7TG7 | pdb_00007tg7

[T:Ag+/Hg2+:T--(pH11-pH7; 60s in metals)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 with Ag+ and Hg2+ for 60s

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

  • Deposited: 2022-01-07 Released: 2023-01-25 
  • Deposition Author(s): Lu, B., Vecchioni, S., Seeman, N.C., Sha, R., Ohayon, Y.P.
  • Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States), Human Frontier Science Program (HFSP), National Aeronautic Space Administration (NASA, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Transmetalation for DNA-Based Molecular Electronics.

De, A.Lu, B.Ohayon, Y.P.Woloszyn, K.Livernois, W.Perren, L.Yang, C.F.Mao, C.Botana, A.S.Hihath, J.Canary, J.W.Sha, R.Anantram, M.P.Vecchioni, S.

(2025) Small 21: e2411518-e2411518

  • DOI: https://doi.org/10.1002/smll.202411518
  • Primary Citation of Related Structures:  
    7TG4, 7TG6, 7TG7, 7TG8, 7TG9, 9MM3, 9MM4, 9MM7, 9MM8, 9MM9, 9MMA, 9MMB, 9MMC, 9MMD

  • PubMed Abstract: 

    The rational design of molecular electronics remains a grand challenge of materials science. DNA nanotechnology has offered unmatched control over molecular geometry, but direct electronic functionalization is a challenge. Here a generalized method is presented for tuning the local band structure of DNA using transmetalation in metal-mediated base pairs (mmDNA). A method is developed for time-resolved X-ray diffraction using self-assembling DNA crystals to establish the exchange of Ag +  and Hg 2+  in T:T base pairs driven by pH exchange. Transmetalation is tracked over six reaction phases as crystal pH is changed from pH 8.0 to 11.0, and vice versa. A detailed computational analysis of the electronic configuration and transmission in the ensuing crystal structures is then performed. This findings reveal a high conductance contrast in the lowest unoccupied molecular orbitals (LUMO) as a result of metalation. The ability to exchange single transition metal ions as a result of environmental stimuli heralds a means of modulating the conductance of DNA-based molecular electronics. In this way, both theoretical and experimental basis are established by which mmDNA can be leveraged to build rewritable memory devices and nanoelectronics.


  • Organizational Affiliation
    • Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA.

Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')21synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3')7synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')7synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')7synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.949α = 90
b = 105.949β = 90
c = 93.791γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Office of Naval Research (ONR)United StatesN000141912596
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United States2106790
Human Frontier Science Program (HFSP)United StatesRPG0010/2017
National Science Foundation (NSF, United States)United StatesDMR-1420073
National Aeronautic Space Administration (NASA, United States)United States2020 NASA Center Innovation Fund

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2025-10-29
    Changes: Database references, Structure summary