7SD7

[C:Hg2+:T] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice

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

  • Deposited: 2021-09-29 Released: 2022-10-05 
  • Deposition Author(s): Vecchioni, S., Lu, B., 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: 3.68 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.

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

(2023) Adv Mater : e2201938-e2201938

  • DOI: https://doi.org/10.1002/adma.202201938
  • Primary Citation of Related Structures:  
    7SD6, 7SD7, 7SD8, 7SDF, 7SDG, 7SDH, 7SDI, 7SDJ, 7SDK, 7SDL, 7SDM, 7SDN, 7SDO, 7SDQ, 7SDS, 7SDT, 7SDU, 7SDV, 7SDW, 7SDX, 7SDY, 7SDZ, 7SE0, 7SE1, 7SE2, 7SE3, 7SE4, 7SE5, 7SG8, 7SG9, 7SGA, 7SGB

  • PubMed Abstract: 

    DNA double helices containing metal-mediated DNA (mmDNA) base pairs have been constructed from Ag + and Hg 2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials has been impractical without a complete lexical and structural description. Here, we explore the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination. We employed the tensegrity triangle to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and elucidated generalized design rules for mmDNA construction. We uncovered two binding modes: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations showed additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates. This article is protected by copyright. All rights reserved.


  • Organizational Affiliation

    Department of Chemistry, New York University, New York, NY, 10003, 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*CP*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*C)-3')6synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')8synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG (Subject of Investigation/LOI)
Query on HG

Download Ideal Coordinates CCD File 
E [auth B]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.587α = 90
b = 105.587β = 90
c = 89.084γ = 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
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: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection