7DO1
Solution structure of a heteromolecular telomeric (3+1) G-quadruplex containing right loop progression
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 | 4 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'), 4.2 mM DNA (5'-D(*TP*TP*AP*GP*GP*G)-3'), 20 mM sodium phosphate, 100 mM sodium chloride, 10 % v/v [U-99% 2H] D2O, 90 % v/v H2O | 90% H2O/10% D2O | 0.1 M | 6.8 | 1 atm | 303 | Bruker AVANCE 600 |
2 | 2D 1H-1H NOESY | 4 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'), 4.2 mM DNA (5'-D(*TP*TP*AP*GP*GP*G)-3'), 20 mM sodium phosphate, 100 mM sodium chloride, 100 % v/v [U-99% 2H] D2O | 100% D2O | 0.1 M | 6.8 | 1 atm | 303 | Bruker AVANCE 600 |
3 | 2D 1H-15N HSQC | 4 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'), 4.2 mM DNA (5'-D(*TP*TP*AP*GP*GP*G)-3'), 20 mM sodium phosphate, 100 mM sodium chloride, 10 % v/v [U-99% 2H] D2O, 90 % v/v H2O | 90% H2O/10% D2O | 0.1 M | 6.8 | 1 atm | 303 | Bruker AVANCE 600 |
4 | 2D 1H-13C HSQC | 4 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'), 4.2 mM DNA (5'-D(*TP*TP*AP*GP*GP*G)-3'), 20 mM sodium phosphate, 100 mM sodium chloride, 100 % v/v [U-99% 2H] D2O | 100% D2O | 0.1 M | 6.8 | 1 atm | 303 | Bruker AVANCE 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 3.6.2 | Bruker Biospin |
2 | chemical shift assignment | CcpNmr Analysis | 2.4.2 | CCPN |
3 | geometry optimization | X-PLOR NIH | 3.0.3 | Schwieters, Kuszewski, Tjandra and Clore |
4 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |