Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 1. DNA nanostructure encoding mNeonGreen for human genome integration. (A) Graphical strategy depiction showing folding of a long unstruc- tured ssDNA into a DNA nanostructure for integration into the genome via CRISPR–Cas9-mediated HDR. (B) Schematic of a 2716-base long template encoding mNeonGreen along with regulatory elements and two 100-base homology arms for genome targeting atan intergenic site on human chromosome 9. (C) Cylindrical model and oxDNA simulations of an 18-helix bundle DNA nanostructure show a decrease in end-to-end distance from 108.98 ± 11.22 nm (ssDNA) to 29.33 ± 9.9 nm (18-helix). (D) AFM characterization of the unstructured ssDNA and the 18-helix DNA nanostructure. Scale bar: 100 nm.

Article Snippet: Imaging was performed with ScanAsyst-Air probes at a typical scan rate of around 1 Hz. oxDNA simulations Simulations of four distinct versions of 18-helix DNA nanostructured HDR templates were performed using the coarse-grained model oxDNA (25), including 50% Staples, Only Top, Open and Complex.

Techniques: CRISPR

Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 4. Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex. Scale bar: 100 nm. (C) Unstructured ssDNA and 18-helix nanostructure templates show increased knock-in efficiency compared to dsDNA. Error bars represent SDs from duplicate experiments. (D) Live cell count shows that unstructured ssDNA and 18-helix nanostructured templates display lower toxicity compared to dsDNA. Error bars represent SDs from duplicate experiments.

Article Snippet: Imaging was performed with ScanAsyst-Air probes at a typical scan rate of around 1 Hz. oxDNA simulations Simulations of four distinct versions of 18-helix DNA nanostructured HDR templates were performed using the coarse-grained model oxDNA (25), including 50% Staples, Only Top, Open and Complex.

Techniques: Knock-In, Cell Counting

Journal: BMC Molecular and Cell Biology

Article Title: Indian medicinal phytocompounds for targeting apoptosis and high-penetrance genes in triple-negative breast cancer: an in-silico exploration

doi: 10.1186/s12860-025-00548-6

Figure Lengend Snippet: Using the IMPPAT database, 300 phytochemicals were considered as potential drug candidates against cancer-related proteins (BRCA1, TP53, etc.) retrieved from the PDB. Eighty-three of these underwent ADMET and toxicity prediction. Molecular docking (using BIOVIA and AutoDock Vina) narrowed the field to six, with binding sites predicted by Protein Plus. Molecular dynamics simulations (using GROMACS) further refined the selection to one promising phytochemical, compared against an approved drug, with final trajectory analysis performed using Xmgrace

Article Snippet: Molecular Dynamics Simulation (MDS) simulations provide insights into the stability of these protein-ligand complexes under physiological conditions.

Techniques: Binding Assay, Selection