7SM9

[U:Hg2+/Ag+:U--pH 10] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution

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

  • Deposited: 2021-10-25 Released: 2022-11-23 
  • 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: 3.24 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals.

Lu, B.Ohayon, Y.P.Woloszyn, K.Yang, C.F.Yoder, J.B.Rothschild, L.J.Wind, S.J.Hendrickson, W.A.Mao, C.Seeman, N.C.Canary, J.W.Sha, R.Vecchioni, S.

(2023) J Am Chem Soc 145: 17945-17953

  • DOI: https://doi.org/10.1021/jacs.3c05478
  • Primary Citation of Related Structures:  
    7SLB, 7SLC, 7SLD, 7SLE, 7SLF, 7SLG, 7SLJ, 7SLK, 7SLL, 7SLM, 7SLN, 7SLO, 7SM0, 7SM1, 7SM2, 7SM3, 7SM4, 7SM5, 7SM6, 7SM7, 7SM8, 7SM9, 7SMA, 7SMB, 7TI3, 7UJZ, 7UK0, 8DX1, 8DX5, 8DX6, 8DX7, 8DX9, 8DXA, 8DXC, 8DXD, 8DXF

  • PubMed Abstract: 

    Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.


  • Organizational Affiliation

    Department of Chemistry, New York University, New York, New York 10003, United States.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

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

Find similar nucleic acids by:  Sequence   |   3D Structure  

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

Find similar nucleic acids by:  Sequence   |   3D Structure  

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

Find similar nucleic acids by:  Sequence   |   3D Structure  

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: 3.24 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.016α = 90
b = 106.016β = 90
c = 93.685γ = 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)FranceRPG0010/2017
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: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references