scholarly journals High precision and high yield fabrication of dense nanoparticle arrays onto DNA origami at statistically independent binding sites

Nanoscale ◽  
2014 ◽  
Vol 6 (22) ◽  
pp. 13928-13938 ◽  
Author(s):  
Sadao Takabayashi ◽  
William P. Klein ◽  
Craig Onodera ◽  
Blake Rapp ◽  
Juan Flores-Estrada ◽  
...  
Keyword(s):  
High Precision ◽  
Steric Hindrance ◽  
Binding Sites ◽  
Dna Origami ◽  
High Yield ◽  
Electrostatic Repulsion ◽  
Nanoparticle Arrays ◽  
Self Assembled

Nanoparticle arrays self-assembled in the absence of site-bridging, steric hindrance, and electrostatic repulsion.

Gold nanostructures based on DNA Origami templates with applications in nanoelectronics and plasmonics

MRS Advances ◽  
2017 ◽  
Vol 2 (64) ◽  
pp. 4017-4023 ◽  
Author(s):  
David D. Ruiz ◽  
Karen L. Cardos ◽  
Gerardo Soto ◽  
Enrique C. Samano
Keyword(s):  
Binding Sites ◽  
Virus Genome ◽  
Dna Origami ◽  
Minimum Size ◽  
Dna Nanostructures ◽  
Nanoparticle Arrays ◽  
M13 Virus ◽  
Dna Binding Sites ◽  
Significant Interest ◽  
Artificial Dna

ABSTRACTA major challenge in nanofabrication is the manipulation and exact placement of nano-objects on a specific template. Artificial DNA nanostructures such as DNA origami have garnered significant interest as templates for incorporating nanomaterials at precise sites while the structures are self-assembled. This work shows the usage of the DNA origami technique in the design and fabrication of nanostructures with the shapes of a circle and a triangle using the third part of the M13 virus genome, named mini-M13, as a scaffold. These DNA origami templates were modified to have DNA binding sites with a uniquely coded sequence. This method is used to attach 5 nm gold nanoparticles functionalized with the complementary DNA sequence. Two new metallic nanostructures with different nanoparticle arrays having minimum size but recognizable morphology are provided. The formation and dimensions of the nanostructures were verified using AFM and agarose gel electrophoresis.

Toward Self-Assembled Plasmonic Devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates

ACS Nano ◽  
2016 ◽  
Vol 10 (5) ◽  
pp. 5374-5382 ◽  
Author(s):  
Fatih N. Gür ◽  
Friedrich W. Schwarz ◽  
Jingjing Ye ◽  
Stefan Diez ◽  
Thorsten L. Schmidt
Keyword(s):  
Gold Nanoparticles ◽  
Dna Origami ◽  
High Yield ◽  
Self Assembled

Nanoscale Self-Assembly Using Ion and Electron Beam Techniques: A Rapid Review

MRS Advances ◽  
2020 ◽  
Vol 5 (64) ◽  
pp. 3507-3520
Author(s):  
Chunhui Dai ◽  
Kriti Agarwal ◽  
Jeong-Hyun Cho
Keyword(s):  
Electron Beam ◽  
Self Assembly ◽  
Ion Beam ◽  
Three Dimensional ◽  
The Self ◽  
Stress Generation ◽  
Rapid Review ◽  
High Yield ◽  
3D Nanostructures ◽  
Self Assembled

AbstractNanoscale self-assembly, as a technique to transform two-dimensional (2D) planar patterns into three-dimensional (3D) nanoscale architectures, has achieved tremendous success in the past decade. However, an assembly process at nanoscale is easily affected by small unavoidable variations in sample conditions and reaction environment, resulting in a low yield. Recently, in-situ monitored self-assembly based on ion and electron irradiation has stood out as a promising candidate to overcome this limitation. The usage of ion and electron beam allows stress generation and real-time observation simultaneously, which significantly enhances the controllability of self-assembly. This enables the realization of various complex 3D nanostructures with a high yield. The additional dimension of the self-assembled 3D nanostructures opens the possibility to explore novel properties that cannot be demonstrated in 2D planar patterns. Here, we present a rapid review on the recent achievements and challenges in nanoscale self-assembly using electron and ion beam techniques, followed by a discussion of the novel optical properties achieved in the self-assembled 3D nanostructures.

Self-Assembled Au Nanoparticle Arrays for Precise Metabolic Assay of Cerebrospinal Fluid

2021 ◽  
Vol 13 (4) ◽  
pp. 4886-4893
Author(s):  
Yuning Wang ◽  
Kun Zhang ◽  
Tongtong Tian ◽  
Weilong Shan ◽  
Liang Qiao ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Au Nanoparticle ◽  
Nanoparticle Arrays ◽  
Self Assembled

scholarly journals Nanomechanics of self-assembled DNA building blocks

Nanoscale ◽  
2021 ◽  
Author(s):  
Michael Penth ◽  
Kordula Schellnhuber ◽  
Roland Bennewitz ◽  
Johanna Blass
Keyword(s):  
Structural Dynamics ◽  
Force Spectroscopy ◽  
Building Blocks ◽  
Dna Origami ◽  
Self Assembled ◽  
High Flexibility

Massive parallel force spectroscopy reveals a surprisingly high flexibility for DNA constructs used in DNA origami. The high flexibility is attributed to the structural dynamics of DNA self-assemblies.

scholarly journals Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

2019 ◽  
Author(s):  
Helen L. Miller ◽  
Sonia Contera ◽  
Adam J.M. Wollman ◽  
Adam Hirst ◽  
Katherine E. Dunn ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Single Molecule ◽  
Targeted Drug Delivery ◽  
Binding Sites ◽  
Dna Origami ◽  
Target Cells ◽  
Dna Nanostructures ◽  
Synthetic Dna ◽  
Drug Molecules ◽  
Targeted Drug

AbstractIntercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.

Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks

2016 ◽  
Vol 8 (45) ◽  
pp. 31239-31247 ◽  
Author(s):  
Saminathan Ramakrishnan ◽  
Sivaraman Subramaniam ◽  
A. Francis Stewart ◽  
Guido Grundmeier ◽  
Adrian Keller
Keyword(s):  
Dna Origami ◽  
Protein Patterns ◽  
Self Assembled

Steric Hindrance Mutagenesis versus Alanine Scan in Mapping of Ligand Binding Sites in the Tachykinin NK1 Receptor

1998 ◽  
Vol 53 (1) ◽  
pp. 166-175 ◽  
Author(s):  
Birgitte Holst ◽  
Sannah Zoffmann ◽  
Christian E. Elling ◽  
Siv A. Hjorth ◽  
Thue W. Schwartz
Keyword(s):  
Ligand Binding ◽  
Steric Hindrance ◽  
Binding Sites ◽  
Nk1 Receptor ◽  
Alanine Scan ◽  
Ligand Binding Sites

scholarly journals Etomidate and Etomidate Analog Binding and Positive Modulation of γ-Aminobutyric Acid Type A Receptors

2018 ◽  
Vol 129 (5) ◽  
pp. 959-969 ◽  
Author(s):  
Megan McGrath ◽  
Zhiyi Yu ◽  
Selwyn S. Jayakar ◽  
Celena Ma ◽  
Mansi Tolia ◽  
...  
Keyword(s):  
Steric Hindrance ◽  
Gabaa Receptors ◽  
Binding Sites ◽  
Phenyl Ring ◽  
Type A ◽  
Binding Pocket ◽  
Aminobutyric Acid ◽  
Substituent Group ◽  
Acid Type ◽  
Site Selective

Abstract Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New Background Naphthalene-etomidate, an etomidate analog containing a bulky phenyl ring substituent group, possesses very low γ-aminobutyric acid type A (GABAA) receptor efficacy and acts as an anesthetic-selective competitive antagonist. Using etomidate analogs containing phenyl ring substituents groups that range in volume, we tested the hypothesis that this unusual pharmacology is caused by steric hindrance that reduces binding to the receptor’s open state. Methods The positive modulatory potencies and efficacies of etomidate and phenyl ring–substituted etomidate analogs were electrophysiology defined in oocyte-expressed α1β3γ2L GABAA receptors. Their binding affinities to the GABAA receptor’s two classes of transmembrane anesthetic binding sites were assessed from their abilities to inhibit receptor labeling by the site-selective photolabels 3[H]azi-etomidate and tritiated R-5-allyl-1-methyl-5-(m-trifluoromethyl-diazirynylphenyl) barbituric acid. Results The positive modulatory activities of etomidate and phenyl ring–substituted etomidate analogs progressively decreased with substituent group volume, reflecting significant decreases in both potency (P = 0.005) and efficacy (P < 0.0001). Affinity for the GABAA receptor’s two β+ − α– anesthetic binding sites similarly decreased with substituent group volume (P = 0.003), whereas affinity for the receptor’s α+ – β–/γ+ – β– sites did not (P = 0.804). Introduction of the N265M mutation, which is located at the β+ − α– binding sites and renders GABAA receptors etomidate-insensitive, completely abolished positive modulation by naphthalene-etomidate. Conclusions Steric hindrance selectively reduces phenyl ring–substituted etomidate analog binding affinity to the two β+ − α– anesthetic binding sites on the GABAA receptor’s open state, suggesting that the binding pocket where etomidate’s phenyl ring lies becomes smaller as the receptor isomerizes from closed to open.

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