6DKL

Crystal Structure of a Rationally Designed Six-Fold Symmetric DNA Scaffold

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

  • Deposited: 2018-05-29 Released: 2018-08-29 
  • Deposition Author(s): Simmons, C.R., Zhang, F., Yan, H.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry.

Zhang, F.Simmons, C.R.Gates, J.Liu, Y.Yan, H.

(2018) Angew Chem Int Ed Engl 57: 12504-12507

  • DOI: https://doi.org/10.1002/anie.201807223
  • Primary Citation of Related Structures:  
    6DKL

  • PubMed Abstract: 

    Programming self-assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self-assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21-base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson-Crick base-pairing. The six-fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self-assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well-defined cavities that are suitable for future applications with immobilized guests.


  • Organizational Affiliation

    School of Molecular Sciences and Biodesign Institution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*AP*TP*GP*CP*AP*CP*A)-3')9synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3')10synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3')11synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3')12synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.408α = 90
b = 68.408β = 90
c = 143.222γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM104960
National Science Foundation (NSF, United States)United States1360635

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references