9MM8 | pdb_00009mm8

[T:Ag+/Hg2+:T--(pH8-pH9.5; 16s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 8 and soaked in pH 9.5 for 16s

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

  • Deposited: 2024-12-20 Released: 2025-10-29 
  • Deposition Author(s): Lu, B., Vecchioni, S.
  • Funding Organization(s): Office of Naval Research (ONR), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.61 Å
  • R-Value Free: 
    0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation   3D Report Full Report


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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: 4.61 Å
  • R-Value Free:  0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.662α = 90
b = 104.662β = 90
c = 94.963γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Office of Naval Research (ONR)United StatesN000141912596
National Science Foundation (NSF, United States)United StatesCCF-2106790
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United StatesGCR-2317843

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release