Chemicals and materials
Silicon wafers (boron doped, p+ type, 0.01 to 0.02 Ω cm) were obtained from Siegert Wafer GmbH (Aachen, Germany). Ethanol (EtOH, 99.6 vol.%) was obtained from Altia Plc. (Porkkalankatu, Finland), and hydrofluoric acid (HF, 38%) from Merck GmbH (Darmstadt, Germany). Sulfuric acid, sodium nitrite, Griess reagent, 4-amino-5-methylamino-2′,7′-difluorofluorescein (DAF-FM), d-glucose, potassium hydroxide, and phosphate-buffered saline (PBS) tablets were purchased from Sigma-Aldrich (St. Louis, MO, USA). Tryptic soy broth (TSB; soybean-casein digest) and nutrient agar were purchased from Thermo-Scientific (Waltham, MA, USA). E. coli (ATCC #25922), P. aeruginosa (ATCC #27853), S. epidermidis (ATCC #35984), and S. aureus (ATCC #29213) were obtained from the American Type Culture Collection (Manassas, VA, USA). For mammalian cell culture, the following reagents were used as received: 0.01 M PBS pH 7.4 (Sigma-Aldrich), DMEM medium, fetal bovine serum (FBS), l-glutamine, penicillin, streptomycin, amphotericin B (all purchased from Life Technologies, Carlsbad, CA, USA), propidium iodide (PI; Sigma-Aldrich), fluorescein diacetate (FDA; Sigma-Aldrich), lactate dehydrogenase (LDH) cytotoxicity assay kit II (Abcam, Cambridge, UK), and trypsin (0.05%, EDTA 0.53 mM, Life Technologies). Cell culture media were prepared using ultrapurified water supplied by a Milli-Q system (Millipore Co., Billerica, MA, USA). NIH/3T3 mouse embryonic fibroblasts (ATCC #CRL-1658) from the American Type Culture Collection were used in these experiments.
Fabrication of THCPSi NPs
THCPSi NPs were fabricated according to the previously reported procedure  from p+ type (0.01 to 0.02 Ω cm) silicon wafers by periodically etching at 50 mA/cm2 (2.2-s period) and 200 mA/cm2 (0.35-s period) in an aqueous 1:1 HF(38%)/EtOH electrolyte for a total etching time of 20 min. Subsequently, the THCPSi films were detached from the substrate by abruptly increasing the current density to electropolishing conditions (250 mA/cm2, 3-s period). The detached multilayer films were then thermally hydrocarbonized under N2/acetylene (1:1, volume) flow at 500°C for 15 min and then cooled down to room temperature under a stream of N2 gas. The THCPSi membranes (1.3 g) were converted to NPs using wet ball milling (ZrO2 grinding jar, Pulverisette 7, Fritsch GmbH, Idar-Oberstein, Germany) in 1 decene (18 mL) overnight. A size separation was performed by centrifugation (1,500 RCF, 5 min) in order to achieve a narrow particle size distribution.
Preparation of NO/THCPSi NPs
Sodium nitrite (10 mM) dissolved in 50 mM PBS (pH 7.4) was mixed with glucose 50 mg/mL. The THCPSi NPs were then added to this buffer solution at different concentrations (ranging from 0.05 to 0.2 mg/mL). Subsequently, the suspension was sonicated for 5 min to ensure particle dispersion and then stirred for 2 h. Upon NO incorporation, the THCPSi NPs were centrifuged at 8,000 RCF for 10 min for collection. Finally, after removing the supernatant, the THCPSi NP pellet was dried by heating at 65°C overnight. The drying temperature was held at 70°C to avoid glucose caramelization [23, 33, 34]. An alternative drying procedure, overnight lyophilization (FD1 freeze dryer, Dynavac Co., MA, USA), was also assessed, as described in the text .
Glucose/THCPSi NPs and sodium nitrite/THCPSi NPs were also prepared following the same procedure as for the NO/THCPSi NPs but omitting either sodium nitrite or d-glucose during NP loading, respectively. All prepared NPs were kept at ambient conditions and were dispersed via sonication for 5 min in PBS before use.
Pore structure analysis
The pore volume, average pore diameter, and specific surface area of the THCPSi NPs were calculated from nitrogen sorption measurements on a TriStar 3000 porosimeter (Micromeritics Inc., Norcross, GA, USA).
Scanning electron microscopy
Morphological studies of THCPSi NPs were carried out by means of scanning electron microscopy (SEM) on a Quanta™ 450 FEG instrument (Hillsboro, OR, USA) by collecting secondary electrons at 30-kV beam energy under high vacuum of 6 × 10-4 Pa. Energy-dispersive X-ray spectroscopy (EDX) measurements were performed using a Link 300 ISIS instrument from Oxford Instruments (detector Si(Li), 30-kV beam energy, resolution 60 eV; Abingdon, Oxfordshire, UK). The samples were prepared by fixing the NPs to the microscope holder, using a conducting carbon strip. In order to conduct SEM and EDX analysis of NO/THCPSi NPs treated and untreated with E. coli, colonies at the desired growth stage were fixed by formaldehyde (4 v/v%) for 2 h on round graphite disks. After rinsing twice with PBS, the disks were attached on a SEM holder and were observed by using the Quanta™ 450 FEG SEM and the Link 300 ISIS EDX (Oxford Instruments).
Dynamic light scattering
The mean particle size and size distribution of NPs were determined by dynamic light scattering (DLS; Zetasizer Nano ZS, Malvern Instruments, Malvern, UK). The analysis was carried out at a temperature of 25°C using NPs dispersed in ultrapurified water. Every sample measurement was repeated 15 times.
Diffuse reflectance infrared Fourier transform (DRIFT) spectra were acquired using a Thermo Nicolet Avatar 370MCT (Thermo Electron Corporation, Waltham, MA, USA) instrument. A smart diffuse reflectance accessory was used for all samples embedded within KBr pellets. The spectra were recorded and analyzed using OMNIC version 7.3 software (Thermo Electron Corp., Waltham, MA, USA). For each spectrum, 128 scans were averaged in the range of 4,000 to 800 cm-1 with a resolution of 4 cm-1. In addition, dipole moments of the chemicals were calculated using the Millsian 2.1 Beta (Millsian, Inc., Cranbury, NJ, USA). Background spectra were blanked using a suitable clean silicon wafer. All spectra were run in dry air to remove noise from CO2 and water vapor.
Generation of NO
A calibration curve for NO was obtained by preparing a saturated solution of NO as described previously by Mesároš et al. . Briefly, 10 mL of PBS (pH 7.4) was degassed using an Ar purge for 60 min. Subsequently, NO was generated by adding 20 mL of 6 M sulfuric acid slowly to 2 g of sodium nitrite in a twin-neck round-bottom flask, which was connected via rubber tubing to a Büchner flask containing KOH solution (to remove NO degradation products, 10% v/v). The Büchner flask was then connected to the flask containing degassed PBS. The NO gas produced was bubbled through the degassed PBS (held at 4°C) for 30 min to produce a saturated NO solution. The solubility of NO in PBS at atmospheric pressure is 1.75 ± 0.02 mM [35–37]. Using Griess reagent , our solution was found to have a concentration of 1.87 mM at 37°C.
Colorimetric assay of nitrite
The presence of nitrite compounds can be detected by the Griess reaction, which results in the formation of a characteristic red pink color. Nitrites react with sulfanilic acid to form a diazonium salt, which then reacts with N-alpha-naphthyl-ethylenediamine to form a pink azo dye [38, 39]. A calibration curve was prepared using dilutions of sodium nitrite between 0.43 and 65 μM in PBS (pH 7.4, temperature 37°C) mixed with equal volumes of the prepared Griess reagent according to the manufacturer’s instructions. The absorbance of the solutions at 540 nm was measured on a HP8453 PDA UV/VIS spectrophotometer (Agilent, Santa Clara, CA, USA).
Fluorimetric determination of NO
To detect the release of NO from PSi NP, the DAF-FM assay was used. DAF-FM is non-fluorescent until it reacts with NO to form a fluorescent benzotrizole. DAF-FM possesses good specificity, sensitivity (approximately 3 nM) and is simple to use [23, 36]. It does not react with the other nitrogen oxides (i.e., NO2- and NO3-) and reactive oxygen species (i.e., O2- and H2O2) .
Fluorescence spectra for all samples were acquired using a LS 55 spectrofluorometer (PerkinElmer, Waltham, MA, USA) with slit widths set at 2.5 nm for both excitation and emission; the photomultiplier voltage was set to 775 V, and a wavelength of 495 nm was used for excitation and 515 nm for emission. In order to prepare an approximate 1 mM stock DAF-FM solution, 1 mg of DAF-FM was dissolved in 250 μL DMSO and then the stock solution (10 μL) was mixed with 90 μL PBS (pH 7.4). Fluorescence was expressed as arbitrary fluorescence units and was measured at the same instrument settings in all experiments.
For the fluorescence-based measurements of NO concentration, a calibration curve was prepared using dilutions of saturated NO solution in PBS between 0.00 and 1.87 mM in PBS (pH 7.4, 37°C). Fresh DAF-FM stock solution was added to the PBS and immediately mixed in an Eppendorf tube in the darkness using a shaker for 2 min and then transferred into a quartz cuvette with a stopper, and the fluorescence was measured after a 5-min incubation.
Nitric oxide release from NO/THCPSi NPs
The prepared NO/THCPSi NPs (0.1 mg/mL) were added to PBS (1 mL), sonicated, and mixed using a test tube shaker. After incubation at 37°C for the sampling interval times specified in the text, the NPs were centrifuged at 12,000 RCF for 5 min and then the supernatant containing the released NO from the NPs was separated and pre-incubated with 2 μL DAF-FM solution (approximately 1 mM) for 2 min at room temperature in the darkness on a test tube shaker (approximately 0.1 RCF). The supernatant containing NO and DAF-FM was subsequently transferred into a cuvette, and fluorescence intensities were measured as described above. The amount of the released NO was calculated using the fluorimetric DAF-FM calibration curve.
Determination of antimicrobial activity
P. aeruginosa, E. coli, and S. aureus were cultured overnight at 37°C in TSB and diluted to a concentration of 108 colony-forming units per milliliter (CFU/mL) based on turbidity (OD600) and further diluted to 104 CFU/mL and 1 mL treated with different concentrations of NO/THCPSi NPs or glucose/THCPSi NPs (control). As a further control, NO/THCPSi NPs (0.1 mg/mL) were added to 0.5 mL of PBS, sonicated for 5 min and then incubated for 2 h to remove NO, centrifuged (12,000 RCF for 5 min), and NO-depleted NO/THCPSi NPs dried at 65°C overnight. Bacteria not treated with NPs were used as negative controls in each experiment.
The NP samples were incubated for 2 h, 4 h (S. aureus; 0.05, 0.1, or 0.2 mg/mL concentration of NPs), and 24 h (P. aeruginosa, E. coli, and S. aureus; 0.1 mg/mL concentration of NPs) at 37°C. S. aureus were then serially diluted and spread-plated on nutrient agar. Bacterial viability was assessed by counting the number of colonies formed on the agar plate. The colony count was normalized by considering the untreated colony (negative) as 100% of bacteria viability. The viability of E. coli and P. aeruginosa after 24 h was determined by turbidity measurements (OD600nm), taking into account background caused by the NPs themselves.
Effect of NO/THCPSi NPs on established biofilms
The reduction in total viable cells recovered from established S. epidermidis biofilms treated with NO/THCPSi NPs was compared to the control biofilms of the same species not treated with the NPs. Glass microscope slides were cut into pieces with surface areas of 24 mm2. The glass pieces were cleaned with 70% ethanol and dried. S. epidermidis was cultured at 37°C in TSB overnight and diluted to 106 CFU/mL. The 106 CFU/mL microbial suspension was then added to each tube containing the glass slide pieces. The vials containing bacteria, broth, and glass slide pieces were placed in a 37°C incubator for biofilm formation. After 24 h, the glass slide pieces were removed from the nutrient broth, rinsed twice in sterile PBS, and individually transferred into new Eppendorf tubes containing a fresh suspension 1 mL of 0.1 mg/mL NO/THCPSi NPs and THCPSi NPs (control) in PBS and returned to the 37°C incubator. After 24 h, the tubes containing glass slide pieces were sonicated in a 125-W ultrasonic cleaner for 5 min to remove the biofilm-forming cells from the slide. The resulting bacterial suspension was subjected to serial tenfold dilutions, and 100 μL of appropriate dilutions was plated onto agar plates, which were then incubated at 37°C overnight. The total number of colonies that grew on each plate was counted, and the number of viable biofilm bacteria removed from each slide was determined.
Mammalian cell viability assay
The cytotoxicity of the NO/THCPSi NPs was evaluated using NIH/3T3 fibroblast cells. The cells were maintained in DMEM supplemented with 10% FBS and 2 mM l-glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, and incubated at 37°C with 5% CO2.
All mentioned procedures for the preparation of NO/THCPSi NPs and glucose/THCPSi NPs were done under sterile conditions within a biological safety cabinet (Bio-cabinet, Aura 2000, Microprocessor Automatic Control, Firenze, Italy).
The NIH/3T3 cells were trypsinized and then seeded into polystyrene 96-well plates (Nalge Nunc International, Penfield, NY, USA) at a density of 3 × 104 cells/mL and then after 24 h, the cultured cells were incubated with NO/THCPSi NPs, glucose/THCPSi NPs, and THCPSi NPs at four different concentrations from 0.05 to 0.2 mg/mL for 48 h.
After the incubation period, the culture medium was separated from the cultured cells and subjected to a LDH assay that was carried out following the manufacturer’s instructions. Moreover, a FDA-PI assay was performed on the cultured cells remaining in the wells. The cells were incubated with fresh medium before adding final concentrations of 15 μg/mL FDA and 5 μM PI for 3 min at 37°C to count the live and dead cells, respectively, using a fluorescence microscope (Eclipse, Ti-S, Nikon, Tokyo, Japan) and determine the percentage of live cells. All experiments were repeated at least three times.
For the NO release tests and bactericidal assays conducted in the related media, n = 3 and the data are expressed as mean values ± standard deviation. Statistical significance between populations was determined by one-way ANOVA followed by Tukey’s multiple comparison post hoc analysis (GraphPad Prism® software). Data from both the FDA-PI and LDH cytotoxicity assays are presented as mean values ± standard error of the mean.