Guiding premise of the experiments and comparison of various polyborates.

<p>(a) Intra-molecular Lewis acid complex formation between boronic species and non-vicinal phosphate groups, located far apart on DNA backbone, leads to a lower gel apparent length. A structural diagram of a region of a single strand of duplex DNA and a smaller schematic cartoon of two duplex DNA fragments illustrate the molecular and topological consequences of complexation. Additional complexes, not depicted here, form due to hydroxyl groups in agarose matrices; in such gels, DNA-borate-agarose complexes are expected. (b) Saturation of DNA backbone with the boronic species prevents intra-molecular Lewis acid complexation. (c) Polyborates are formed at high boric acid concentrations. Mass-to-charge ratio increases and electromobility decreases (denoted by upward arrow) with the number of borates in each complex.</p

Evidence for Lewis acid complexation and improved borate electrophoresis at pH 6.5.

<p>DNA fragments of 4 kb, 1 kb and 200 bp are marked by arrowheads approximating the leading edges of the bands, and the 12 kb band is marked at the center of the lagging edge. The sizes of all fragments of the ladder were, in bp, 100, 200, 300, 400, 500, 650, 850, 1000, 1650, and 2000 through 12,000 in 1000-bp increments. (a) Electrophoretic separation for anions of differing Lewis acid character. (b) Separation using borates at different pHs, given a constant migration for the 200 bp band. (c) Separation (in 2% agarose) of bands from 100 bp to 1000 bp in 6.5 pH borate.</p

Compression ratios for anions tested and comparison of borate buffers at different pHs.

<p>(a) Compression ratios for various anions and borates at different pH. For the similar germanium compounds, the ramp above their data depicts that the hydroxide is expected to have the greater Lewis acid character. For the incremental linear chain carboxylic acid series (formate, acetate, propionate), the ramps above their data similarly depict that formate has the highest, and acetate the second-highest, expected Lewis acid character among this series. The ramps do not pertain to the other histogram data. (b) Conductivity of the buffer as a function of time, measured as current at constant voltage of 350 V. (c) Temperature in the anodic chamber as a function of time. (d) Electrophoretic run speed, represented as the distance traveled from the well by 12 kb and 1.6 kb bands in an 80 min run.</p

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Additional file 3: Figure S3. Ki67 staining. BRCA1mut and Non-Carrier organoids were stained with Ki67 to measure proliferation

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Additional file 1: Figure S1. Immunofluorescent co-staining in BRCA1mut and Non-carrier organoids. Immunofluorescent staining was done for ER (red) and PR (red) along with myoepithelial/basal marker αSMA (green) and DAPI (blue) to visualize the nuclei. Scale bar, 100 μm

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Additional file 6: Figure S6. Notch signaling GSEA plot. Notch signaling signature genes are positively enriched in the BRCA1mut organoids treated with E2+P4 (N=4) versus Non-carrier organoids treated with E2+P4 (N=4). p=0.22, NES=1.23

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Additional file 2: Figure S2. Immunofluorescent negative controls. BRCA1mut and Non-Carrier organoids were fluorescently stained with no primary antibody and Alexa-Fluor 555 (red) and 488 (green) secondary antibody and DAPI (blue) to visualize the nuclei. Scale bar, 100 μm

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Additional file 8: Table S1. Patient information

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Additional file 4: Figure S4. Correlation between top 3% most variant genes in comparison groups. Normalized expression mean of Non-carrier E2+P4 (N=4) vs BRCA1mut E2+P4 (N=4), Non-carrier E+ P (N=4) vs Non-carrier+TPA (N=4), BRCA1mut E2+P4 (N=4) vs BRCA1mut + TPA (N=4)

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Additional file 9: Table S2. qRT-PCR primer sequences