scholarly journals Low-cost, bottom-up fabrication of large-scale single-molecule nanoarrays by DNA origami placement

2020 ◽  
Author(s):  
Rishabh M. Shetty ◽  
Sarah R. Brady ◽  
Paul W. K. Rothemund ◽  
Rizal F. Hariadi ◽  
Ashwin Gopinath
Keyword(s):  
High Throughput ◽  
Single Molecule ◽  
Large Scale ◽  
Low Cost ◽  
Maximum Yield ◽  
Dna Origami ◽  
Top Down ◽  
Statistical Limit ◽  
Macro Scale ◽  
Self Assembled

Large-scale nanoarrays of single biomolecules enable high-throughput assays while unmasking the underlying heterogeneity within ensemble populations. Until recently, creating such grids which combine the unique advantages of microarrays and single-molecule experiments (SMEs) has been particularly challenging due to the mismatch between the size of these molecules and the resolution of top-down fabrication techniques. DNA Origami Placement (DOP) combines two powerful techniques to address this issue: (i) DNA origami, which provides a ∼ 100-nm self-assembled template for single-molecule organization with 5 nm resolution, and (ii) top-down lithography, which patterns these DNA nanostructures, transforming them into functional nanodevices via large-scale integration with arbitrary substrates. Presently, this technique relies on state-of-the-art infrastructure and highly-trained personnel, making it prohibitively expensive for researchers. Here, we introduce a bench-top technique to create meso-to-macro-scale DNA origami nanoarrays using self-assembled colloidal nanoparticles, thereby circumventing the need for top-down fabrication. We report a maximum yield of 74%, two-fold higher than the statistical limit of 37% imposed on non-specific molecular loading alternatives. Furthermore, we provide a proof-of-principle for the ability of this nanoarray platform to transform traditionally low-throughput, stochastic, single-molecule assays into high-throughput, deterministic ones, without compromising data quality. Our approach has the potential to democratize single-molecule nanoarrays and demonstrates their utility as a tool for biophysical assays and diagnostics.

scholarly journals Absolute and arbitrary orientation of single-molecule shapes

Science ◽  
2021 ◽  
Vol 371 (6531) ◽  
pp. eabd6179
Author(s):  
Ashwin Gopinath ◽  
Chris Thachuk ◽  
Anya Mitskovets ◽  
Harry A. Atwater ◽  
David Kirkpatrick ◽  
...  
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Large Scale ◽  
Dna Origami ◽  
Excitation Light ◽  
Optical Cavities ◽  
Large Scale Integration ◽  
Unique Maximum ◽  
Modular Platform ◽  
Scale Integration

DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is challenging: Large numbers of freely diffusing devices must be fixed at desired locations with desired alignment. We present a DNA origami molecule whose energy landscape on lithographic binding sites has a unique maximum. This property enabled device alignment within 3.2° on silica surfaces. Orientation was absolute (all degrees of freedom were specified) and arbitrary (the orientation of every molecule was independently specified). The use of orientation to optimize device performance was shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration was demonstrated with an array of 3456 DNA origami with 12 distinct orientations that indicated the polarization of excitation light.

scholarly journals Nanoscale patterning of self-assembled monolayer (SAM)-functionalised substrates with single molecule contact printing

Nanoscale ◽  
2017 ◽  
Vol 9 (39) ◽  
pp. 15098-15106 ◽  
Author(s):  
M. Sajfutdinow ◽  
K. Uhlig ◽  
A. Prager ◽  
C. Schneider ◽  
B. Abel ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Gold Films ◽  
Self Assembled Monolayer ◽  
Contact Printing ◽  
Nanoscale Patterning ◽  
Self Assembled

DNA origami stamps print biomolecules onto SAM-coated gold filmsviabioconjugation in a process called single molecule contact printing.

scholarly journals Broad-scale Applications of the Raspberry Pi: A Review and Guide for Biologists

2021 ◽  
Author(s):  
Jolle Wolter Jolles
Keyword(s):  
Scientific Community ◽  
Large Scale ◽  
Low Cost ◽  
Ease Of Use ◽  
Plant Phenotyping ◽  
Raspberry Pi ◽  
Ecosystem Monitoring ◽  
Diverse Range ◽  
Wide Range ◽  
Macro Scale

The field of biology has seen tremendous technological progress in recent years, fuelled by the exponential growth in processing power and high-level computing, and the rise of global information sharing. Low-cost single-board computers are predicted to be one of the key technological advancements to further revolutionise this field. So far, an overview of current uptake of these devices and a general guide to help researchers integrate them in their work has been missing. In this paper I focus on the most widely used single board computer, the Raspberry Pi. Reviewing its broad applications and uses across the biological domain shows that since its release in 2012 the Raspberry Pi has been increasingly taken up by biologists, both in the lab, the field, and in the classroom, and across a wide range of disciplines. A hugely diverse range of applications already exist that range from simple solutions to dedicated custom-build devices, including nest-box monitoring, wildlife camera trapping, high-throughput behavioural recordings, large-scale plant phenotyping, underwater video surveillance, closed-loop operant learning experiments, and autonomous ecosystem monitoring. Despite the breadth of its implementations, the depth of uptake of the Raspberry Pi by the scientific community is still limited. The broad capabilities of the Raspberry Pi, combined with its low cost, ease of use, and large user community make it a great research tool for almost any project. To help accelerate the uptake of Raspberry Pi’s by the scientific community, I provide detailed guidelines, recommendations, and considerations, and 30+ step-by-step guides on a dedicated accompanying website (raspberrypi-guide.github.io). I hope with this paper to generate more awareness about the Raspberry Pi and thereby fuel the democratisation of science and ultimately help advance our understanding of biology, from the micro- to the macro-scale.

scholarly journals An Open-Source Framework for Automated High-Throughput Cell Biology Experiments

2021 ◽  
Vol 9 ◽  
Author(s):  
Pavel Katunin ◽  
Jianbo Zhou ◽  
Ola M. Shehata ◽  
Andrew A. Peden ◽  
Ashley Cadby ◽  
...  
Keyword(s):  
Open Source ◽  
High Throughput ◽  
Cell Biology ◽  
Large Scale ◽  
Low Cost ◽  
Fluorescent Labeling ◽  
Open Source Framework ◽  
Open Source Hardware ◽  
High Degree ◽  
Data Analysis Methods

Modern data analysis methods, such as optimization algorithms or deep learning have been successfully applied to a number of biotechnological and medical questions. For these methods to be efficient, a large number of high-quality and reproducible experiments needs to be conducted, requiring a high degree of automation. Here, we present an open-source hardware and low-cost framework that allows for automatic high-throughput generation of large amounts of cell biology data. Our design consists of an epifluorescent microscope with automated XY stage for moving a multiwell plate containing cells and a perfusion manifold allowing programmed application of up to eight different solutions. Our system is very flexible and can be adapted easily for individual experimental needs. To demonstrate the utility of the system, we have used it to perform high-throughput Ca2+ imaging and large-scale fluorescent labeling experiments.

Large-scale synthesis of mesoporous carbon microspheres with controllable structure and nitrogen doping using a spray drying method

RSC Advances ◽  
2014 ◽  
Vol 4 (107) ◽  
pp. 62662-62665 ◽  
Author(s):  
Xu Li ◽  
Jianguo Zhou ◽  
Jitong wang ◽  
Wenming Qiao ◽  
Licheng Ling ◽  
...  
Keyword(s):  
Spray Drying ◽  
High Throughput ◽  
Mesoporous Carbon ◽  
Nitrogen Doping ◽  
Large Scale ◽  
Low Cost ◽  
Carbon Microspheres ◽  
Drying Method ◽  
Spherical Morphology ◽  
Large Mesopores

A low-cost and high-throughput spray drying method was developed to produce mesoporous carbon microspheres with controllable structure and nitrogen doping. The obtained microspheres have spherical morphology, controllable nitrogen doping (0–7 wt%) and large mesopores.

scholarly journals Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

2016 ◽  
Vol 113 (44) ◽  
pp. E6749-E6756 ◽  
Author(s):  
P. Benjamin Stranges ◽  
Mirkó Palla ◽  
Sergey Kalachikov ◽  
Jeff Nivala ◽  
Michael Dorwart ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Dna Synthesis ◽  
Lipid Bilayers ◽  
High Throughput ◽  
Single Molecule ◽  
Low Cost ◽  
Electrode Array ◽  
Oxide Semiconductor ◽  
Sequencing Platform ◽  
Sequencing By Synthesis

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin–polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.

scholarly journals Raman Enhancement of Nanoparticle Dimers Self-Assembled Using DNA Origami Nanotriangles

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1684
Author(s):  
Sergio Kogikoski ◽  
Kosti Tapio ◽  
Robert Edler von Zander ◽  
Peter Saalfrank ◽  
Ilko Bald
Keyword(s):  
Raman Scattering ◽  
Single Molecule ◽  
Resonance Effect ◽  
Field Enhancement ◽  
Surface Enhanced Raman Scattering ◽  
Dna Origami ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering ◽  
Self Assembled

Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor (EF). Herein we obtained the EFs for gold nanoparticle dimers of 60 and 80 nm diameter, respectively, self-assembled using DNA origami nanotriangles. Cy5 and TAMRA were used as surface-enhanced Raman scattering (SERS) probes, which enable the observation of individual nanoparticles and dimers. EF distributions are determined at four distinct wavelengths based on the measurements of around 1000 individual dimer structures. The obtained results show that the EFs for the dimeric assemblies follow a log-normal distribution and are in the range of 106 at 633 nm and that the contribution of the molecular resonance effect to the EF is around 2, also showing that the plasmonic resonance is the main source of the observed signal. To support our studies, FDTD simulations of the nanoparticle’s electromagnetic field enhancement has been carried out, as well as calculations of the resonance Raman spectra of the dyes using DFT. We observe a very close agreement between the experimental EF distribution and the simulated values.

scholarly journals Scalable and High-Throughput Top-Down Manufacturing of Optical Metasurfaces

Sensors ◽  
2020 ◽  
Vol 20 (15) ◽  
pp. 4108
Author(s):  
Taejun Lee ◽  
Chihun Lee ◽  
Dong Kyo Oh ◽  
Trevon Badloe ◽  
Jong G. Ok ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Practical Application ◽  
Large Area ◽  
Top Down ◽  
Optical Components ◽  
New Techniques ◽  
Recent Developments ◽  
Device Applications ◽  
Manufacturing Methods

Metasurfaces have shown promising potential to miniaturize existing bulk optical components thanks to their extraordinary optical properties and ultra-thin, small, and lightweight footprints. However, the absence of proper manufacturing methods has been one of the main obstacles preventing the practical application of metasurfaces and commercialization. Although a variety of fabrication techniques have been used to produce optical metasurfaces, there are still no universal scalable and high-throughput manufacturing methods that meet the criteria for large-scale metasurfaces for device/product-level applications. The fundamentals and recent progress of the large area and high-throughput manufacturing methods are discussed with practical device applications. We systematically classify various top-down scalable patterning techniques for optical metasurfaces: firstly, optical and printing methods are categorized and then their conventional and unconventional (emerging/new) techniques are discussed in detail, respectively. In the end of each section, we also introduce the recent developments of metasurfaces realized by the corresponding fabrication methods.

Sign in / Sign up

Export Citation Format

Share Document