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- PDB-2l13: mini-haipin of AT basepairs having a C12-alkyl linker forming the... -

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Basic information

Entry
Database: PDB / ID: 2l13
Titlemini-haipin of AT basepairs having a C12-alkyl linker forming the loop region
ComponentsDNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')
KeywordsDNA / mini-hairpin / alkyl chain / C12 / dodecyl / synthetic hybrid
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, matrix relaxation
Model detailsminimized average, model 1
AuthorsSiegmund, K.H. / Hariharan, M. / Lewis, F.D.
CitationJournal: J.Phys.Chem.B / Year: 2011
Title: Conformation of a dodecane DNA hairpin linker. Multiple gauche bonds cover the bases.
Authors: Siegmund, K. / Hariharan, M. / Lewis, F.D.
History
DepositionJul 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)3,9241
Polymers3,9241
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)11 / 80structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: DNA chain DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')


Mass: 3923.739 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The C12-alkyl linker enables the short sequence to form a stable mini-hairpin. Ring-currents of the neighboring base-pair made assignment for all methylene protons possible. The position of ...Details: The C12-alkyl linker enables the short sequence to form a stable mini-hairpin. Ring-currents of the neighboring base-pair made assignment for all methylene protons possible. The position of the last terminal base-pair is not well defined due to end-fraying and the resulting lack of a sufficient number of constraints.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
14.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-1, 100% D2O100% D2O
24.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
4.2 mMDNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-11
4.2 mMDNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-22
Sample conditionsIonic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
Sparky3.113Goddardpeak integration
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, matrix relaxation / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 11

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