DNA nanoassemblies, such as DNA origamis, hold promise in biosensing, drug delivery, nanoelectronic circuits, and biological computing, which require suitable methods for migration and precision positioning. Insulator-based dielectrophoresis (iDEP) has been demonstrated as a powerful migration and trapping tool for μm- and nm-sized colloids as well as DNA origamis. However, little is known about the polarizability of origami species, which is responsible for their dielectrophoretic migration. Here, we report the experimentally determined polarizabilities of the six-helix bundle origami (6HxB) and triangle origami by measuring the migration times through a potential landscape exhibiting dielectrophoretic barriers. The resulting migration times correlate to the depth of the dielectrophoretic potential barrier and the escape characteristics of the origami according to an adapted Kramer's rate model, allowing their polarizabilities to be determined. We found that the 6HxB polarizability is larger than that of the triangle origami, which correlates with the variations in charge density of both origamis. Further, we discuss the orientation of both origami species in the dielectrophoretic trap and discuss the influence of diffusion during the escape process. Our study provides detailed insight into the factors contributing to the migration through dielectrophoretic potential landscapes, which can be exploited for applications with DNA and other nanoassemblies based on dielectrophoresis.

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.5b02524DOI Listing

Publication Analysis

Top Keywords

six-helix bundle
8
escape characteristics
8
dielectrophoretic trap
8
dna nanoassemblies
8
dna origamis
8
origami species
8
triangle origami
8
migration times
8
dielectrophoretic potential
8
origami
7

Similar Publications

A DNA Origami Pivot Hinge Driven by DNA Intercalators.

ACS Nano

January 2025

Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.

Article Synopsis
  • The DNA origami technique allows for the creation of nanoscale structures that can change shape dynamically.
  • A new design features a hinge mechanism that pivots based on the concentration of DNA intercalators, using gold nanoparticles for support.
  • This pivoting motion can be adjusted and repeated, potentially leading to the development of advanced nanosensors and actuators that amplify tiny movements caused by molecular interactions.
View Article and Find Full Text PDF

Protein mimics of fusion core from SARS-CoV-1 can inhibit SARS-CoV-2 entry.

Biochem Biophys Res Commun

December 2024

Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China. Electronic address:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the genus Betacoronavirus (subgenus Sarbecovirus) and shares significant genomic and phylogenetic similarities with severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1). SARS-CoV-2 infection occurs through membrane fusion between the virus and host cell membranes, which is facilitated by the spike glycoprotein subunit 2 (S2). The folding of three heptad-repeat regions 1 (HR1) into a central trimeric core structure, along with the binding of three heptad-repeat regions 2 (HR2) in an antiparallel manner within the groove formed between the HR1 regions, which provides the driving force for membrane fusion.

View Article and Find Full Text PDF

Cryo-EM structure and polar assembly of the PS2 S-layer of .

bioRxiv

September 2024

Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium.

Article Synopsis
  • - The study focuses on Corynebacteriales, which have a unique outer membrane structure made of mycolic acids, and explores the mysterious 'S-layer' that enhances this membrane.
  • - Researchers isolated the PS2 S-layer and used advanced 3D cryoEM techniques to reveal its structure, consisting of hexameric core units and trimeric lattice arrangements that contribute to a semipermeable membrane.
  • - The findings provide insights into S-layer functions and evolution within Corynebacteriales, suggesting potential for developing bioengineered materials that utilize these membrane properties.
View Article and Find Full Text PDF

Alpaca-derived nanobody targeting the hydrophobic pocket of the HIV-1 gp41 NHR broadly neutralizes HIV-1 by blocking six-helix bundle formation.

Curr Res Microb Sci

July 2024

Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China.

Article Synopsis
  • The hydrophobic pocket of HIV-1 gp41 NHR is essential for forming a six-helix bundle during viral fusion, making it a prime target for drug design.
  • However, the size of traditional antibodies like IgG prevents them from fitting into this pocket during the crucial fusion process.
  • Nanobodies (Nbs), specifically Nb-172, have been developed to target this region and show promising neutralizing effects against various HIV-1 strains, suggesting their potential as a therapeutic option.
View Article and Find Full Text PDF

ADS-J21 is a novel HIV-1 entry inhibitor targeting gp41.

Curr Res Microb Sci

July 2024

Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China.

Article Synopsis
  • HIV-1 envelope glycoprotein gp41 is crucial for the virus to fuse with host cells, making it a target for anti-HIV drugs.
  • A new compound named ADS-J21 has been developed, which shares a similar Y-shaped structure with the previously studied ADS-J1 but has a lower molecular weight and shows effective activity against various HIV-1 strains.
  • Research showed that ADS-J21 works by blocking the formation of a critical structure (the six-helix bundle) in gp41, paving the way for it to be optimized as a small-molecule fusion inhibitor.
View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!