Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field

Li, Chen Yu; Hemmig, Elisa A.; Kong, Jinglin; Yoo, Jejoong; Hernández‐Ainsa, Silvia; Keyser, Ulrich F.; Aksimentiev, Aleksei

doi:10.1021/nn505825z

Cited by 93 publications

(109 citation statements)

References 80 publications

Supporting

Mentioning

102

Contrasting

Order By: Relevance

“…It is noteworthy that the presence of intense negative electrostatic force field is strongly blocking the avenue of numerous applications in nanosensor and nanomedicine . It was confirmed by our preliminary study, the labeling efficiency was not only strongly relied on the shape of origami, but also on the amounts and position of capture probes M3′.…”

Section: Resultssupporting

confidence: 71%

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label

Liu

Pan

Wen

et al. 2017

Small

View full text Add to dashboard Cite

The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established. Here, as a further confirmatory research to explore the sensitivity and applicability of this assay, differentially predesigned DNA origami shape ID probes are also developed for precisely HBV genotyping. Through the specific identification of visualized DNA origami nanostructure with clinical HBV DNA samples, the genetic variation information of genotypes can be directly identified under AFM. As a proof-of-concept, five genotype B and six genotype C are detected in 11 HBV-infected patients' blood DNA samples of Han Chinese population in the single-blinded test. The AFM image-based DNA origami shape ID genotyping approach shows high specificity and sensitivity, which could be promising for virus infection diagnosis and precision medicine in the future.

show abstract

Section: Resultssupporting

confidence: 71%

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label

Liu

Pan

Wen

et al. 2017

Small

View full text Add to dashboard Cite

show abstract

“…The calculations of local densities and ion fluxed were performed on a 50 × 50 × 76 cubic grid using a previously described method. 55,59,114 …”

Section: Methodsmentioning

confidence: 99%

Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization

Cressiot¹,

Greive

et al. 2017

ACS Nano

Self Cite

View full text Add to dashboard Cite

Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics, and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein’s insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal’s DNA-ratchet function.

show abstract

“…The local current in each grid element was calculated as: 70

I_{j} = \sum_{j} q_{j} \times f_{j, k},

where j denotes a particular ion species (K + or Cl − ), q j denotes the ion charge, k the x, y or z -directions, and f j,k the flux of ionic species j along the k -coordinate. Next, the 3D density and ionic flux data was averaged along an azimuthal coordinate in a cylindrical coordinate system to obtain the mean density and the mean flux in the r - z plane.…”

Section: Methodsmentioning

confidence: 99%

Modulation of Molecular Flux Using a Graphene Nanopore Capacitor

Shankla

Aksimentiev²

2017

J. Phys. Chem. B

Self Cite

View full text Add to dashboard Cite

Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations we show that the charge state of such a graphene nanopore capacitor can regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the the sign of the charge assigned to both plates of the capacitor. Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the bias driving the transmembrane current. Facilitated by dynamic inversion of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.

show abstract

Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field

Cited by 93 publications

References 80 publications

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label

Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization

Modulation of Molecular Flux Using a Graphene Nanopore Capacitor

Contact Info

Product

Resources

About