8UY5

[ZP] Self-assembling DNA crystal with expanded genetic code using C,A,T,G, Z and P nucleotides

Summary for 8UY5

• Entry DOI: 10.2210/pdb8uy5/pdb
• Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*(DP)P*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*GP*TP*AP*(DZ)P*A)-3'), DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3'), ... (4 entities in total)
• Functional Keywords: tensegrity triangle, dna nanotechnology, synthetic biology, aegis, dna, zp
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 12841.43

Authors

Vecchioni, S.,Sha, R.,Ohayon, Y.P.,Hernandez, C. (deposition date: 2023-11-13, release date: 2025-01-22)

Primary citation

Vecchioni, S.,Ohayon, Y.P.,Hernandez, C.,Hoshika, S.,Mao, C.,Benner, S.A.,Sha, R.
Six-Letter DNA Nanotechnology: Incorporation of Z - P Base Pairs into Self-Assembling 3D Crystals.
Nano Lett., 24:14302-14306, 2024

PubMed Abstract: Artificially expanded genetic information systems (AEGIS) were developed to expand the diversity and functionality of biological systems. Recent experiments have shown that these expanded DNA molecular systems are robust platforms for information storage and retrieval as well as useful for basic biotechnologies. In tandem, nucleic acid nanotechnology has seen the use of information-based "semantomorphic" encoding to drive the self-assembly of a vast array of supramolecular devices. To establish the effectiveness of AEGIS toward nanotechnological applications, we investigated the ability of a six-letter alphabet composed of A:T, G:C and synthetic : (, 6-amino-3-(1'-β-d-2'-deoxy ribofuranosyl)-5-nitro-(1)-pyridin-2-one; , 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-(8)-4-one) base pairs to engage in 3D self-assembly. We found that crystals could be programmably assembled from AEGIS oligomers. We conclude that unnatural base pairs can be used for the topological self-assembly of crystals. We anticipate the expansion of AEGIS-based nucleic acid nanotechnologies to enable the development of novel nanomaterials, high-fidelity signal cascades, and dynamic nanoscale devices.

PubMed: 39471314
DOI: 10.1021/acs.nanolett.4c03949

Experimental method

X-RAY DIFFRACTION (3.562 Å)