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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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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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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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