8D93

[2T7] Self-assembling tensegrity triangle with R3 symmetry at 2.96 A resolution, update and junction cut for entry 3GBI

Summary for 8D93

• Entry DOI: 10.2210/pdb8d93/pdb
• Related: 3GBI
• Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3'), DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3'), DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3'), ... (4 entities in total)
• Functional Keywords: tensegrity triangle, dna nanotechnology, nanomaterials, linking number, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 12797.42

Authors

Vecchioni, S.,Woloszyn, K.,Lu, B.,Sha, R.,Ohayon, Y.P.,Seeman, N.C. (deposition date: 2022-06-09, release date: 2023-01-25, Last modification date: 2023-10-25)

Primary citation

Vecchioni, S.,Lu, B.,Janowski, J.,Woloszyn, K.,Jonoska, N.,Seeman, N.C.,Mao, C.,Ohayon, Y.P.,Sha, R.
The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles.
Small, 19:e2206511-e2206511, 2023

PubMed Abstract: The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its "tensegrity" nature to its three rotationally stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two-thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed turn inter-junction segments, yielding right-handed, antiparallel, "J1" junctions. Here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one-third of a helical turn is reported. It is found that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction-the "L1" junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. A Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length is identified. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.

PubMed: 36585389
DOI: 10.1002/smll.202206511

Experimental method

X-RAY DIFFRACTION (2.96 Å)