6UDN image
Entry Detail
PDB ID:
6UDN
Keywords:
DNA
Title:
Crystal Structure of a Self-Assembling DNA Scaffold Containing TA Sticky Ends and Rhombohedral Symmetry
Biological Source:
Source Organism:
synthetic construct
PDB Version:
Deposition Date:
2019-09-19
Release Date:
2020-09-23
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.60 Å
R-Value Free:
0.25
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
H 3
6UDN validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
Chain IDs:B (auth: A)
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*TP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')
Chain IDs:A (auth: B)
Chain Length:21
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*TP*AP*TP*CP*AP*GP*AP*TP*G)-3')
Chain IDs:C
Chain Length:9
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*GP*TP*CP*AP*G)-3')
Chain IDs:D
Chain Length:5
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
ARS
Primary Citation
A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Angew.Chem.Int.Ed.Engl. 59 18619 18626 (2020)
PMID: 32533629 DOI: 10.1002/anie.202005505

Abstact

DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.

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Disease

Primary Citation of related structures
6U40
6UAL