1C32

SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER		140 mM NACL	7.0	1 atm	15
2	PE-COSY	140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER		140 mM NACL	7.0	1 atm	15
3	ROESY	140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER		140 mM NACL	7.0	1 atm	15
4	BASD-TOCSY	140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER		140 mM NACL	7.0	1 atm	15
5	WATERGATED NOESY	140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER		140 mM NACL	7.0	1 atm	15

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500
2	Varian	UNITYPLUS	400

NMR Refinement
Method	Details	Software
STRUCTURE REFINEMENT OF THE DNA WAS PERFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS.	303 NOE VOLUME CONSTRAINTS FROM THE 100 MS AND 498 NOE FROM THE 250 MS NOESY DATA WERE USED. IN ADDITION 10 NOE CONSTRAINTS INVOLVING THE IMINO PROTONS OF RESIDUES G1, G5, G6, G8, G10, G14, AND G15 WERE USED AS DISTANCE CONSTRAINTS. FOUR HYDROGEN BONDS WERE USED FOR EACH GUANINE INVOLVED IN A QUARTET. EXPERIMENTAL COUPLING CONSTANTS WERE USED TO GENERATE 45 DIHEDRAL CONSTRAINTS, 15 FROM BASHD-TOCSY EXPERIMENTS (H3*-31P), AND 30 FROM PE-COSY DATA (H1*-C1*- C2*-1H2* AND H1*-C1*-C2*-2H2*). ADDITIONAL CONSTRAINTS WERE USED TO KEEP THE PURINE RINGS PLANAR. THE STARTING STRUCTURE USED WAS THE STRUCTURE OBTAINED IN A PREVIOUS REFINEMENT. THE NON-BONDED INTERACTION CUT-OFF WAS SET TO 11.5 A, USING X-PLOR PROTOCOLS. THE ACTIVE DISTANCE OF THE SWITCHING FUNCTIONS WAS 7.5 TO 10.5 A. THE DISTANCE CUT-OFF FOR THE HYDROGEN BONDING INTERACTIONS WAS 7.5 A. THE SWITCHING FUNCTION FOR HYDROGEN BONDING INTERACTIONS WAS ACTIVE FROM 4.0 TO 6.5 A. THE ENERGY OF THE STARTING STRUCTURE WAS MINIMIZED IN 200 STEPS OF POWELL'S CONJUGATE GRADIENT MINIMIZATION. THE RELAXATION MATRIX REFINEMENTS WERE CARRIED OUT IN VACUUM AT 300K WITH A RELATIVE WEIGHTING OF ALL THE EXPERIMENTAL CONSTRAINTS (NOE, DISTANCE AND DIHEDRAL) OF 60 KCAL/MOL. SUBSEQUENTLY, A 100 PS RELAXATION MATRIX TRAJECTORY WAS CONDUCTED WITH STRUCTURES SAVED EVERY 2 PS. THE TRAJECTORIES STABILIZED AFTER 30 PS. UPON COMPLETION OF THE SIMULATION AN ADDITIONAL 200 STEP CONJUGATE GRADIENT MINIMIZATION WAS CONDUCTED TO PRODUCE THE FINAL STRUCTURES. THE ROOT MEAN SQUARE DEVIATION {OF WHAT?} WAS CALCULATED TO BE 0.14. THE NOE CROSS-PEAK VOLUMES OF THE STRUCTURES OBTAINED BETWEEN 80-100 PS AT INTERVALS OF 2 PS WERE BACKCALCULATED USING THE FELIX 970 SOFTWARE PACKAGE (MSI INC.) PARAMETERS USED IN THE BACKCALCULATION PROTOCOL ARE AS FOLLOWS: A CORRELATION TIME OF 5.0 NS, A Z-LEAKAGE RATE OF 3.0 S-1 AND A DISTANCE CUT OFF OF 7.5 A. NOE SPECTRA OF THESE 10 STRUCTURES WERE THEN BACKCALCULATED AND AVERAGED. 40 NOE INTENSITIES FROM THE EXPERIMENTAL NOESY SPECTRA WERE USED TO NORMALIZE THE BACKCALCULATED TO THE THEORETICAL NOES. THE NORMALIZATION AND AVERAGING PROCESSES WERE CONDUCTED ON A IN HOUSE PROGRAM. THE RMS, R AND Q VALUES OF THE AVERAGED STRUCTURE THAT ARE 0.28, 0.68 AND 0.30.	VNMR

NMR Ensemble Information
Conformer Selection Criteria	80-88 AND 91-100 PS STRUCTURES FORM TRAJECTORY
Conformers Calculated Total Number	10
Conformers Submitted Total Number	10
Representative Model	10 (100ps structure)

Additional NMR Experimental Information
Details	THIS FILE CONTAINS THE COORDINATES OF 10 STRUCTURES FROM 80-88 AND 91-100 PS.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR	6.1B	VARIAN
2	processing	VNMR	6.1B	VARIAN
3	processing	Felix	970	MSI
4	refinement	Felix	970	MSI
5	structure solution	X-PLOR	3.1	BRUNGER
6	refinement	X-PLOR	3.1	BRUNGER