Nanoscope 5 multimode 8

A Bruker Nanoscope V MultiMode 8 atomic force microscope is used with Peak-Force Tapping™ mode. In this mode, a force curve is obtained at every pixel of the image. The peak force is used as a feedback parameter in order to image topography. The sample can be scanned at lower forces and with shorter contact time, thus protecting delicate samples. For imaging in air, a silicon cantilever is used (resonance frequency = 70 kHz, spring constant = 0.4 N/m and tip radius = 2 nm). The experiments were performed at room temperature. Images are processed using Nanoscope Analysis software, which consists of subtracting the average of each line in order to remove planar artifacts. The scan range used was 1 μm × 1 μm and 2 μm × 2 μm at 512 × 512 pixels and at 1024 × 1024 pixels, respectively. To quantify the atomic force microscopy (AFM) images, DNA molecules were traced and analyzed with NCTracer, software developed by the Neurogeometry Lab at Northeastern University (22 (link),23 ).
To characterize the persistence length p of the DNA in the absence and in the presence of HMO1, orientation differences, θ, for various locations along the DNA were measured as function of contour length, L, and fit to the 2D WLC model

The optical properties of GQDs were characterized by Horiba Duetta. The time-resolved PL spectra were characterized with a Horiba FluoroMax. Raman spectra were performed by an Anton Paar Cora 5001 with 532 nm. FT-IR spectra were obtained by using a Thermo Scientific iS50. XPS spectra were assessed utilizing a Thermo ESCALAB 250Xi spectrometer. AFM images was recorded with ScanAsyst air mode using Nanoscope V Multimode 8 (Bruker).

AFM images were recorded in air by using a Nanoscope V Multimode 8 (Bruker, Santa Barbara, CA, USA) in PeakForce Tapping (PFT) mode using Scanasyst-Air probes (Bruker). Continuous force–distance curves were thus recorded with an amplitude of 100–300 nm at low frequency (1–2 kHz). PFT mode decreases the lateral and shear forces. Images were recorded at 2048 × 2048 pixels at a line rate of 1.5 Hz. Images shown in the figures are representative of three different and independent samples. The ‘particle analysis’ tool in the Nanoscope Analysis software (version 1.50) was used to determine the heights of the adsorbed mRNPs from at least three independent samples. Basically, for each particle of interest, the particle analysis tool measured the maximum height of the particle. The length of nucleoprotein filaments was measured by using the ImageJ software manually.
Indicated amounts of proteins and nucleic acids were incubated in 20 μl of binding buffer (10 mM Hepes, pH 7.5, 30 mM KCl, 1 mM Putrescine) for 5 min at room temperature. Putrescine, a natural polyamine, was added to the buffer to adsorb mRNPs on mica (36 (link)). Then, samples were deposited on the mica surface and dried. The method is described in details in ref. (36 (link)).

A Nanoscope V Multimode 8 (Bruker, Santa Barbara, CA) in PeakForce Tapping (PFT) mode using Scanasyst-Air probes (Bruker) was used to record AFM images in air. Continuous force-distance curves were thus recorded with an amplitude of 100–300 nm at low frequency (1–2 kHz). The point of using the PFT mode is to decrease the lateral and shear forces. Images were recorded at 2048 × 2048 pixels at a line rate of 1.5 Hz.
To adsorb the proteins and DNA on mica, putrescine (Pu²⁺) was added to the solution (20 mM Tris–HCl, pH 7.4 containing 25 mM KCl, 0.5 mM DTT, and 2 mM MgCl₂) to a final concentration of 1 mM, after which a 10 μL droplet was deposited on the surface of freshly cleaved mica at room temperature for 30 s and dried for AFM imaging as described previously (Singatulina et al., 2019 (link)).

Samples used for AFM analysis, including CS, WPI, and WPI-CS complexes, were prepared as described in the preceding section. AFM was performed using a Nanoscope V Multimode 8 (Bruker Corporation, USA). Data was analyzed using the NanoScope analysis software.

The Bi₂S₃ powder (99%) and Te (99.8%) were purchased from Sigma-Aldrich and used directly as evaporation sources. Bi₂S₃ and Te films were deposited using the same thermal evaporator via a standard procedure. The substrate temperature was maintained at RT, and the vacuum pressure before evaporation was ~3 × 10⁻⁶ Torr. The distance between the substrate and Bi₂S₃/Te-loaded tungsten boat was ~20 cm. The thickness of the Bi₂S₃/Te film was monitored during deposition. The as-deposited samples were then annealed at different temperatures for 30 min in a N₂-filled glove box. The crystal structures of the films on glass were analyzed using XRD with Cu Kα radiation (Bruker D8 ADVANCE). AFM images were obtained using a Nanoscope V Multimode 8 (Bruker, Newark, DE, United States of America) on Si substrates. Optical absorption spectra were obtained using a UV–visible spectrophotometer (V-770, JASCO). Samples for HRTEM characterization were prepared using a focused ion beam (FIB). The images and FFT patterns were obtained using HRTEM (JEOL JEM 2100 F). XPS analysis was performed using a PHI 5000 VersaProbe instrument (Ulvac-PHI, Japan). The depth element distribution was measured by SIMS (IMS 6 F, CAMECA). The Hall measurements of the films were performed in an N₂-filled glove box using the van der Pauw method with a 0.51 T magnet at RT.