Quantum energy filter

Samples were analyzed using a NanoWizard ULTRA Speed AFM (JPK Instruments) mounted on an inverted optical microscope (Nikon Eclipse TE2000-U or Zeiss AxioObserver.A1), or equipped with a JPK TopViewOptics. Samples were imaged in buffer at ambient temperature in amplitude-modulation or phase-modulation AC mode. Fast-scanning high-resonant ultra-short cantilevers (USC-F0.3-k0.3, NanoWorld) with a nominal resonance frequency of 300 kHz in air, spring constant of 0.3 N/m, reflective chromium/gold-coated silicon chip, and high-density carbon tips with a radius of curvature of 10 nm were used. Prior to deposition on substrate, RNA and HBDs molecules were incubated in filtered nuclear-like buffer (NLB; 5 mM NaCl, 140 mM K⁺, 0.5 mM Mg²⁺, 10⁻⁴ mM Ca²⁺, pH = 7.2) for 30 min at 37°C. For cryo-EM, HOTAIR-bearing grids were plunge-frozen in liquid ethane cooled by liquid nitrogen, using a Leica EM-GP plunger (4 sec blotting time, 80% humidity), and imaged at liquid nitrogen temperature on an FEI Tecnai TF20 electron microscope operated at 200 kV with a Gatan side entry 626 cryo-holder. Images were recorded on a K2 Summit direct detector (Gatan) mounted at the end of a GIF Quantum energy filter (Gatan). Images were collected in counting mode, at a calibrated magnification of 16,218 yielding a pixel size of 3.083 Å. Additional detailed methods can be found in the Supplemental Notes.