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Solution NMR structure of the d(GGGTTGGGTTTTGGGTGGG) quadruplex in sodium conditions
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 5 mM DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), 20 mM sodium phosphate 93% H2O/7% D2O 25 7.8 ambient atm 278 2 2D 1H-1H NOESY 5 mM DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), 20 mM sodium phosphate 100% D2O 25 7.8 ambient atm 293 3 2D 1H-1H TOCSY 5 mM DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), 20 mM sodium phosphate 100% D2O 25 7.8 ambient atm 293 4 2D DQF-COSY 5 mM DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), 20 mM sodium phosphate 100% D2O 25 7.8 ambient atm 293 5 2D [1H-13C] H1(C5)H8 JR HMBC 5 mM DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), 20 mM sodium phosphate 93% H2O/7% D2O 25 7.8 ambient atm 278 6 2D [1H-31P]-HSQC 5 mM DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), 20 mM sodium phosphate 100% D2O 25 7.8 ambient atm 293
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian VNMRS 500 500
NMR Refinement Method Details Software simulated annealing, molecular dynamics Felix
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 processing Felix Accelrys Software Inc. 2 chemical shift assignment Sparky Goddard 3 data analysis Sparky Goddard 4 structure solution X-PLOR Brunger 5 refinement X-PLOR Brunger 6 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 7 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 8 data analysis MOLMOL Koradi, Billeter and Wuthrich 9 collection VnmrJ Varian