8E4D

[U:Ag+:U] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice

Summary for 8E4D

• Entry DOI: 10.2210/pdb8e4d/pdb
• Related: 7SD8
• Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*A)-3'), DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3'), ... (5 entities in total)
• Functional Keywords: tensegrity triangle, self-assembling crystal, metal-mediated mismatch, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 12867.23

Authors

Vecchioni, S.,Lu, B.,Seeman, N.C.,Sha, R.,Ohayon, Y.P. (deposition date: 2022-08-18, release date: 2023-04-05, Last modification date: 2024-04-03)

Primary citation

Vecchioni, S.,Lu, B.,Livernois, W.,Ohayon, Y.P.,Yoder, J.B.,Yang, C.F.,Woloszyn, K.,Bernfeld, W.,Anantram, M.P.,Canary, J.W.,Hendrickson, W.A.,Rothschild, L.J.,Mao, C.,Wind, S.J.,Seeman, N.C.,Sha, R.
Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.
Adv Mater, 35:e2210938-e2210938, 2023

PubMed Abstract: DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag and Hg ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

PubMed: 37268326
DOI: 10.1002/adma.202210938

Experimental method

X-RAY DIFFRACTION (4.19 Å)