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- PDB-6ycv: 2'-F-riboguanosine and LNA modified hybrid type G-quadruplex with... -

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Basic information

Entry
Database: PDB / ID: 6ycv
Title2'-F-riboguanosine and LNA modified hybrid type G-quadruplex with V-loop
ComponentsDNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GF2))-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')
KeywordsDNA / G-quadruplex / V-loop / LNA / 2'-F-riboguanosine
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsWeisz, K. / Haase, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE 1933/15-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design.
Authors: Haase, L. / Weisz, K.
History
DepositionMar 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GF2))-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,0181
Polymers7,0181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area540 Å2
ΔGint2 kcal/mol
Surface area3830 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GF2))-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')


Mass: 7018.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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
111isotropic11D 1H
121isotropic12D 1H-1H NOESY
232isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
252isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM F14L15, 90% H2O/10% D2OF14L1590% H2O/10% D2O
solution20.4 mM F14L15, 100% D2OF14L15_ex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMF14L15natural abundance1
0.4 mMF14L15natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
115 mM308K7 1 atm308 K
215 mM313K7 1 atm313 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
TopSpin4.0.4Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
X-PLOR NIH2.49Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing3
molecular dynamics4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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