3GBI image
Deposition Date 2009-02-19
Release Date 2009-09-01
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3GBI
Keywords:
Title:
The Rational Design and Structural Analysis of a Self-Assembled Three-Dimensional DNA Crystal
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
4.02 Å
R-Value Free:
0.30
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
H 3
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:A
Chain Length:21
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
Chain IDs:B
Chain Length:7
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
Chain IDs:C
Chain Length:6
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
Chain IDs:D
Chain Length:8
Number of Molecules:1
Biological Source:
Ligand Molecules
Primary Citation
From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.
Nature 461 74 77 (2009)
PMID: 19727196 DOI: 10.1038/nature08274

Abstact

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.

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