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- PDB-2n5p: Universal base control oligonucleotide structure -

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Basic information

Entry
Database: PDB / ID: 2n5p
TitleUniversal base control oligonucleotide structure
Components
  • DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')
  • DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')
KeywordsDNA / Nucleic Acid / Universal Base / Synthetic Base
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics, matrix relaxation, distance geometry
Model detailsfewest violations, model1
AuthorsSpring-Connell, A.M. / Evich, M.G. / Seela, F. / Germann, M.W.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog.
Authors: Spring-Connell, A.M. / Evich, M.G. / Debelak, H. / Seela, F. / Germann, M.W.
History
DepositionJul 23, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')
B: DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,4722
Polymers5,4722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

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


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Control DNA oligonucleotide for the universal base. This sequence contains a dA in place of the UB at position 5.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY 75 ms
1212D Low Flip COSY
1312D 1H-13C HSQC
1412D 1H-1H constant time NOESY
1512D 1H-1H TOCSY
1612D 1H-31P CORR
1711D 1H
2821D 1H 1-1 jump and return
1911D 31P
11012D 1H-1H NOESY 150 ms
11112D 1H-1H NOESY 250 ms

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O
21 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 mM sodium chloride, 10 mM sodium phosphate, 90 % H2O, 10 % 100% deuterium D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')-11
1 mMDNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')-21
100 %D2O-3100% Deuterium1
100 mMsodium chloride-41
10 mMsodium phosphate-51
1 mMDNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')-62
1 mMDNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')-72
100 mMsodium chloride-82
10 mMsodium phosphate-92
90 %H2O-102
10 %D2O-11100% deuterium2
Sample conditionsIonic strength: 100 / pH: 6.79 / Pressure: ambient / Temperature: 294 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
XwinNMRBruker Biospincollection
CORMAThomas Jamesrefinement
CORMAThomas Jamesdata analysis
MARDIGRASThomas Jamesdata analysis
MARDIGRASThomas Jamesrefinement
RefinementMethod: molecular dynamics, matrix relaxation, distance geometry
Software ordinal: 1
Details: AMBER 9 restrained MD simulations, MARDIGRAS, CORMA for comparisons of structure to NOE data (Rx values).
NMR constraintsNA alpha-angle constraints total count: 16 / NA beta-angle constraints total count: 16 / NA delta-angle constraints total count: 18 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 18 / NA sugar pucker constraints total count: 90 / NOE constraints total: 143 / NOE intraresidue total count: 78 / NOE sequential total count: 66 / Hydrogen bond constraints total count: 46
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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