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SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA
90% H2O/10% D2O
~50mM
6.8
ambient
298
2
3D_15N-separated_NOESY
2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA
90% H2O/10% D2O
~50mM
6.8
ambient
298
3
3D_15N-separated_NOESY
2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA
100% D2O
4
DQF-COSY
2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA
100% D2O
5
31P-1H HetCor
2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA
100% D2O
6
2D 13C-filtered NOESY
2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA
100% D2O
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AMX
500
NMR Refinement
Method
Details
Software
simulated annealing and molecular dynamics refinement
structures were calculated using 313 conformationally restrictive NOE distance constraints (i.e., intra-residue sugar-sugar NOEs are not included), 20 H-bond base pair constraints, 30 backbone dihedral restraints, and dihedral restraints to restrict sugar pucker conformation. Parameter file was modified to incorporate bond-length, bond-angle, charge, van der Waal's radius for the Rp phosphoryl sulfur atoms located 5' to each adenine in the sequence. [Jaroszewski, JW., et al., Anti-Cancer Drug Design ( 1992) 7, 253; Florian, J. et al., J. Am. Chem. Soc. (1998) 120, 7959].
UXNMR
NMR Ensemble Information
Conformer Selection Criteria
back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number
30
Conformers Submitted Total Number
10
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
Details
The structure was determined using standard 2D homonuclear and 2D/3D heteronuclear techniques. Filtered experiments used to identify inter-residue NOEs involving unlabeled A residues