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- PDB-9gdm: Solution structure of a silver ion mediated DNA duplex with unive... -

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Basic information

Entry
Database: PDB / ID: 9gdm
TitleSolution structure of a silver ion mediated DNA duplex with universal 7-deazapurine substitutions
ComponentsODNI-Ag
KeywordsDNA / 7-deazaadenine / 7-deazaguanine / silver-mediated base pairing / oligonucleotide / metallo-DNA
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsJavornik, U. / Plavec, J. / Galindo, M.A.
Funding support Slovenia, Spain, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-1704 Slovenia
Ministry of Economy and Competitiveness (MINECO)PID2020-120186RB-I00 Spain
CitationJournal: Nat Commun / Year: 2024
Title: Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs.
Authors: Javornik, U. / Perez-Romero, A. / Lopez-Chamorro, C. / Smith, R.M. / Dobado, J.A. / Palacios, O. / Bera, M.K. / Nyman, M. / Plavec, J. / Galindo, M.A.
History
DepositionAug 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ODNI-Ag
B: ODNI-Ag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,60914
Polymers7,3152
Non-polymers1,29412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable, mass spectrometry, The deconvoluted mass spectrum for the reaction between duplex I and AgI ions showed the peaks for duplex I (7281.0 g/mol) with 7- ...Evidence: NMR Distance Restraints, not applicable, mass spectrometry, The deconvoluted mass spectrum for the reaction between duplex I and AgI ions showed the peaks for duplex I (7281.0 g/mol) with 7-12 AgI ions (106.9 a.u) bound, demonstrating the formation of I-Ag complexes, including the saturated system with twelve metal ions., SAXS, Scattering data consistent with model of a duplex with silver ions in bound in the interior.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain ODNI-Ag


Mass: 3657.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ag
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D NOESY
122isotropic12D NOESY
132isotropic12D 1H-1H COSY
142isotropic12D 1H-1H TOCSY
152isotropic12D 1H-31P HPCOSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3, 90% H2O/10% D2OSample was titrated with silver nitrate to induce transition to metallated structure.odnIAg_h2o_sample90% H2O/10% D2O
solution20.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3, 100% D2OSample was titrated with silver nitrate to induce transition to metallated structure.odnIAg_d2o_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDNAnatural abundance1
100 mMNaClO4natural abundance1
100 mMTRISnatural abundance1
14.5 mMAgNO3natural abundance1
0.8 mMDNAnatural abundance2
100 mMNaClO4natural abundance2
100 mMTRISnatural abundance2
14.5 mMAgNO3natural abundance2
Sample conditionsDetails: standard expt. conditions / Ionic strength: 100 mM / Label: room_temp / pH: 8.6 / PH err: 0.4 / Pressure: 1 bar / Pressure err: 0.05 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Varian VNMRSVarianVNMRS8002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.2Agilentcollection
TopSpin4.1Brukercollection
TopSpin4.1Brukerprocessing
Amber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JL (National Magnetic Resonance Facility at Madison)chemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JL (National Magnetic Resonance Facility at Madison)peak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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