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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'A21synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'B7synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*GP*CP*TP*GP*CP)-3'C6synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'D8synthetic construct
        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

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • 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