Journal: The Journal of Biological Chemistry

Article Title: PhuS conformational dynamics are essential for DNA binding and heme-responsive control of the prrF operon in Pseudomonas aeruginosa

doi: 10.1016/j.jbc.2026.111314

Figure Lengend Snippet: Characterization of the heme binding properties of the PhuS R25 A variant . A , CD spectra of 10 μM apo-proteins ( left panel ) and holo-proteins ( right panel ) dialyzed in 1 mM potassium phosphate (pH 7.4). PhuS WT and PhuS R25 A spectra shown in blue and red, respectively. B , UV-Visible spectra of holo-WT and holo-R25 A protein in 20 mM Tris (pH 8.0) containing 150 mM NaCl. C , Tryptophan fluorescence quenching of WT PhuS and R25A PhuS. 1 μM of apo-WT PhuS or apo-R25 A PhuS was titrated with increasing concentrations (0 μM–12.8 μM) of heme. Samples were excited at 295 nm and emission was monitored at 337 nm. Relative binding was calculated by dividing the difference in fluorescence by the initial unbound fluorescence emission. The binding constant (K d ) was fit to a one-site binding model in Graphpad Prism by plotting relative binding as a function of heme concentration.

Article Snippet: 30 PM of oligonucleotides were added and incubated further at 37 ̊C for another 20 min. After the incubation, the protein-DNA binding reactions were run on a 10% Tris glycine polyacrylamide native gel (Bio-Rad).

Techniques: Binding Assay, Variant Assay, Circular Dichroism, Fluorescence, Concentration Assay

Journal: bioRxiv

Article Title: In Vivo Selection of anti-glioblastoma DNA aptamer-drug conjugates in an orthotopic patient-derived xenograft model

doi: 10.64898/2026.02.16.706148

Figure Lengend Snippet: A. Chemical structure of PEG4-Val-Cit-PAB-MMAE conjugated to the 5’ end of a DNA aptamer. B. A polyacrylamide denaturing gel post-stained with SYBR gold showing that MMAE-PAB-Val-Cit-PEG4 can be conjugated to DNA primers by trans-cyclooctene-tetrazine (TCO-Tz) click chemistry. C. Confirmation of MMAE structural stability by LC-MS following 20 rounds of thermal cycling conditions. ISTD= internal standard D. Confirmation that Taq polymerase could incorporate a 5’MMAE conjugated DNA primer. Two PCR reactions were run: one with an unmodified forward primer (lanes 2-6) and one with 5’MMAE conjugated forward primer (lanes 7-11). Samples were taken throughout the PCR reaction and run on a native polyacrylamide gel and post-stained with SYBR gold. p=primers, mp = 5’MMAE conjugated primer, and *=amplicon

Article Snippet: Solutions were subjected to electrophoresis through 8% native polyacrylamide gels (29:1 acrylamide:bisacrylamide Bio-Rad #1610146) and stained with SYBR gold (Invitrogen #S11494).

Techniques: Staining, Liquid Chromatography with Mass Spectroscopy, Amplification

Journal: bioRxiv

Article Title: In Vivo Selection of anti-glioblastoma DNA aptamer-drug conjugates in an orthotopic patient-derived xenograft model

doi: 10.64898/2026.02.16.706148

Figure Lengend Snippet: A. A schematic diagram of the in vivo SELEX with an ApDC library. B. Native polyacrylamide gel shift assay detecting the presence of MMAE with an anti-MMAE antibody in the naïve library used for Round 1 and the final library used for Round 10. -F = free library, -S = shifted library due to anti-MMAE antibody-ApDC complex C. Top 10 sequences by area under the curve at Round 10 from NGS. D. Biodistribution of the top 5 sequences identified at Round 10 in the Round 10 mouse.

Article Snippet: Solutions were subjected to electrophoresis through 8% native polyacrylamide gels (29:1 acrylamide:bisacrylamide Bio-Rad #1610146) and stained with SYBR gold (Invitrogen #S11494).

Techniques: In Vivo, Gel Shift

Journal: bioRxiv

Article Title: In Vivo Selection of anti-glioblastoma DNA aptamer-drug conjugates in an orthotopic patient-derived xenograft model

doi: 10.64898/2026.02.16.706148

Figure Lengend Snippet: Mice were injected I.P. with 350 µl of 1 µM ApDC/aptamer cocktail (50 pmol per sequence) or vehicle. The cocktail was composed of the 5 top ApDC candidates, a scrambled sequence of ApDC 1, and the negative control aptamer sequence used in our previous in vivo SLELEX. 4 h post-injection, the mice were euthanized and thoroughly perfused prior to organ harvest. Tumor was detected by GFP positive staining. Aptamers were isolated from organs and detected with sequence specific PCR primers. A. Denaturing polyacrylamide gel stained with SYBR gold confirming the size shift and purity of the ApDCs in the cocktail injected into the mice. B. The amount of ApDCs and negative control aptamer detected in the GFP positive brain tumor. C. Comparison of the levels of ApDCs detected in the brain tumor compared to other areas of the brain. D. Levels of aptamer detected in tissues sensitive to anti-tubulin agents like MMAE. E. Whole organ biodistribution of the candidates across 5 mice. *= comparison to ApDC 6. ‡ = comparison to Ap 7. *p<0.05; **p<0.01, ***p<0.001, and ****p<0.0001.

Article Snippet: Solutions were subjected to electrophoresis through 8% native polyacrylamide gels (29:1 acrylamide:bisacrylamide Bio-Rad #1610146) and stained with SYBR gold (Invitrogen #S11494).

Techniques: Injection, Sequencing, Negative Control, In Vivo, Staining, Isolation, Comparison