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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 | ||||||||||||||||||||
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Title | mini-haipin of AT basepairs having a C12-alkyl linker forming the loop region | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / mini-hairpin / alkyl chain / C12 / dodecyl / synthetic hybrid | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / simulated annealing, matrix relaxation | Model details | minimized average, model 1 | ![]() Siegmund, K.H. / Hariharan, M. / Lewis, F.D. | ![]() ![]() Title: Conformation of a dodecane DNA hairpin linker. Multiple gauche bonds cover the bases. Authors: Siegmund, K. / Hariharan, M. / Lewis, F.D. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 96.1 KB | Display | ![]() |
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PDB format | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 294 KB | Display | ![]() |
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Full document | ![]() | 345.4 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3923.739 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: 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. | ||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing, matrix relaxation / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 80 / Conformers submitted total number: 11 |