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 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

Starting Model: experimental
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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 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • 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

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Ligand Structure Quality Assessment 


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