ABSTRACT
Linear double-stranded DNA polymers coding for synthetic genes immobilized on a surface form a brush as a center for cell-free gene expression, with DNA density 102-103 fold higher than in bulk solution reactions. A brush localizes the transcription-translation machinery in cell extracts or in cell-free reconstituted reactions from purified components, creating a concentrated source of RNA and proteins. Newly synthesized molecules can form circuits regulating gene expression in the same brush or adjacent ones. They can also assemble into functional complexes and machines such as ribosomal units, then analyzed by capture on prepatterned antibodies or by cascaded reactions. DNA brushes are arranged as a single center or multiple ones on a glass coverslip, in miniaturized compartments carved in silicon wafers, or in elastomeric microfluidic devices. Brushes create genetically programmable artificial cells with steady-state dynamics of protein synthesis. Here, we provide the basic procedure for surface patterning, DNA immobilization, capture of protein products on antibody traps and fluorescent imaging. The method of DNA brush surface patterning enables simple parallelization of cell-free gene expression reactions for high throughput studies with increased imaging sensitivity.
Subject(s)
DNA , Polymers , DNA/genetics , Gene Expression , RNA , RibosomesABSTRACT
The assembly of protein machines in cells is precise, rapid, and coupled to protein synthesis with regulation in space and time. The assembly of natural and synthetic nanomachines could be similarly controlled by genetic programming outside the cell. Here, we present quasi-two-dimensional (2D) silicon compartments that enable programming of protein assembly lines by local synthesis from surface-immobilized DNA brushes. Using this platform, we studied the autonomous synthesis and assembly of a structural complex from a bacteriophage and a bacterial RNA-synthesizing machine. Local synthesis and surface capture of complexes provided high assembly yield and sensitive detection of spatially resolved assembly intermediates, with the 3D geometry of the compartment and the 2D pattern of brushes dictating the yield and mode of assembly steps. Localized synthesis of proteins in a single gene brush enhances their interactions, and displacement of their genes in separated brushes leads to step-by-step surface assembly. This methodology enables spatial regulation of protein synthesis, and deciphering, reconstruction and design of biological machine assembly lines.
Subject(s)
Bacteriophage T4/genetics , Immobilized Nucleic Acids/genetics , Multiprotein Complexes/biosynthesis , Multiprotein Complexes/genetics , Protein Engineering/instrumentation , Protein Engineering/methods , Cell-Free System , DNA-Directed RNA Polymerases/genetics , DNA-Directed RNA Polymerases/metabolism , Equipment Design , Escherichia coli/genetics , Gene Silencing , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Promoter Regions, Genetic , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Silicon , Viral Proteins/genetics , Viral Proteins/metabolismABSTRACT
We study for the first time the resonant torsional behaviors of inorganic nanotubes, specifically tungsten disulfide (WS2) and boron nitride (BN) nanotubes, and compare them to that of carbon nanotubes. We have found WS2 nanotubes to have the highest quality factor (Q) and torsional resonance frequency, followed by BN nanotubes and carbon nanotubes. Dynamic and static torsional spring constants of the various nanotubes were found to be different, especially in the case of WS2, possibly due to a velocity-dependent intershell friction. These results indicate that inorganic nanotubes are promising building blocks for high-Q nanoelectromechanical systems (NEMS).
