Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

7NPN

B-brick bare in 5 mM Mg2+

This is a non-PDB format compatible entry.
Summary for 7NPN
Entry DOI10.2210/pdb7npn/pdb
EMDB information12467 12468 12469 12470 12471 12472 12473 12474 12475 12476 12516
DescriptorSCAFFOLD STRAND, STAPLE STRAND, ... (79 entities in total)
Functional Keywordsdna origami, dna
Biological sourcesynthetic construct
More
Total number of polymer chains79
Total formula weight1847040.38
Authors
Bertosin, E.,Stoemmer, P.,Feigl, E.,Wenig, M.,Honemann, M.,Dietz, H. (deposition date: 2021-02-27, release date: 2021-03-31, Last modification date: 2024-07-10)
Primary citationBertosin, E.,Stommer, P.,Feigl, E.,Wenig, M.,Honemann, M.N.,Dietz, H.
Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures.
Acs Nano, 15:9391-9403, 2021
Cited by
PubMed Abstract: Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), pseudoatomic model fitting, and single-molecule mass photometry to study oligolysine and polyethylene glycol (PEG)-oligolysine-coated multilayer DNA origami objects. The coatings preserve coarse structural features well on a resolution of multiple nanometers but can also induce deformations such as twisting and bending. Higher-density coatings also led to internal structural deformations in the DNA origami test objects, in which a designed honeycomb-type helical lattice was deformed into a more square-lattice-like pattern. Under physiological ionic strength, where the uncoated objects disassembled, the coated objects remained intact but they shrunk in the helical direction and expanded in the direction perpendicular to the helical axis. Helical details like major/minor grooves and crossover locations were not discernible in cryo-EM maps that we determined of DNA origami coated with oligolysine and PEG-oligolysine, whereas these features were visible in cryo-EM maps determined from the uncoated reference objects. Blunt-ended double-helical interfaces remained accessible underneath the coating and may be used for the formation of multimeric DNA origami assemblies that rely on stacking interactions between blunt-ended helices. The ionic strength requirements for forming multimers from coated DNA origami differed from those needed for uncoated objects. Using single-molecule mass photometry, we found that the mass of coated DNA origami objects prior to and after incubation in low ionic strength physiological conditions remained unchanged. This finding indicated that the coating effectively prevented strand dissociation but also that the coating itself remained stable in place. Our results validate oligolysine coatings as a powerful stabilization method for DNA origami but also reveal several potential points of failure that experimenters should watch to avoid working with false premises.
PubMed: 33724780
DOI: 10.1021/acsnano.0c10137
PDB entries with the same primary citation
Experimental method
ELECTRON MICROSCOPY (10.38 Å)
Structure validation

227561

PDB entries from 2024-11-20

PDB statisticsPDBj update infoContact PDBjnumon