Experiment: 2M39

The solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	2.5 mM 5'-R((C5L)P(G48)P(C5L)P(G48)P(A44)P(A44)P(T39)P(T39)P(C5L)P(G48)P(C5L))-D(P(DG))-3', 100 mM potassium chloride	90% H2O/10% D2O	100	7.0	ambient	278
2	2D NOESY	2.5 mM 5'-R((C5L)P(G48)P(C5L)P(G48)P(A44)P(A44)P(T39)P(T39)P(C5L)P(G48)P(C5L))-D(P(DG))-3', 100 mM potassium chloride	100% D2O	100	7.0	ambient	303
3	2D DQF-COSY	2.5 mM 5'-R((C5L)P(G48)P(C5L)P(G48)P(A44)P(A44)P(T39)P(T39)P(C5L)P(G48)P(C5L))-D(P(DG))-3', 100 mM potassium chloride	100% D2O	100	7.0	ambient	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	Unity Inova	600

NMR Refinement
Method	Details	Software
simulated annealing, energy minimization	STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. 3',5'-PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O2' OF EACH RIBOSE MODIFIED BY METHOXYETHYL.	VNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	50
Conformers Submitted Total Number	9
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND HETERONUCLEAR TECHNIQUES.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR	6.1B	Varian
2	processing	VNMR	6.1B	Varian
3	processing	Felix	2000	Accelrys Software Inc.
4	structure solution	Amber	7	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollman
5	refinement	Amber	7	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollman