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 9MMA | pdb_00009mma

[T:Ag+/Hg2+:T--(pH9.5-pH11; 20s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 9.5 and soaked in pH 11 for 20s

  • 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: 5.03 Å
  • R-Value Free: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9MMA

This is version 1.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 13 kDa 
  • Atom Count: 860 
  • Modeled Residue Count: 42 
  • Deposited Residue Count: 42 
  • Unique nucleic acid chains: 4

Macromolecules

Find similar nucleic acids by:  Sequence
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
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')7synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.03 Å
  • R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.402α = 90
b = 104.402β = 90
c = 95.175γ = 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
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