5M4W
Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleotide found in regulatory region of the PLEKHG3 human gene with G11 to I11 mutation, d(GCGAGGGAGCIAGGG),VK34_I11
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 mM LiCl | 90% H2O/10% D2O | 100 mM | 6 | 1 atm | 273 | Varian Uniform NMR System 800 |
2 | 1D 1H-15N HSQC | 1 mM residue specific 15N labeled DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 mM LiCl | 90% H2O/10% D2O | 100 mM | 6 | 1 atm | 273 | Varian Uniform NMR System 600 |
3 | 2D 1H-15N HSQC | 1 mM residue specific 15N labeled DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 mM LiCl | 90% H2O/10% D2O | 100 mM | 6 | 1 atm | 273 | Varian Uniform NMR System 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | Uniform NMR System | 600 |
2 | Varian | Uniform NMR System | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard |