5VY7

A self-assembling L-form DNA crystal lattice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.

Simmons, C.R.Zhang, F.MacCulloch, T.Fahmi, N.Stephanopoulos, N.Liu, Y.Seeman, N.C.Yan, H.

(2017) J. Am. Chem. Soc. 139: 11254-11260

  • DOI: 10.1021/jacs.7b06485
  • Primary Citation of Related Structures:  5VY6

  • PubMed Abstract: 
  • The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for sol ...

    The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.


    Organizational Affiliation

    Department of Chemistry, New York University , New York, New York 10003, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*CP*TP*CP*A)-3')A21synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3')B6synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*T)-3')C8synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')D7synthetic construct
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
0DG
Query on 0DG
A, B, C, D
L-DNA LINKINGC10 H14 N5 O7 P

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0DA
Query on 0DA
A, B, C
L-DNA LINKINGC10 H14 N5 O6 P

--

0DT
Query on 0DT
A, B, C, D
L-DNA LINKINGC10 H15 N2 O8 P

--

0DC
Query on 0DC
A, B, C, D
L-DNA LINKINGC9 H14 N3 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.238 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 68.584α = 90.00
b = 68.584β = 90.00
c = 55.737γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-05-24 
  • Released Date: 2017-08-09 
  • Deposition Author(s): Simmons, C.R., Yan, H.

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references