6WK7

Crystal Structure Analysis of a poly(thymine) DNA duplex

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2020-04-15 Released: 2020-07-22 
  • Deposition Author(s): Li, Q., Zhao, J., Liu, L., Mandal, S., Rizzuto, F.J., He, H., Wei, S., Jonchhe, S., Sleiman, H.F., Mao, H., Mao, C.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Science Foundation (NSF, United States), National Institutes of Health/National Cancer Institute (NIH/NCI), Natural Sciences and Engineering Research Council (NSERC, Canada), Office of Naval Research, Banting Postdoctoral Fellowships, Canada Research Chairs

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.263 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials.

Li, Q.Zhao, J.Liu, L.Jonchhe, S.Rizzuto, F.J.Mandal, S.He, H.Wei, S.Sleiman, H.F.Mao, H.Mao, C.

(2020) Nat Mater 19: 1012-1018

  • DOI: https://doi.org/10.1038/s41563-020-0728-2
  • Primary Citation of Related Structures:  
    6WK7

  • PubMed Abstract: 

    The diversity of DNA duplex structures is limited by a binary pair of hydrogen-bonded motifs. Here we show that poly(thymine) self-associates into antiparallel, right-handed duplexes in the presence of melamine, a small molecule that presents a triplicate set of the hydrogen-bonding face of adenine. X-ray crystallography shows that in the complex two poly(thymine) strands wrap around a helical column of melamine, which hydrogen bonds to thymine residues on two of its three faces. The mechanical strength of the thymine-melamine-thymine triplet surpasses that of adenine-thymine base pairs, which enables a sensitive detection of melamine at 3 pM. The poly(thymine)-melamine duplex is orthogonal to native DNA base pairing and can undergo strand displacement without the need for overhangs. Its incorporation into two-dimensional grids and hybrid DNA-small-molecule polymers highlights the poly(thymine)-melamine duplex as an additional tool for DNA nanotechnology.


  • Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, IN, USA.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')A [auth B],
B [auth C]
6synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.665α = 90
b = 67.665β = 90
c = 67.665γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AX2Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21974111
National Science Foundation (NSF, United States)United StatesCBET-1904921
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesNIH 1R01CA236350
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--
Office of Naval ResearchUnited StatesN00014-15-1-2707
Banting Postdoctoral FellowshipsCanada--
Canada Research ChairsCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description