3GBI

The Rational Design and Structural Analysis of a Self-Assembled Three-Dimensional DNA Crystal

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.02 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.246 

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This is version 1.2 of the entry. See complete history. 


Literature

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.

Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C., Seeman, N.C.

(2009) Nature 461: 74-77

  • DOI: 10.1038/nature08274
  • Primary Citation of Related Structures:  
    3GBI

  • PubMed Abstract: 

    • We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world ...

    We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 A resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

    Organizational Affiliation: 

    Department of Chemistry, New York University, New York 10003, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')A 21N/A
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')B 7N/A
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')C 6N/A
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')D 8N/A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.02 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.246 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.161α = 90
b = 107.161β = 90
c = 93.144γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description