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- PDB-8r6d: A quadruplex-duplex hybrid with a three-layered hybrid-2 G-quadru... -

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Basic information

Entry
Database: PDB / ID: 8r6d
TitleA quadruplex-duplex hybrid with a three-layered hybrid-2 G-quadruplex topology
ComponentsDNA (31-MER)
KeywordsDNA / (3+1) hybrid / hybrid-2 / G-quadruplex / Quadruplex-duplex hybrid
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsVianney, Y.M. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)410497337 Germany
CitationJournal: Adv Sci / Year: 2024
Title: Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions.
Authors: Vianney, Y.M. / Dierks, D. / Weisz, K.
History
DepositionNov 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2024Group: Database references / Category: citation / database_2 / Item: _citation.journal_volume / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)9,7711
Polymers9,7711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable, native gel electrophoresis, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (31-MER)


Mass: 9771.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D DQF-COSY
131isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM DNA (31-MER), 90% H2O/10% D2O298 K, 20 mM potassium phosphate buffer + 100 mM KCl, pH 7.0.Sample 1 - Natural abundance90% H2O/10% D2O
solution20.2 mM [U-10% 13C; U-10% 15N]-Gua DNA (31-MER), 90% H2O/10% D2O298 K, 20 mM potassium phosphate buffer + 100 mM KCl, pH 7.0.selectively labeled 10% 13C and 15N dG90% H2O/10% D2O
solution30.2 mM [U-10% 15N]-Gua DNA (31-MER), 90% H2O/10% D2O298 K, 20 mM potassium phosphate buffer + 100 mM KCl, pH 7.0.selectively labeled 10% 15N dG90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA (31-MER)natural abundance1
0.2 mMDNA (31-MER)[U-10% 13C; U-10% 15N]-Gua2
0.2 mMDNA (31-MER)[U-10% 15N]-Gua3
Sample conditionsDetails: 298 K, 20 mM potassium phosphate buffer + 100 mM KCl, pH 7.0
Ionic strength: 120 mM / Label: condition1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin4.0.7Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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