Synthesis of aptamer-paclitaxel conjugates: The AS1411-PTX were synthesized as described in supporting information. Briefly, redox-responsive di-acids were constructed firstly. Then, the di-acids were conjugated to PTX, to afford carboxylic acid derivatives. Subsequently, the carboxylic acid derivatives obtained were further conjugated to amino-DNA. This conjugation process resulted in the formation of diverse types of aptamer-paclitaxel conjugates (ApDCs).
Drug release assays: ApDCs (0.15 nmol) was dissolved in PBS (0.1×, 60 µL), DTT (10 mM, 60 µL) and H2O2 (1 mM, 60 µL), respectively. The mixture was incubated at 37 °C. At timed intervals, the intact ApDCs were assayed utilizing an Agilent 1290 HPLC system along with UV detector set at 260 nm. Phase A was ACN, and phase B was TEAA (50 mM). The gradient was run from 2% to 55% of phase A in 30 minutes for the YMC-Triart C18 column (3 mm, 150 mm×4.6 mm) at a flow rate of 0.5 mL·min-1 with ambient column temperature. The percentage of intact ApDCs was normalized with the initial amount treated as 100%.
CCK-8 assay for cell viability: To identify the most efficient ApDC in tumor cells, the cell viability assay will be conducted using a Cell Counting Kit-8 (CCK8, Dojindo). According to the provided protocol, MDA-MB-231, 4T1, SKOV-3, MIHA, MCF7, MCF10A cells will be seeded in 96-well plates with approximately 5,000 cells in each well and incubated overnight for adherence. Solutions of ApDCs and controls will be made up in medium. The media of cells will be removed, and the solutions will be added for 72 h incubation at 37 °C. At the end of the incubation, 100 µL of culture medium containing 10% of CCK8 solution will be added to each well. The plates will be read after additional 2 h incubation by a spectrometer at 450 nm.
Cellular apoptosis assays: To analyze the different phases of apoptosis, cells were seeded in 6-well plates and treated with ApDCs and corresponding controls for 48 h, respectively. Following the treatment period, cells were harvested, rinsed with cold PBS, and resuspended in 100 μL 1× Annexin-V binding buffer. Next, 5 μL Annexin-V–FITC (fluorescein isothiocyanate) and 5 μL PI (propidium iodide) were added to the cell suspension and incubated at room temperature for 15 min in the dark with gentle vertexing. Quantitative determination was performed using a flow cytometer. By analyzing the fluorescence signals obtained from the flow cytometer, we were able to assess the proportion of cells undergoing early apoptosis (Annexin-V positive, PI negative), late apoptosis (Annexin-V positive, PI positive), and necrosis (PI positive) in response to the treatment with ApDCs and respective controls.
ELONA for relative binding ability: To analyze the binding ability of the modified AS1411 to nulceolin,160 ng nucleolin protein was coated to 96-well microtiter plate in SELEX B&W buffer (1 mM MgCl2 and 0.05% Tween 20 in 1×PBS, 100 µL) by incubating at 4 °C overnight. The plate was then blocked with blocking buffer (0.1% Tween 20 and 1% BSA in 1×PBS) for 1 h at room temperature and washed with SELEX B&W buffer for 4 times. Then, biotinylated aptamers (1 μM) in SELEX B&W buffer (100 µL) were added into each well and incubated for 45 min at room temperature with continuous gentle shaking. After binding, the plate was washed with SELEX B&W buffer for 4 times to remove non-specific and very weak binding. 0.01% streptavidin-HRP (100 µL) was added to each well and incubated for 30 min and washed with washing buffer (1 mM MgCl2, 0.1% Tween 20 and 0.1% BSA in 1×PBS, 100 µL) for 4 times. TMB (50 µL) was added to each well and incubated for 20 min. The reaction was stopped by adding H2SO4 (2 M, 50 µL). Absorbance at 450 nm was measured with microplate reader. The absorbance of modified AS1411 was normalized to unmodified AS1411 with the initial amount treated as 100%.
SPR assay for binding affinity: The nucleolin protein was immobilized onto a CM5 chip according to manufacturer′s protocol. Briefly, the surface of chip was activated using a mixture of 0.5 M N-hydroxysuccinimide (NHS) and 0.1 M 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) in a 1:1 volume ratio, followed by addition of nucleolin diluted in 10 mM sodium acetate (pH=5.0). For the interaction analysis between ApDCs and nucleolin, ApDCs were diluted with 1×PBS ranged from 0.156-10 mM. Seven consecutive injections of equal volume were performed to ensure the same binding signals, followed by regeneration using 50 mM sodium hydroxide (NaOH). The sodium hydroxide (Kd) was determined using a GE Biacore X100 SPR System.
Confocal assays for cellular endocytosis: MDA-MB-231 cells were seeded in a 24-well plate at a density of 2 × 105 cells per well and incubate overnight. Then, the cells were incubated with Cy5-labeled AS1411, FA, ASP and FASP, each at a concentration of 250 nM. The cells were then incubated at 37 °C for a duration of 4 hours to allow for aptamer internalization. During the final 15 minutes of the incubation period, a volume of 2 μg·mL−1 Hoechst 33342 (blue) then was added to the cells. Following the incubation, the cells were carefully washed to remove any unbound or extracellular aptamers. Subsequently, the cells were visualized using confocal microscopy.
FCM assays for cellular uptake: MDA-MB-231, MCF7 and MCF10A cells were seeded in a 10 cm dish at a density of 2.0 × 105 cells and incubated overnight. The cells were washed three times with PBS and harvested with Accutase. Then, the cells were treated with Cy5-labeled AS1411, FAS1411, ASP and FASP FASP at a concentration of 250 nM for 3 hours. The cellular uptake level of the FASP and controls were analyzed using flow cytometry in the APC channel.
Animal study for antitumor efficacy in vivo: The Laboratory Animal House of Hong Kong Baptist University provided housing for the mice used in this study. The animal facility maintained a regulated environment with controlled temperature and a 12-hour light/dark cycle, while food and water were freely accessible to the mice throughout the study. Prior to conducting any experiments, a minimum of one week was allocated for the mice to acclimate to their new environment. All in vivo studies were conducted in compliance with ethical guidelines and received approval from the Animal Experimentation Ethics Committee of the Hong Kong Baptist University (REC/22-23/0401).
Eight-week-old female BALB/c nude mice were inoculated subcutaneously with 1 × 107 MDA-MB-231 cells in the armpit. After tumors were observed within 3 weeks, the mice were randomly divided into three groups (seven mice in each group) for further experimentation. The mice were administered with FASP, ASP, PTX, FTSP, FUDR twice a week for three weeks via subcutaneous injection at a dosage of 1.5 µmol·kg−1, and the vehicle group was administered with equivolume of PBS. Tumor size and body weight were measured twice a week, with intervals of 3-4 days. At the end of the treatment, the mice were euthanized, and the tumors were weighted. The blood samples were obtained for biochemical analyses.
Animal study for biodistribution effect in vivo: The biodistribution studies were performed in MDA-MB-231 inoculated BALB/c nude mice. After tumors were observed within 3 weeks, the mice were randomly divided into two groups for further experimentation. The mice were administered with Cy5 labeled FASP and FTSP via subcutaneous injection at a dosage of 0.5 µmol·kg−1. After 4 hours, the mice were euthanized. The heart, liver, spleen, lung, kidney and tumor were obtained for images utilizing Imaging Station Maestro 2 (CRI, MA, USA).
Statistical analysis: All variables were expressed as mean ± standard deviation. One-way ANOVA with Tukey’s post-hoc test was performed to determine the inter-group differences in the study variables. All the statistical data were analyzed by GraphPad Prism, and P < 0.05 was considered to be statistically significant. For the in vivo experiments, the animals were grouped randomly and blindly to researchers.