Detailed DSSR results for the G-quadruplex: PDB entry 8tvz

PDB id

8tvz

Class

RNA

Method

cryo-EM (5.94 Å)

Summary

RNA origami 3-helix tile traptamer

Reference

Vallina NS, McRae EKS, Geary C, Andersen ES (2024): "An RNA origami robot that traps and releases a fluorescent aptamer." Sci Adv, 10, eadk1250. doi: 10.1126/sciadv.adk1250.

Abstract

RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems.

G4 notes

1 G-tetrad

 1 glyco-bond=--ss sugar=-3-3 groove=-w-n planarity=0.426 type=other  nts=4 GGGG C.G94,C.G98,C.G277,C.G272

 1 type=lateral   helix=#-1 nts=5 GUCGG C.G94,C.U95,C.C96,C.G97,C.G98
 2 type=lateral   helix=#-1 nts=6 GUAGAG C.G272,C.U273,C.A274,C.G275,C.A276,C.G277