Journal: Scientific Reports

Article Title: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

doi: 10.1038/s41598-021-90629-1

Figure Lengend Snippet: Circular dichroism (CD) spectra of tC (green), tC O (red), 2CNqA (blue), pA (dark gray), Cy3 (violet), and unmodified U (black dotted line) gapmers hybridized to the RNA target T. The duplex concentration was 4 µM and the spectra were collected at 10–15 °C to ensure full hybridization. Insets: A zoom-out indicating the region (black rectangle) of the main figure. ( a ) Single-labeled gapmers. ( b ) Double-labeled gapmers. To illustrate the similarity to the A-form CD signature, an RNA:RNA duplex (red dashed line, normalized, see Material and Methods section for sequence) is included.

Article Snippet: For knockdown analysis of the gapmers, 384-well plates coated with Poly-D-Lysin (Corning, 354,663) were seeded with 7,000 HEK 293-GLP1R cells in 35 μL per well.

Techniques: Circular Dichroism, Concentration Assay, Hybridization, Labeling, Sequencing

Journal: Scientific Reports

Article Title: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

doi: 10.1038/s41598-021-90629-1

Figure Lengend Snippet: Normalized UV–vis absorption spectra (solid lines) and emission spectra (dashed lines) of the tC-2 (green), tC O -2 (red), 2CNqA-2 (blue), pA-2 (black), and Cy3 (violet) gapmers.

Article Snippet: For knockdown analysis of the gapmers, 384-well plates coated with Poly-D-Lysin (Corning, 354,663) were seeded with 7,000 HEK 293-GLP1R cells in 35 μL per well.

Techniques:

Journal: Scientific Reports

Article Title: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

doi: 10.1038/s41598-021-90629-1

Figure Lengend Snippet: Fluorescence quantum yield (Φ F , red bars) and lifetime (τ F , green bars) of the single-stranded (plain bars) and RNA-bound (striped bars) gapmers. Presented values are mean ± standard deviation from two independent replicates. The corresponding numeric data are provided in Supplementary Table .

Article Snippet: For knockdown analysis of the gapmers, 384-well plates coated with Poly-D-Lysin (Corning, 354,663) were seeded with 7,000 HEK 293-GLP1R cells in 35 μL per well.

Techniques: Fluorescence, Standard Deviation

Journal: Scientific Reports

Article Title: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

doi: 10.1038/s41598-021-90629-1

Figure Lengend Snippet: Confocal microscopy images of live HEK 293 T cells continuously exposed to unformulated gapmers (3 µM) for 24 h. Samples were excited at 405 nm (emission: 407–700 nm) for FBA detection and at 561 nm (emission: 563–700 nm) for Cy3 detection. Scale bars are 20 µm.

Article Snippet: For knockdown analysis of the gapmers, 384-well plates coated with Poly-D-Lysin (Corning, 354,663) were seeded with 7,000 HEK 293-GLP1R cells in 35 μL per well.

Techniques: Confocal Microscopy