DSSR-enabled G4 identification/annotation

PDB-id: 9eoq
Class: DNA
Method: cryo-EM (7.5 Å)
Summary: cryo-EM structure of a 1033 scaffold base DNA origami nanostructure v4 and tba
Reference: Khoshouei A, Kempf G, Mykhailiuk V, Griessing JM, Honemann MN, Kater L, Cavadini S, Dietz H (2024): "Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM." Nano Lett., 24, 5031-5038. doi: 10.1021/acs.nanolett.4c00915.
Abstract: DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.
G4 notes: 1 G-tetrad

 1 type=lateral   helix=#-1 nts=4 GTAG A.DG16,A.DT17,A.DA18,A.DG19
 2 type=lateral   helix=#-1 nts=7 GGGCAGG A.DG19,A.DG20,A.DG21,A.DC22,A.DA23,A.DG24,A.DG25
 3 type=lateral   helix=#-1 nts=4 GTTG A.DG25,A.DT26,A.DT27,A.DG28

DSSR-enabled G4 identification/annotation: PDB entry 9eoq

Summary information and primary citation

Cartoon-block schematics in six views (download the tarball)

List of 1 G-tetrad

List of 3 non-stem G4-loops (including the two closing Gs)