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- PDB-6syk: Guanine-rich oligonucleotide with 5'- and 3'-GC ends form G-quadr... -

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Basic information

Entry
Database: PDB / ID: 6syk
TitleGuanine-rich oligonucleotide with 5'- and 3'-GC ends form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pair
ComponentsGCnCG
KeywordsDNA / G-quadruplex / A(GGGG)A hexad / GCGC-quartet / 5'- and 3'-GC ends
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsPavc, D. / Wang, B. / Spindler, L. / Drevensek-Olenik, I. / Plavec, J. / Sket, P.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research Agency Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly.
Authors: Pavc, D. / Wang, B. / Spindler, L. / Drevensek-Olenik, I. / Plavec, J. / Sket, P.
History
DepositionSep 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCnCG
B: GCnCG


Theoretical massNumber of molelcules
Total (without water)8,9042
Polymers8,9042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1540 Å2
ΔGint2 kcal/mol
Surface area4420 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain GCnCG


Mass: 4451.877 Da / Num. of mol.: 2 / 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
212isotropic12D NOESY
222isotropic22D NOESY
333isotropic12D NOESY
343isotropic22D NOESY
353isotropic22D TOCSY
262isotropic22D DQF-COSY
373isotropic22D 1H-31P COSY
181isotropic22D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM 8% 13C, 8% 15N GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2OSite-specific 13C,15N labelled samples used for unambiguous assignment13C15N_sample90% H2O/10% D2O
solution21 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2Ounlabelled_sample90% H2O/10% D2O
solution31 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2Ounlabelled_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGCnCG8% 13C, 8% 15N1
175 mMsodium chloridenatural abundance1
10 mMsodium phosphate buffernatural abundance1
1 mMGCnCGnatural abundance2
175 mMsodium chloridenatural abundance2
10 mMsodium phosphate buffernatural abundance2
1 mMGCnCGnatural abundance3
175 mMsodium chloridenatural abundance3
10 mMsodium phosphate buffernatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1175 mM13C15N_sample_conditions6.81 atm298 K
2175 mMunlabelled_sample_conditions6.81 atm298 K
3175 mMunlabelled_sample_D2O_conditions6.81 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent Agilent Technologies VNMRS 800 MHz NMR spectrometerAgilentAgilent Technologies VNMRS 800 MHz NMR spectrometer8001
Agilent Agilent Technologies DD2 600 MHz NMR spectrometerAgilentAgilent Technologies DD2 600 MHz NMR spectrometer6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
VNMRVarianchemical shift assignment
SparkyGoddardpeak picking
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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