Zero-mode waveguides: Sub-wavelength nanostructures for single molecule studies at high concentrations

Methods ◽  
2008 ◽  
Vol 46 (1) ◽  
pp. 11-17 ◽  
Author(s):  
Jose M. Moran-Mirabal ◽  
Harold G. Craighead
Keyword(s):  
Single Molecule ◽  
Zero Mode ◽  
Single Molecule Studies ◽  
High Concentrations ◽  
Sub Wavelength

scholarly journals Nanoaperture fabrication via colloidal lithography for single molecule fluorescence imaging

2019 ◽  
Author(s):  
Ryan M. Jamiolkowski ◽  
Kevin Y Chen ◽  
Shane A. Fiorenza ◽  
Alyssa M. Tate ◽  
Shawn H. Pfeil ◽  
...  
Keyword(s):  
Single Molecule ◽  
Self Assembly ◽  
Zero Mode ◽  
Thin Metal Film ◽  
Polystyrene Microspheres ◽  
Single Molecule Fluorescence ◽  
Fluorescence Studies ◽  
Observation Volume ◽  
Sophisticated Equipment ◽  
Sub Wavelength

AbstractIn single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling fabrication of thousands of ZMWs in parallel without sophisticated equipment. Polystyrene 1 μm dia. microbeads self-assemble on a glass slide into a hexagonal array, forming a mask for the deposition of metallic posts in the inter-bead interstices. The width of those interstices (and subsequent posts) is adjusted within 100-300 nm by partially fusing the beads at the polystyrene glass transition temperature. The beads are dissolved in toluene, aluminum or gold cladding is deposited around the posts, and those are dissolved, leaving behind an array ZMWs. Parameter optimization and the performance of the ZMWs are presented. By using colloidal self-assembly, typical laboratories can make use of sub-wavelength ZMW technology avoiding the availability and expense of sophisticated clean-room environments and equipment.

Single-molecule detection and radiation control in solutions at high concentrations via a heterogeneous optical slot antenna

Nanoscale ◽  
2014 ◽  
Vol 6 (15) ◽  
pp. 9103-9109 ◽  
Author(s):  
Chenglong Zhao ◽  
Yongmin Liu ◽  
Jing Yang ◽  
Jiasen Zhang
Keyword(s):  
Single Molecule ◽  
Emission Rate ◽  
Zero Mode ◽  
Single Molecule Detection ◽  
Slot Antenna ◽  
Radiation Control ◽  
High Concentrations

A heterogeneous optical slot antenna significantly enhances the single-molecule excitation and emission rate, which enables single-molecule detection in solutions at high concentrations, compared to a conventional zero-mode waveguide.

Design and Fabrication of Linear-shaped Zero Mode Waveguides for Single Molecule Observation of Kinesin and Fluorescent ATP

2017 ◽  
Vol 137 (6) ◽  
pp. 159-164
Author(s):  
Kazuya Fujimoto ◽  
Yuki Morita ◽  
Ryota Iino ◽  
Michio Tomishige ◽  
Hirofumi Shintaku ◽  
...  
Keyword(s):  
Single Molecule ◽  
Zero Mode

scholarly journals Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

2021 ◽  
Vol 22 (5) ◽  
pp. 2398
Author(s):  
Wooyoung Kang ◽  
Seungha Hwang ◽  
Jin Young Kang ◽  
Changwon Kang ◽  
Sungchul Hohng
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Facilitated Diffusion ◽  
One Dimensional ◽  
Bacterial Transcription ◽  
Fluorescence Measurements ◽  
Dimensional Diffusion ◽  
Single Molecule Studies ◽  
Hopping Diffusion

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

Breaking Down the Supramolecular Ensemble: Single-Molecule Studies of the Concentration Dependence of Main-Chain Supramolecular Polymer Molecular Weight Distributions on Surfaces

2010 ◽  
Vol 63 (4) ◽  
pp. 624
Author(s):  
Michael J. Serpe ◽  
Jason R. Whitehead ◽  
Stephen L. Craig
Keyword(s):  
Molecular Weight ◽  
Single Molecule ◽  
Monomer Concentration ◽  
Supramolecular Polymer ◽  
Force Microscopy ◽  
Molecular Weight Distributions ◽  
Atomic Force ◽  
Multi Stage ◽  
Single Molecule Studies ◽  
Supramolecular Ensemble

Single molecule atomic force microscopy (AFM) studies of oligonucleotide-based supramolecular polymers on surfaces are used to examine the molecular weight distribution of the polymers formed between a functionalized surface and an AFM tip as a function of monomer concentration. For the concentrations examined here, excellent agreement with a multi-stage open association model of polymerization is obtained, without the need to invoke additional contributions from secondary steric interactions at the surface.

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