Journal: bioRxiv

Article Title: Unveiling DNA Origami Interaction Dynamics on Living Cell Surfaces by Single Particle Tracking

doi: 10.1101/2024.12.23.628980

Figure Lengend Snippet: Immunostaining of the EGFR on Hek 293T cells (left) and the MDA MD 468 cells (right). Images were taken via confocal laser scanning microscopy.

Article Snippet: The MDA-MB-468 (ATCC cat. HTB-132) and Hek 293T (ATCC cat. CRL-3519) cell lines were cultured in Thermo ScientificTM NuncTM Cell Culture Treated Flasks with Filter Caps.

Techniques: Immunostaining, Confocal Laser Scanning Microscopy

Journal: bioRxiv

Article Title: Unveiling DNA Origami Interaction Dynamics on Living Cell Surfaces by Single Particle Tracking

doi: 10.1101/2024.12.23.628980

Figure Lengend Snippet: a) Schematic representation of the experimental findings on NR selectivity: the differential binding profile between the targeted cell line (MDA MD 468) and the non-targeted cell line (Hek 293T) with the targeted NRs (NRs_18Ab and NRs_18Apt). For the MDA MD 468 cells, binding events with the targeted NRs are characterized by very long trajectories, indicating specific binding, while the binding trajectories with the Hek 293T are typically much shorter, indicating non-specific binding. b) Representative image of NRs_18Ab trajectories at 60 minutes after their incubation with MDA MD 468 and Hek 293T cells. Cell contours are indicated by the dotted line. Color bar indicates the diffusion coefficients (ranging from 0 to 4 µm 2 /s). c) Scatter plot of all the binding events for non-functionalized NRs, NR_18Ab and NR_18Apt (i.e. all the trajectories with D ≤ 1), plotted against their respective trajectory length (y-axis). d) Bar plot displaying the differential specific binding percentage between MDA MD 468 and Hek 293T for the different NR designs (NR_18Ab and NR_18Apt) at 3 distinct time points (10 min, 30 min and 60 min). Results are shown as the mean +-standard error of the mean. n = 3 biological replicates (per biological replicate, the trajectories of 5 different movies were combined, i.e. 5 technical replicates) *: significant difference between groups with p ≤ 0.05, ** : significant difference between groups with p ≤ 0.01, *** : significant difference between groups with p ≤ 0.001.

Article Snippet: The MDA-MB-468 (ATCC cat. HTB-132) and Hek 293T (ATCC cat. CRL-3519) cell lines were cultured in Thermo ScientificTM NuncTM Cell Culture Treated Flasks with Filter Caps.

Techniques: Binding Assay, Incubation, Diffusion-based Assay

Journal: bioRxiv

Article Title: Unveiling DNA Origami Interaction Dynamics on Living Cell Surfaces by Single Particle Tracking

doi: 10.1101/2024.12.23.628980

Figure Lengend Snippet: a) Scheme of the binding kinetics between targeted NRs (NR_18Ab and NR_18Apt) and cells (left panel). The corresponding formula of the binding kinetics is displayed in the right panel. b) Comparison of the total number of specific binding events between NRs with 8 or 18 binding ligands (antibody or aptamer) in both MDA MD 468 and Hek 293T cells. The amount of binding events can be directly related to k on . c) Example of the exponential decay fitting for the binding time of NR functionalized with 18 antibodies in MDA MD 468 cells, where dotted line represents the fitted courve and the corresponding equation is displayed. d) τ B values obtained via an exponential decay fitting of all the binding events for each NR design and cell type. This value is inversely proportional to k off . A comparison was made between NRs with 8 or 18 binding ligands (antibody or aptamer) in both MDA MD 468 or Hek 293T. Results are shown as mean fitted value, where error bars represent the standard error of the fitting for each NR design in the different cell lines.

Article Snippet: The MDA-MB-468 (ATCC cat. HTB-132) and Hek 293T (ATCC cat. CRL-3519) cell lines were cultured in Thermo ScientificTM NuncTM Cell Culture Treated Flasks with Filter Caps.

Techniques: Binding Assay, Comparison

Journal: Nature Communications

Article Title: Branched-chain α-keto acids impair glucose-stimulated insulin secretion in pancreatic β-cells under diabetes by reactivating the LDHA-lactate axis

doi: 10.1038/s41467-026-70004-2

Figure Lengend Snippet: a 3D diagram of the binding modes between human dimeric LDHA (PDB: 8FW6) and KIC, KMV, and KIV. The binding free energy of each molecule is shown. Chain A is colored orange; Chain B is magenta; KIC, KMV, and KIV are represented as green stick models; hydrogen bonds are indicated by blue dashed lines. b Representative surface plasmon resonance (SPR) assay showing the binding interactions between human recombinant LDHA protein and KIC, KMV, KIV and pyruvate (Pyr). Sensorgrams illustrate the binding and dissociation phases, with equilibrium dissociation constant (K D ) values calculated to assess binding strength. c Protein crosslinking assay for tetrameric, dimeric, and monomeric forms of LDHA in whole-cell lysates of mouse islets (470 size-matched islets per sample) and INS-1E cells incubated with vehicle or BCKA (30 μM each of KIC, KMV and KIV) for 48 h. Glutaraldehyde was added to the cell lysate as a crosslinking agent to stabilize protein interactions. d Effect of BCKA on the dimerization and tetramerization of recombinant human LDHA protein. Monomeric LDHA control was prepared by heating at 99 °C for 5 min. e 293 T cells were transfected with empty vector, or plasmids overexpressing LDHA WT or Ser210A (1MUT), Ser202A/Ser210A/Thr307A (3 MUT) or Gly 203 A/Gly208A/Asn205A/Ser 210 A (4 MUT). The cell lysates were incubated with 0, 0.2 mM or 2 mM BCKA, followed by DARTS analysis of proteinase K (PK)-mediated LDHA degradation. Protein abundance in total cell lysates (TCL) was visualized using silver staining. c–e Each experiment was independently repeated at least three times with similar results.

Article Snippet: 293 T cells (Procell, Cat# CM-0005) were cultured in DMEM (Gibco, Cat# 12800082) supplemented with 10% FBS, 1% penicillin-streptomycin.

Techniques: Binding Assay, SPR Assay, Recombinant, Incubation, Control, Transfection, Plasmid Preparation, Quantitative Proteomics, Silver Staining