8GH5

Implementing Logic Gates in DNA Crystal Engineering

• PDB DOI: https://doi.org/10.2210/pdb8GH5/pdb
• NAKB: 8GH5

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


• Deposited: 2023-03-09 Released: 2023-06-07 
• Deposition Author(s): Zhang, C., Paluzzi, V.E., Sha, R., Jonoska, N., Mao, C.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.284 
• R-Value Work: 0.226 
• R-Value Observed: 0.230 

Literature

Implementing Logic Gates by DNA Crystal Engineering.

Zhang, C., Paluzzi, V.E., Sha, R., Jonoska, N., Mao, C.

(2023) Adv Mater 35: e2302345-e2302345

• PubMed: 37220213 
• DOI: https://doi.org/10.1002/adma.202302345
• Primary Citation of Related Structures:  
  8GH5


• PubMed Abstract: 
  

  DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.

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Organizational Affiliation: 

Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 9.62 kDa 
• Atom Count: 650 
• Modelled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*CP*G)-3')	A	5	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*TP*GP*GP*A)-3')	B, E	6	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*CP*GP*A)-3')	C	5	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*AP*CP*G)-3')	D	5	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*CP*TP*C)-3')	F	5	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.284 
• R-Value Work: 0.226 
• R-Value Observed: 0.230 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.26	α = 90
b = 51.238	β = 90
c = 105.514	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Zhang, C., Paluzzi, V.E., Sha, R., Jonoska, N., Mao, C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CCF-2107393
National Science Foundation (NSF, United States)	United States	CCMI-2025187
National Science Foundation (NSF, United States)	United States	2106790
National Science Foundation (NSF, United States)	United States	2107267

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references
• Version 1.2: 2023-10-25
  Changes: Refinement description