Imaging was performed with a
MultiMode AFM Nanoscope IV system (Bruker Instruments, Santa Barbara, CA, USA) in tapping mode under ambient conditions. The images were recorded at a scanning rate of 1.5 Hz using an
RTESPA-300 probe (Bruker Nano Inc., CA, USA) with a resonance frequency of ∼320 kHz and a spring constant of ∼40 N/m. Images were processed using the FemtoScan Online software package (Advanced Technologies Center, Moscow, Russia). Only nonoverlapping ring structures were used for analysis to avoid any influence of possible distortion due to the close proximity of other nanostructures. The cross-sectional tool was used to analyze a distance through the center of a close-up specific ring structure. Two orthogonal cross sections were taken vertically and horizontally to the image orientation. The maximum-to-maximum distance in the cross section was measured, which reports on the distance between segments of nucleic acids in the RNA ring assembly. The deformation factor (DF) was calculated as the ratio of the longer measured distance to the shorter one. The DF was then plotted as a histogram for various designs of the RNA ring nanoassemblies.
Sajja S., Chandler M., Fedorov D., Kasprzak W.K., Lushnikov A., Viard M., Shah A., Dang D., Dahl J., Worku B., Dobrovolskaia M.A., Krasnoslobodtsev A., Shapiro B.A, & Afonin K.A. (2018). Dynamic Behavior of RNA Nanoparticles Analyzed by AFM on a Mica/Air Interface. Langmuir : the ACS journal of surfaces and colloids, 34(49), 15099-15108.