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- PDB-8r6g: A quadruplex-duplex hybrid with a three-layered chair G-quadruple... -

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Basic information

Entry
Database: PDB / ID: 8r6g
TitleA quadruplex-duplex hybrid with a three-layered chair G-quadruplex topology
ComponentsDNA (33-MER)
KeywordsDNA / (2+2) antiparallel topology / 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 13, 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 (33-MER)


Theoretical massNumber of molelcules
Total (without water)10,4691
Polymers10,4691
Non-polymers00
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 (33-MER)


Mass: 10468.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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
144isotropic12D 1H-15N HSQC
155isotropic12D 1H-15N HSQC
165isotropic12D 1H-13C HSQC
276isotropic12D 1H-15N HSQC
183isotropic12D 1H-1H NOESY
193isotropic12D DQF-COSY
1102isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.3 mM DNA (33-MER), 90% H2O/10% D2Onatural abundance90% H2O/10% D2O
solution20.52 mM DNA (33-MER), 90% H2O/10% D2Onatural abundance290% H2O/10% D2O
solution30.5 mM DNA (33-MER), 100% D2Onatural abundance3100% D2O
solution40.22 mM [U-10% 15N]Gua DNA (33-MER), 90% H2O/10% D2O15N-Gua90% H2O/10% D2O10% selective enriched
solution50.22 mM [U-10% 13C; U-10% 15N]-Gua DNA (33-MER), 90% H2O/10% D2O15N/13C-Gua90% H2O/10% D2O10% selective enriched
solution60.6 mM [U-10% 15N]Ade DNA (33-MER), 90% H2O/10% D2O15NAde3090% H2O/10% D2O10% selective enriched
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMDNA (33-MER)natural abundance1
0.52 mMDNA (33-MER)natural abundance2
0.5 mMDNA (33-MER)natural abundance3
0.22 mMDNA (33-MER)[U-10% 15N]Gua4
0.22 mMDNA (33-MER)[U-10% 13C; U-10% 15N]-Gua5
0.6 mMDNA (33-MER)[U-10% 15N]Ade6
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1293 K 20 mM potassium phosphate buffer + 100 mM KCl, pH 7.0120 mMcondition171 atm293 K
2278 K 10 mM potassium phosphate buffer, pH 7.010 mMcondition271 atm278 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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