ISDA

Deposition Date 2024-03-15

Release Date 2024-04-24

Last Version Date 2024-05-08

Entry Detail

PDB ID:

9EOQ

Keywords:

DNA

Title:

Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

7.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (42-MER)
Chain IDs:A
Chain Length:42
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')
Chain IDs:B
Chain Length:15
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM.

Khoshouei, A, Kempf, G, Mykhailiuk, V, Griessing, J.M, Honemann, M.N, Kater, L, Cavadini, S, Dietz, H.Show

Nano Lett. 24 5031 5038 (2024)

PMID: 38602296 DOI: 10.1021/acs.nanolett.4c00915

Abstact

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.

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Primary Citation of related structures