021/nn400020z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanopores have been utilized to detect the conformation and dynamics of polymers, including DNA and RNA. Biological pores are extremely reproducible at the atomic level with uniform channel sizes. The channel of the bacterial virus phi29 DNA-packaging motor is a natural conduit for the transportation of double-stranded DNA (dsDNA) and has the largest diameter among the well-studied biological channels. The larger channel facilitates translocation of dsDNA and offers more space for further channel modification and conjugation. Interestingly, the relatively large wild-type channel, which translocates dsDNA, cannot detect single-stranded nucleic acids (ssDNA or ssRNA) under the current experimental conditions. Herein, we reengineered this motor channel by removing the internal loop segment of the channel. The modification resulted in two classes of channels. One class was the same size as the wild-type channel, while the other class had a cross-sectional area about 60% of the wild-type. This smaller channel was able to detect the real-time translocation of single-stranded nucleic acids at single-molecule level. While the wild-type connector exhibited a one-way traffic property with respect to dsDNA translocation, the loop-deleted connector was able to translocate ssDNA and ssRNA with equal competencies from both termini. This finding of size alterations in reengineered motor channels expands the potential application of the phi29 DNA-packaging motor in nanomedicine, nanobiotechnology, and high-throughput single-pore DNA sequencing.
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Affiliation(s)
- Jia Geng
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
| | - Huaming Fang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
- Address correspondence to: Peixuan Guo, University of Kentucky, Department of Pharmaceutical Sciences, 789 S. Limestone Avenue, Room # 565, Lexington, KY, USA 40536-0596, , Phone:859-218-0128, Fax:859-257-1307
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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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Haque F, Lunn J, Fang H, Smithrud D, Guo P. Real-time sensing and discrimination of single chemicals using the channel of phi29 DNA packaging nanomotor. ACS NANO 2012; 6:3251-3261. [PMID: 22458779 PMCID: PMC3337346 DOI: 10.1021/nn3001615] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A highly sensitive and reliable method to sense and identify a single chemical at extremely low concentrations and high contamination is important for environmental surveillance, homeland security, athlete drug monitoring, toxin/drug screening, and earlier disease diagnosis. This article reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of 12 protein subunits encircled into a 3.6 nm channel as a path for dsDNA to enter during packaging and to exit during infection. The connector has previously been inserted into a lipid bilayer to serve as a membrane-embedded channel. Herein we report the modification of the phi29 channel to develop a class of sensors to detect single chemicals. The lysine-234 of each protein subunit was mutated to cysteine, generating 12-SH ring lining the channel wall. Chemicals passing through this robust channel and interactions with the SH group generated extremely reliable, precise, and sensitive current signatures as revealed by single channel conductance assays. Ethane (57 Da), thymine (167 Da), and benzene (105 Da) with reactive thioester moieties were clearly discriminated upon interaction with the available set of cysteine residues. The covalent attachment of each analyte induced discrete stepwise blockage in current signature with a corresponding decrease in conductance due to the physical blocking of the channel. Transient binding of the chemicals also produced characteristic fingerprints that were deduced from the unique blockage amplitude and pattern of the signals. This study shows that the phi29 connector can be used to sense chemicals with reactive thioesters or maleimide using single channel conduction assays based on their distinct fingerprints. The results demonstrated that this channel system could be further developed into very sensitive sensing devices.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536
| | - Jennifer Lunn
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45267
| | - Huaming Fang
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536
| | - David Smithrud
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45267
| | - Peixuan Guo
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536
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Slastnikova TA, Rosenkranz AA, Gulak PV, Schiffelers RM, Lupanova TN, Khramtsov YV, Zalutsky MR, Sobolev AS. Modular nanotransporters: a multipurpose in vivo working platform for targeted drug delivery. Int J Nanomedicine 2012; 7:467-82. [PMID: 22346349 PMCID: PMC3277434 DOI: 10.2147/ijn.s28249] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Modular nanotransporters (MNT) are recombinant multifunctional polypeptides created to exploit a cascade of cellular processes, initiated with membrane receptor recognition to deliver selective short-range and highly cytotoxic therapeutics to the cell nucleus. This research was designed for in vivo concept testing for this drug delivery platform using two modular nanotransporters, one targeted to the α-melanocyte-stimulating hormone (αMSH) receptor overexpressed on melanoma cells and the other to the epidermal growth factor (EGF) receptor overexpressed on several cancers, including glioblastoma, and head-and-neck and breast carcinoma cells. Methods In vivo targeting of the modular nanotransporter was determined by immuno-fluorescence confocal laser scanning microscopy and by accumulation of 125I-labeled modular nanotransporters. The in vivo therapeutic effects of the modular nanotransporters were assessed by photodynamic therapy studies, given that the cytotoxicity of photosensitizers is critically dependent on their delivery to the cell nucleus. Results Immunohistochemical analyses of tumor and neighboring normal tissues of mice injected with multifunctional nanotransporters demonstrated preferential uptake in tumor tissue, particularly in cell nuclei. With 125I-labeled MNT{αMSH}, optimal tumor:muscle and tumor:skin ratios of 8:1 and 9.8:1, respectively, were observed 3 hours after injection in B16-F1 melanoma-bearing mice. Treatment with bacteriochlorin p-MNT{αMSH} yielded 89%–98% tumor growth inhibition and a two-fold increase in survival for mice with B16-F1 and Cloudman S91 melanomas. Likewise, treatment of A431 human epidermoid carcinoma-bearing mice with chlorin e6- MNT{EGF} resulted in 94% tumor growth inhibition compared with free chlorin e6, with 75% of animals surviving at 3 months compared with 0% and 20% for untreated and free chlorin e6-treated groups, respectively. Conclusion The multifunctional nanotransporter approach provides a new in vivo functional platform for drug development that could, in principle, be applicable to any combination of cell surface receptor and agent (photosensitizers, oligonucleotides, radionuclides) requiring nuclear delivery to achieve maximum effectiveness.
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Affiliation(s)
- Tatiana A Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Moscow, Russia
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Ishikawa J, Fujita Y, Maeda Y, Furuta H, Ikawa Y. GNRA/receptor interacting modules: Versatile modular units for natural and artificial RNA architectures. Methods 2011; 54:226-38. [DOI: 10.1016/j.ymeth.2010.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 12/25/2022] Open
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Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA. A boost for the emerging field of RNA nanotechnology. ACS NANO 2011; 5:3405-18. [PMID: 21604810 PMCID: PMC3102291 DOI: 10.1021/nn200989r] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This Nano Focus article highlights recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, which took place in Cleveland, OH, USA (October 23-25, 2010) ( http://www.eng.uc.edu/nanomedicine/RNA2010/ ), chaired by Peixuan Guo and co-chaired by David Rueda and Scott Tenenbaum. The conference was the first of its kind to bring together more than 30 invited speakers in the frontier of RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics. A special invited talk on the well-established principles of DNA nanotechnology was arranged to provide models for RNA nanotechnology. An Administrator from National Institutes of Health (NIH) National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer discussed the current nanocancer research directions and future funding opportunities at NCI. As indicated by the feedback received from the invited speakers and the meeting participants, this meeting was extremely successful, exciting, and informative, covering many groundbreaking findings, pioneering ideas, and novel discoveries.
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Affiliation(s)
- Girish C. Shukla
- Center for Gene Regulation in Health and Disease, Department of Biological Sciences, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Farzin Haque
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Yitzhak Tor
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Jean-Jacques Toulmé
- Université Bordeaux Segalen, INSERM U869, Bâtiment 3A 1er étage, 33076 Bordeaux Cedex, France
| | - Hervé Isambert
- Institut Curie, Research Division, CNRS UMR 168, 11 rue P. & M. Curie, 75005 Paris, France
| | - Peixuan Guo
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Scott A. Tenenbaum
- College of Nanoscale Science & Engineering, University at Albany-SUNY, Albany, New York 12203, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
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Abstract
PURPOSE OF REVIEW The field of pharmaceutical and medical nanotechnology has grown rapidly in recent decades and offers much promise for therapeutic advances. This review is intended to serve as a quick summary of the major areas in the therapeutic application of nanotechnology. RECENT FINDINGS Nanotechnology for therapeutic application falls into two broad categories of particulate systems and nanoengineered devices. Recent studies appear to focus on the development of multifunctional particles for drug delivery and imaging and the development of nanotechnology-based biosensors for diagnostic applications. Cancer treatment and diagnosis appears to be the principal focus of many of these applications, but nanotechnology is also finding application in tissue engineering and surface engineering of medical implants. SUMMARY Particulate drug delivery systems in general appear to be poised for increased use in the clinic, whereas nanoengineered implants and diagnostic sensors might well be the next major wave in the medical use of nanotechnology.
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Bibliography. Neonatology and perinatology. Current world literature. Curr Opin Pediatr 2011; 23:253-7. [PMID: 21412083 DOI: 10.1097/mop.0b013e3283454167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Like DNA, RNA can be designed and manipulated to produce a variety of different nanostructures. Moreover, RNA has a flexible structure and possesses catalytic functions that are similar to proteins. Although RNA nanotechnology resembles DNA nanotechnology in many ways, the base-pairing rules for constructing nanoparticles are different. The large variety of loops and motifs found in RNA allows it to fold into numerous complicated structures, and this diversity provides a platform for identifying viable building blocks for various applications. The thermal stability of RNA also allows the production of multivalent nanostructures with defined stoichiometry. Here we review techniques for constructing RNA nanoparticles from different building blocks, we describe the distinct attributes of RNA inside the body, and discuss potential applications of RNA nanostructures in medicine. We also offer some perspectives on the yield and cost of RNA production.
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Affiliation(s)
- Peixuan Guo
- Nanobiomedical Center, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45221, USA.
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