5M1L
Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene
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 | 0.8 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 6.0 | 1 atm | 273 | Varian Uniform NMR System 800 |
2 | 1D 1H-15N HSQC | 0.8 mM [10 % 15N] residue specific Gua DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 6.0 | 1 atm | 273 | Varian Uniform NMR System 600 |
3 | 2D 1H-15N HSQC | 0.8 mM [10 % 15N] residue specific Gua DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 6.0 | 1 atm | 273 | Varian Uniform NMR System 600 |
4 | 2D 1H-13C HSQC | 0.8 mM [10% 13C] residues specific adenine DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 6.0 | 1 atm | 273 | Varian Uniform NMR System 800 |
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 Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 10 |
Computation: NMR Software | ||||
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# | 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 |