5IX7

Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.398 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A metallo-DNA nanowire with uninterrupted one-dimensional silver array

Kondo, J.Tada, Y.Dairaku, T.Hattori, Y.Saneyoshi, H.Ono, A.Tanaka, Y.

(2017) Nat Chem 9: 956-960

  • DOI: 10.1038/nchem.2808

  • PubMed Abstract: 
  • The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The di ...

    The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal-DNA hybrid duplexes by a bottom-up approach. Here we describe a metallo-DNA nanowire-whose structure was solved by high-resolution X-ray crystallography-that consists of dodecamer duplexes held together by four different metal-mediated base pairs (the previously observed C-Ag-C, as well as G-Ag-G, G-Ag-C and T-Ag-T) and linked to each other through G overhangs involved in interduplex G-Ag-G. The resulting hybrid nanowires are 2 nm wide with a length of the order of micrometres to millimetres, and hold the silver ions in uninterrupted one-dimensional arrays along the DNA helical axis. The hybrid nanowires are further assembled into three-dimensional lattices by interactions between adenine residues, fully bulged out of the double helix.


    Organizational Affiliation

    Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3')A12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
AG
Query on AG

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Download CCD File 
A
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBR
Query on CBR
A
DNA LINKINGC9 H13 Br N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.398 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 30.150α = 90.00
b = 30.150β = 90.00
c = 118.420γ = 120.00
Software Package:
Software NamePurpose
AutoSolphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
MEXTJapan24245037
MEXTJapanS1201015
Murata Science FoundationJapan--

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references