8UY5 | pdb_00008uy5

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

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2023-11-13 Released: 2025-01-22 
  • Deposition Author(s): Vecchioni, S., Sha, R., Ohayon, Y.P., Hernandez, C.
  • Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 
    0.172 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Six-Letter DNA Nanotechnology: Incorporation of Z - P Base Pairs into Self-Assembling 3D Crystals.

Vecchioni, S.Ohayon, Y.P.Hernandez, C.Hoshika, S.Mao, C.Benner, S.A.Sha, R.

(2024) Nano Lett 24: 14302-14306

  • DOI: https://doi.org/10.1021/acs.nanolett.4c03949
  • Primary Citation Related Structures: 
    8UY5

  • 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 Z : P ( Z , 6-amino-3-(1'-β-d-2'-deoxy ribofuranosyl)-5-nitro-(1 H )-pyridin-2-one; P , 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-(8 H )-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.


  • Organizational Affiliation
    • Department of Chemistry, New York University, New York, New York 10003, United States.

Macromolecule Content 

  • Total Structure Weight: 12.84 kDa 
  • Atom Count: 861 
  • Modeled Residue Count: 42 
  • Deposited Residue Count: 42 
  • Unique nucleic acid chains: 4

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
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')21synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*GP*TP*AP*(DZ)P*A)-3')7synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')7synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')7synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free:  0.172 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.274α = 90
b = 106.274β = 90
c = 94.462γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Office of Naval Research (ONR)United StatesN000141912596
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United States2106790
National Science Foundation (NSF, United States)United StatesCCF-2106790
National Science Foundation (NSF, United States)United StatesGCR-2317843

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release