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- PDB-2l8i: A biocompatible backbone modification? - Structure and dynamics o... -

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Basic information

Entry
Database: PDB / ID: 2l8i
TitleA biocompatible backbone modification? - Structure and dynamics of a triazole-linked DNA duplex
Components
  • DNA (5'-D(*CP*GP*AP*CP*G*(2L8)P*TP*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*CP*AP*AP*AP*CP*GP*TP*CP*G)-3')
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsEl-Sagheer, A. / Brown, T. / Ernsting, N. / Dehmel, L. / Griesinger, C. / Mugge, C.
CitationJournal: Chemistry / Year: 2011
Title: Structure and Dynamics of Triazole-Linked DNA: Biocompatibility Explained.
Authors: Dallmann, A. / El-Sagheer, A.H. / Dehmel, L. / Mugge, C. / Griesinger, C. / Ernsting, N.P. / Brown, T.
History
DepositionJan 13, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*TP*GP*CP*AP*AP*AP*CP*GP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*CP*G*(2L8)P*TP*GP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,9452
Polymers7,9452
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3976.599 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*AP*CP*G*(2L8)P*TP*GP*CP*AP*GP*C)-3')


Mass: 3968.682 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-13C HMQC
1532D 1H-13C HMQC
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM DNA strand I, 3 mM DNA strand II, 99,98 % [U-100% 2H] D2O, 150 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O
23 mM DNA strand I, 3 mM DNA strand II, 10 % [U-99% 2H] D2O, 90 % H2O, 150 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
33 mM DNA strand I, 3 mM DNA strand II, 99,98 % [U-100% 2H] D2O, 20 mg/ml Pf1 phage, 150 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMDNA strand I-11
3 mMDNA strand II-21
99.98 %D2O-3[U-100% 2H]1
150 mMsodium chloride-41
10 mMsodium phosphate-51
3 mMDNA strand I-62
3 mMDNA strand II-72
10 %D2O-8[U-99% 2H]2
90 %H2O-92
150 mMsodium chloride-102
10 mMsodium phosphate-112
3 mMDNA strand I-123
3 mMDNA strand II-133
99.98 %D2O-14[U-100% 2H]3
20 mg/mLPf1 phage-153
150 mMsodium chloride-163
10 mMsodium phosphate-173
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.84Keller and Wuthrichchemical shift assignment
CARA1.84Keller and Wuthrichpeak picking
TOPSPIN2.1Bruker Biospincollection
TOPSPIN2.1Bruker Biospinprocessing
X-PLOR_NIH2.2Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR_NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: 20000K
NMR constraintsNOE constraints total: 351
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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