Journal: ACS Photonics

Article Title: Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

doi: 10.1021/acsphotonics.1c01825

Figure Lengend Snippet: Label-free detection using a plasmon resonance shift. (a) Scheme of a DNA molecule electrophoretically driven through a plasmonic nanopore and detected by optical backscattering from the plasmonic antenna. (b) Typical TEM image of the plasmonic nanopore which consists of a gold dimer antenna with a nanopore at the gap center. The inset shows a TEM image of zoom of the nanogap region. (a, b) Reprinted with permission from ref . Copyright 2018 American Chemical Society. (c) Scheme of a DNA translocated through an inverted bowtie nanoantenna and detected by both the ionic current through the nanopore and the light transmitted through an inverted bowtie nanoantenna. Reprinted with permission from ref . Copyright 2019 American Chemical Society. (d) Scheme of double nanohole apertures. (e) Single-strand DNA trapping event in the double nanohole with no intermediate step. (f) A hairpin DNA trapping event in the double nanohole shows the unzipping with an intermediate step of ∼0.1 s. (g) Energy reaction diagram of trapping and unzipping of a DNA hairpin; k , Boltzmann constant; T , temperature; U , energy. (d–g) Reprinted with permission from ref . Copyright 2014 OSA.

Article Snippet: Single-molecule DNA sequencing technologies include single-molecule fluorescence detection mostly used by PacBio and label-free resistive pulse sensing (RPS) in biological nanopores used by the Oxford Nanopore Technologies.

Techniques:

Journal: ACS Photonics

Article Title: Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

doi: 10.1021/acsphotonics.1c01825

Figure Lengend Snippet: Surface-enhanced Raman spectroscopic sensing in nanopore/nanoslit. (a) Schematic illustration of DNA threading through a nanopore with a bowtie antenna, the SERS signal of a DNA base will be enhanced when it passes through the nanopore located in the hot spot. Reprinted with permission from ref . Copyright 2015 American Chemical Society. (b) Schematic illustration of gold plasmonic nanopores synthesized at the tip of a glass nanopipette. When molecules driven by electrophoresis translocate through the gold nanopores, SERS signals will be generated. Reprinted with permission from ref . Copyright 2019 American Chemical Society. (c) Schematic representation of the setup for nanoslit SERS. The inset shows a top-view SEM image of the nanoslit structure, consisting of an inverted prism nanoslit cavity with Bragg-mirror gratings. The scale bar is 1 μm. (d) SERS spectra of four DNA nucleotides. Each spectrum was averaged from 100 spectra, with a nucleotide solution of 1 × 10 –3 M. (c, d) Reprinted with permission from ref . Copyright 2018 Springer Nature; http://creativecommons.org/licenses/by/4.0 .

Article Snippet: Single-molecule DNA sequencing technologies include single-molecule fluorescence detection mostly used by PacBio and label-free resistive pulse sensing (RPS) in biological nanopores used by the Oxford Nanopore Technologies.

Techniques: Synthesized, Electrophoresis, Generated

Journal: ACS Photonics

Article Title: Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

doi: 10.1021/acsphotonics.1c01825

Figure Lengend Snippet: Electroplasmonic trapping for single-molecule SERS. (a) Schematic of the flow-through setup that allows a single gold nanourchin to flow through and be trapped under transmembrane bias at a plasmonic resonance upon 785 nm laser excitation. (b) Under laser illumination hot spot forms between AuNU and the nanopore sidewall, inside of which the SERS signal of analytes will be generated. (c) TEM image of the AuNU. The scale bar is 10 nm. (a–c) Reprinted with permission from ref . Copyright 2020 Wiley-VCH. (d) Schematic illustration of the electro-plasmonic forces exerted on an AuNU in the nanohole under bias, both of which have negative surface charges. The trapping is due to a balance between the electrophoretic (F EP ), electro-osmotic (F EO ), and optical (F OF ) forces. White arrows indicate the zeta potentials on the AuNU (ζ np ) and the nanohole wall (ζ hole ), respectively, and d is the distance between the particle tip and nanohole wall. (e) Simulated electromagnetic field intensity distributions of the AuNU coupled with the nanohole. The color bar represents the enhancement of the electromagnetic field intensity. (f) Magnified view of the electromagnetic field intensity at one tip of the AuNU. The scale bar is 2 nm. (d–f) Reprinted with permission from ref . Copyright 2019 Springer Nature; http://creativecommons.org/licenses/by/4.0 .

Article Snippet: Single-molecule DNA sequencing technologies include single-molecule fluorescence detection mostly used by PacBio and label-free resistive pulse sensing (RPS) in biological nanopores used by the Oxford Nanopore Technologies.

Techniques: Generated

Journal: ACS Photonics

Article Title: Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

doi: 10.1021/acsphotonics.1c01825

Figure Lengend Snippet: (a) Schematic illustration of AuNU trapped inside of a gold nanopore under laser illumination. (b) Schematic illustration of a SERS hot spot generated between the nanopore side wall and AuNU with physically adsorbed vasopressin molecules. (c) Schematic illustration of a vasopressin molecule partially excited by a subnanometer hot spot. Physically adsorbed on the gold surface, the molecule will change orientation, position, and conformation inside the subnanometer hot spot under laser illumination. (d) SERS time series extracted from 1400 spectra produced by adsorbing vasopressin submonolayer on the gold nanourchins and trapping them in the nanohole. The color bar represents the signal-to-baseline intensity of the Raman modes. The blue dotted lines indicate (e) the parts of Arg, Pro, and Cys that are excited by the hot spot. (f) The Arg and Pro are excited by the hot spot and (g) only the Pro is excited in the hot spot. The left panels are the SERS spectrum with peaks showing corresponding vibration modes. The right panels illustrate the corresponding molecule position and conformation inside of the hot spot. (a, b, and d) Reprinted with permission from ref . Copyright 2020 Wiley-VCH.

Article Snippet: Single-molecule DNA sequencing technologies include single-molecule fluorescence detection mostly used by PacBio and label-free resistive pulse sensing (RPS) in biological nanopores used by the Oxford Nanopore Technologies.

Techniques: Generated, Produced

Journal: ACS Photonics

Article Title: Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

doi: 10.1021/acsphotonics.1c01825

Figure Lengend Snippet: (a) A subnanometer nanopore was used to detect a denatured protein with a rod-like structure. Reprinted with permission from ref . Copyright 2016 Springer Nature. (b) Current traces of a solid-state nanopore at different pH values for positive and negative applied bias. Reprinted with permission from ref . Copyright 2010 American Chemical Society. (c) Simulation of the electro-osmotic flow velocity distribution in a truncated pyramidal nanopore under a positive (left) and negative bias (right). Reprinted with permission from ref . Copyright 2019 Springer Nature. (d) Scheme of a DNA origami sphere docked on a nanopore under an electric bias inducing an electro-osmotic flow that traps proteins. Reprinted with permission from ref . Copyright 2021 Springer Nature.

Article Snippet: Single-molecule DNA sequencing technologies include single-molecule fluorescence detection mostly used by PacBio and label-free resistive pulse sensing (RPS) in biological nanopores used by the Oxford Nanopore Technologies.

Techniques:

Journal: Cell Reports

Article Title: PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells

doi: 10.1016/j.celrep.2020.107957

Figure Lengend Snippet: PTPN2 Deficiency Enhances Programmed Expansion of Briefly Stimulated Effector T Cells (A–D) PTPN2-deficient or WT OT-I T cells were activated in vitro with SIINFEKL, H-2Kb, and CD80 expressing artificial APCs (MEC.B7.SigOVA) for 1 (A and B), 2 (C), and 7 (D) days. Activated T cells (10 5 ) were then transferred into antigen-free CD45-congenic C57BL/6J host mice. (A and B) Frequency of OT-I among total CD8 T cells was determined 7 days post-transfer (A). Bar graphs in (B) show the representative phenotype of five individual mice of the recovered OT-I T cells. (C and D) Frequency of OT-I among total CD8 T cells was determined 5 days post-transfer. (E) Hosts were grafted as in (A), but 7 days after the transfer they received 10 6 CD45-congenic, carboxyfluorescein succinimidyl ester (CFSE)-labeled target splenocytes that were pulsed with SIINFEKL peptide and 10 6 CD45-congenic unpulsed control splenocytes which served as a reference population. The plots show the calculated frequency of residual peptide-pulsed target cells at 6 h post-injection in the spleen. (F) Same setup as (E), but 10 5 Ova- and GFP-expressing RMA cells and antigen-negative mCherry-expressing RMA cells were intraperitoneally (i.p.) injected. The ratio of GFP versus mCherry RMA cells in the peritoneal fluid was determined by flow cytometry 2 days after the transfer. (G) The left plot shows the OT-I T cell numbers recovered per spleen at 20 h post-transfer and at 7 days post-transfer of 10 5 activated WT versus KO OT-I T cells. The plot to the right shows the ratio of KO/WT OT-I T cells at 6 h post-transfer of 10 6 naive T cells. The data are representative of five (A and B) or two (C and G) independent experiments with 3–5 mice each. Dots in all panels represent data from a mouse and horizontal lines the mean. Statistical analysis: unpaired t test, ∗∗∗∗ p ≤ 0.00001, ∗∗∗ p ≤ 0.0001, ∗∗ p ≤ 0.001, ∗ p ≤ 0.01, ns p ≥ 0.05.

Article Snippet: For E 4 × 10 6 CFSE labeled splenocytes pulsed with SIINFEKL peptide (EMC microcollections) or unpulsed control splenocytes were co-injected i.v. as target cells.

Techniques: In Vitro, Expressing, Labeling, Control, Injection, Flow Cytometry

Journal: Cell Reports

Article Title: PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells

doi: 10.1016/j.celrep.2020.107957

Figure Lengend Snippet:

Article Snippet: For E 4 × 10 6 CFSE labeled splenocytes pulsed with SIINFEKL peptide (EMC microcollections) or unpulsed control splenocytes were co-injected i.v. as target cells.

Techniques: Virus, Recombinant, Software