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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'B7synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*GP*CP*TP*GP*CP)-3'C6synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
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 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 106.437α = 90.00
b = 106.437β = 90.00
c = 95.154γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Database references
  • Version 1.2: 2013-07-10
    Type: Database references