4B8D

TENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.79 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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This is version 1.4 of the entry. See complete history. 


Literature

Enzymatic Production of 'Monoclonal Stoichiometric' Single-Stranded DNA Oligonucleotides

Ducani, C., Kaul, C.D., Moche, M., Shih, W.M., Hogberg, B.

(2013) Nat Methods 10: 647

  • DOI: https://doi.org/10.1038/nmeth.2503
  • Primary Citation of Related Structures:  
    4B8D

  • PubMed Abstract: 

    Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. Here we present the 'monoclonal stoichiometric' (MOSIC) method for enzyme-mediated production of DNA oligonucleotides. We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides.

    • Organizational Affiliation: 

    Swedish Medical Nanoscience Center, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'21synthetic construct
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'7synthetic construct
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*GP*CP*TP*GP*CP)-3'6synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.79 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.437α = 90
b = 106.437β = 90
c = 95.154γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2013-07-10
    Changes: Database references
  • Version 1.3: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description