ISDA

Entry Detail

PDB ID:

7UL8

Keywords:

DNA

Title:

[T:Au+:T--pH 11] Metal-mediated DNA base pair in tensegrity triangle

Biological Source:

Source Organism:

synthetic construct

PDB Version:

Deposition Date:

2022-04-04

Release Date:

2023-04-05

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

4.22 Å

R-Value Free:

0.34

R-Value Work:

0.25

R-Value Observed:

0.26

Space Group:

H 3

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
Chain IDs:A
Chain Length:21
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3')
Chain IDs:B
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
Chain IDs:C
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
Chain IDs:D
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.

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, 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.Show

Adv Mater 35 e2210938 e2210938 (2023)

PMID: 37268326 DOI: 10.1002/adma.202210938

Abstact

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ 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.

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Primary Citation of related structures