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- PDB-6ijw: SOLUTION NMR STRUCTURE OF A DODECAMERIC dsDNA COMPLEXED WITH A NI... -

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Basic information

Entry
Database: PDB / ID: 6ijw
TitleSOLUTION NMR STRUCTURE OF A DODECAMERIC dsDNA COMPLEXED WITH A NIR FLUORESCENT PROBE QCy-DT
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / dsDNA / ligand / QCy-DT
Function / homologyChem-QCY / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGanguly, S. / Basu, G.
CitationJournal: Biochemistry / Year: 2021
Title: DNA Minor Groove-Induced cis - trans Isomerization of a Near-Infrared Fluorescent Probe.
Authors: Ganguly, S. / Murugan, N.A. / Ghosh, D. / Narayanaswamy, N. / Govindaraju, T. / Basu, G.
History
DepositionOct 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7693
Polymers7,3272
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1430 Å2
ΔGint-4 kcal/mol
Surface area4540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-QCY / 2,2'-{(4-hydroxy-1,3-phenylene)di[(E)ethene-2,1-diyl]}bis(3-methyl-1,3-benzothiazol-3-ium)


Mass: 442.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22N2OS2 / Feature type: SUBJECT OF INVESTIGATION

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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 1H-1H TOCSY
131isotropic12D DQF-COSY
142isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H TOCSY
162isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY, 90% H2O/10% D2OThe DNA was annealed in a buffer containing 10mM sodium phosphate and 10mM sodium chloride (pH 7.0). The ligand was dissolved in the same buffer. The DNA and ligand was mixed in a 1:1 ratio for the experiments.1H_sample90% H2O/10% D2O
solution2300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY, 100% D2OThe solution containing 1:1 mixture of dsDNA and ligand was lyophilised and redissolved in 100% D2O solution.1H_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')natural abundance1
300 uMQCYnatural abundance1
300 uMDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')[U-2H]2
300 uMQCY[U-2H]2
Sample conditionsIonic strength: 10mM NaCl mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinpeak picking
SparkyGoddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 4

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