2A5P
Monomeric parallel-stranded DNA tetraplex with snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, NMR, 8 struct.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 1H-1H NOESY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
2 | 1H-1H TOCSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
3 | 1H-31P COSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
4 | 1H-1H COSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
5 | 1H-15N JRHMQC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
6 | 1H-15N HMBC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
7 | 1H-13C JRHM 1H-13C HMBC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
8 | 1H-13C HSQC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
9 | 1H-13C sHMBC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
10 | 1H-31P TOCSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | VARIAN UNITY INOVA | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
DISTANCE GEOMETRY AND SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT AND RELAXATION MATRIX INTENSITY REFINEMENT | XPLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 8 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6 AVERAGING OPTION. EIGHT BEST STRUCTURES SELECTED ON THE BASIS OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND FAVOURABLE NON-BONDED ENERGY TERMS WERE FURTHER OPTIMIZED WITH RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE PROPORTION 1:4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE THEN SLOWLY COOLED TO 300K IN 14 PS AND EQUILIBRATED AT 300K FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND TRIAD BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. THE DIHEDRAL AND HYDROGEN-BONDING RESTRAINTS FOR TETRADS, WERE MAINTAINED THROUGHOUT. ALL EIGHT STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES OF NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED AT 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE FORCE CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED FROM 0 TO 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE DISTANCE FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 to 16. AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING STRUCTURES WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS FOR EXCHANGEABLE PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS WERE MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE SET FOR TETRAD (1 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A-2). |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | XPLOR | 3.851 | AT BRUNGER |
2 | collection | VNMR | 6.0 | VARIAN |
3 | processing | Felix | 2000 | ACCELRYS |