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- PDB-9hio: RKEC1 DNA aptamer bound to dopamine -

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Basic information

Entry
Database: PDB / ID: 9hio
TitleRKEC1 DNA aptamer bound to dopamine
ComponentsRKEC1 DNA (27-MER)
KeywordsDNA / Aptamer / Dopamine / Complex / Biosensor
Function / homologyL-DOPAMINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsLargy, E. / Kaiyum, Y.A. / Chao, E.H.P. / Vialet, B. / Johnson, P.E. / Mackereth, C.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other governmentFrance Canada Research Fund Canada
CitationJournal: Biorxiv / Year: 2025
Title: Unconventional DNA architecture in a dopamine–bound aptamer complex
Authors: Chao, E.H.P. / Largy, E. / Kaiyum, Y.A. / Nguyen, M.D. / Vialet, B. / Dauphin-Ducharme, P. / Johnson, P.E. / Mackereth, C.D.
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RKEC1 DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5882
Polymers8,4341
Non-polymers1531
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain RKEC1 DNA (27-MER)


Mass: 8434.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RKEC1 is derived from a longer dopamine-binding DNA aptamer identified using capture-SELEX
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
Has ligand of interestY
Has protein modificationN

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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
222isotropic12D 1H-1H NOESY
232isotropic12D 1H-1H TOCSY
242isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution12 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride, 90% H2O/10% D2ONatural abundance complex of RKEC1 and dopamine in waterH2O90% H2O/10% D2O
solution22 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride, 100% D2ONatural abundance complex of RKEC1 and dopamine in D2OD2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRKEC1 DNA (27-MER)natural abundance1
2.25 mML-DOPAMINEnatural abundance1
20 mMsodium phosphatenatural abundance1
140 mMsodium chloridenatural abundance1
2 mMmagnesium chloridenatural abundance1
2 mMRKEC1 DNA (27-MER)natural abundance2
2.25 mML-DOPAMINEnatural abundance2
20 mMsodium phosphatenatural abundance2
140 mMsodium chloridenatural abundance2
2 mMmagnesium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1162 mM278K7.41 atm278 K
2162 mM298K7.41 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz / Details: CP TCI

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKY1.47Lee, Tonelli and Markleychemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Amber24Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
NMRFAM-SPARKY1.47Lee, Tonelli and Markleypeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinalDetails
simulated annealing6Note that the deposited ambig.tbl, unambig.tbl and dihedrals.tbl were used with ARIA/CNS
simulated annealing2note that H5' and H5'' were freely swapped during this step
molecular dynamics3Note that the final refinement with AMBER, and therefore the deposited ensemble, only used the unambig.tbl restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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