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- PDB-8r6h: A quadruplex-duplex hybrid with a three-layered hybrid-2 G-quadru... -

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Basic information

Entry
Database: PDB / ID: 8r6h
TitleA quadruplex-duplex hybrid with a three-layered hybrid-2 G-quadruplex topology complexed with Phen-DC3
ComponentsDNA (34-MER)
KeywordsDNA / (3+1) hybrid / intercalation / Phen-DC3 / Quadruplex-duplex hybrid
Function / homologyChem-PQ3 / DNA / 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 2.0May 15, 2024Group: Database references / Non-polymer description / Category: chem_comp / database_2 / Item: _chem_comp.formula / _database_2.pdbx_DOI
Revision 2.1Jul 10, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9392
Polymers10,3891
Non-polymers5511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable, native gel electrophoresis, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 (34-MER)


Mass: 10388.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PQ3 / N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide / Phen-DC3


Mass: 550.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H26N6O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
142isotropic12D 1H-15N HMQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.92 mM DNA (34-MER), 90% H2O/10% D2Owith 1 eq. Phen-DC3natural abundance90% H2O/10% D2O
solution20.22 mM [U-10% 15N]dG DNA (34-MER), 90% H2O/10% D2Owith 1 eq. Phen-DC3selectively labeled 15N dG90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.92 mMDNA (34-MER)natural abundance1
0.22 mMDNA (34-MER)[U-10% 15N]dG2
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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