Journal: bioRxiv

Article Title: Nuclear Myosin VI stabilises Ku-associated DNA ends during nonhomologous end joining

doi: 10.64898/2026.09.01.748478

Figure Lengend Snippet: (A) Example STORM render images of MVI and Ku80 under non-treated, cisplatin treatment (65 µM 4 h) and combined Cisplatin+TIP (65 µM and 25 µM 4 h) in HeLa cells (scale bar 2 μm). The Ku80 staining denotes the nucleus region which was taken forward for cluster analysis. (B) Cluster analysis of Ku80 nuclear organisation. Individual data points correspond to the average value for a cell ROI (n = 17). ****p <0.0001 by one-way ANOVA and Tukey’s multiple comparisons test. (C) Representative colocalisation heatmap of MVI and Ku80 clusters following cisplatin treatment/ DoC values of 1 are perfectly colocalised and -1 are separated from each other. (D) Histogram of DoC scores for Ku80 colocalised with MVI and MVI colocalised with Ku80. (E) Illustration of the DNA oligonucleotide, labelled with Atto550 and AlexaFluor647, designed for an in vitro DSB. The proteins are presented in hypothetical arrangements to bridge the DNA oligonucleotides to generate a FRET signal. (F) Representation of ALEX smFRET, whereby when the two oligonucleotides diffuse into the confocal volume, the lasers alternate the excitation during the transit, allowing the determination of smFRET and the presence of both dyes. (G) Representation of photon bursts for Donor detector, Acceptor detector and the resulting FRET burst. (H) Plots of FRET efficiency vs stoichiometry for 20 pM DNA oligonucleotides in the presence of 500 nM Ku70/80, then 500 nM XRCC4 (I) and 500 nM MVI plus 1 µM F-actin (J). (K) The number of FRET bursts for each experimental condition stated. **p<0.01 ****p <0.0001 by one-way ANOVA and Tukey’s multiple comparisons test. Error bars represent SEM.

Article Snippet: Filamentous Actin was purchased from Cytoskeleton Inc (AKF99).

Techniques: Staining, In Vitro

Journal: International Journal of Molecular Sciences

Article Title: Quantum Dots Interaction with α-Actinin via Experimental Observations and Computational Predictions

doi: 10.3390/ijms27136070

Figure Lengend Snippet: Quenching of intrinsic fluorescence of α-actinin in the presence of CdSe/ZnS QDs. ( A ) The intrinsic fluorescence of α-actinin when treated with different concentrations of QDs. This experiment represents one of the triplicated experiments. ( B ) The K d estimation between α-actinin and QDs using the one site–total binding analysis. The graph represents the mean and the standard error in triplicate.

Article Snippet: For all the assays, we homogenized 50 μg α-actinin (Cytoskeleton Inc., Denver, CO, USA) in 50 μL cold sterile deionized water to prepare a stock concentration of 1 mg/mL (10 μM) and kept it on ice.

Techniques: Fluorescence, Binding Assay

Journal: International Journal of Molecular Sciences

Article Title: Quantum Dots Interaction with α-Actinin via Experimental Observations and Computational Predictions

doi: 10.3390/ijms27136070

Figure Lengend Snippet: Native PAGE of α-actinin in the presence of CdSe/ZnS QDs. ( A ) Representative Native gel of 1 µM α-actinin incubated with increasing concentrations of QDs (9–571.4 nM). ( B ) Quantification of α-actinin band intensity, where n = 3. ( C ) Graph of α-actinin band intensity decrease as QD concentration increases. Data were fitted using the Hill equation to model the apparent K d . The graph represents the mean and the standard error in triplicate. * p < 0.05, **** p < 0.0001.

Article Snippet: For all the assays, we homogenized 50 μg α-actinin (Cytoskeleton Inc., Denver, CO, USA) in 50 μL cold sterile deionized water to prepare a stock concentration of 1 mg/mL (10 μM) and kept it on ice.

Techniques: Clear Native PAGE, Incubation, Concentration Assay

Journal: International Journal of Molecular Sciences

Article Title: Quantum Dots Interaction with α-Actinin via Experimental Observations and Computational Predictions

doi: 10.3390/ijms27136070

Figure Lengend Snippet: DLS intensity distribution of ( A ) CdSe/ZnS QDs, ( B ) BSA, ( C ) BSA–QDs, ( D ) α-actinin, ( E ) α-actinin–QDs.

Article Snippet: For all the assays, we homogenized 50 μg α-actinin (Cytoskeleton Inc., Denver, CO, USA) in 50 μL cold sterile deionized water to prepare a stock concentration of 1 mg/mL (10 μM) and kept it on ice.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Quantum Dots Interaction with α-Actinin via Experimental Observations and Computational Predictions

doi: 10.3390/ijms27136070

Figure Lengend Snippet: Spin-down assay to assess α-actinin-mediated actin bundling in the presence of QDs. The assay was performed at low-speed centrifugation (7000 rpm). ( A ) SDS gel showing actin bundling assessment. The supernatant (S) and pellet (P) of each sample are located next to each other. ( B ) Quantification of the actin band intensity from the pellet of each sample, where n = 4. Statistical analysis was carried out using Dunnett’s multiple comparisons test, * p < 0.05, ** p < 0.01.

Article Snippet: For all the assays, we homogenized 50 μg α-actinin (Cytoskeleton Inc., Denver, CO, USA) in 50 μL cold sterile deionized water to prepare a stock concentration of 1 mg/mL (10 μM) and kept it on ice.

Techniques: Spin Down Assay, Centrifugation, SDS-Gel

Journal: International Journal of Molecular Sciences

Article Title: Quantum Dots Interaction with α-Actinin via Experimental Observations and Computational Predictions

doi: 10.3390/ijms27136070

Figure Lengend Snippet: Electrostatic patch placement of coated QDs on α-actinin shown via ( A ) Ribbon diagram and ( B ) Electrostatic patch model. The structure of α-actinin was generated using AlphaFold (UniProt ID: A0A5F9DPI3, ~30–40 nm length) , with the electrostatic patch model used to identify potential QD (~6 nm diameter) interaction regions. The surface coloring represents electrostatic charge distribution, where red indicates negatively charged regions, blue indicates positively charged regions and white indicates the neutral regions. While the figures indicate all the potential binding sites collectively, molecular dynamics simulation was performed with a single QD interacting with α-actinin at one patch at a time.

Article Snippet: For all the assays, we homogenized 50 μg α-actinin (Cytoskeleton Inc., Denver, CO, USA) in 50 μL cold sterile deionized water to prepare a stock concentration of 1 mg/mL (10 μM) and kept it on ice.

Techniques: Generated, Binding Assay