1I34

SOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TWO DIAGONAL LOOPS CONNECTING GGGG TETRADS FLANKED BY G-(T-T) TRIAD AND T-T-T TRIPLE

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	NOESY	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
2	TOCSY	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
3	DQF-COSY	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
4	COSY-45	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
5		5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
6		5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
7		5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
8		5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
9		5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00
10		5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER	90% H2O/10% D2O	150mM NACL	6.80	1 atm	278.00

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	VARIAN UNITY INOVA	600

NMR Refinement
Method	Details	Software
DISTANCE GEOMETRY AND SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT AND RELAXATION MATRIX INTENSITY REFINEMENT	A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED EXPERIMENTALLY SPECIFIED AS NOE. FOURTEEN STRUCTURES WERE IDENTIFIED BASED ON THE CRITERION ACCEPTABLE COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATIONS AND FAVORABLE NON-BONDED ENERGY. THE VARIATION IN ENERGIES WITHIN THIS SUBSET OF STRUCTURES WAS 46 KCAL/MOL AND WAS SEPARATED FROM THE REMAINING STRUCTURES BY A GAP OF 200 KCAL/MOL. THE TEN BEST STRUCTURES FROM THIS SUBSET OF FOURTEEN 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 2.8 PS AND EQUILIBRATED AT 300K FOR 12 PS. SOFT PLANARITY RESTRAINTS WERE SWITCHED OFF BEFORE THE EQUILIBRATION STAGE.THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO 3000 STEPS OF MINIMIZATION. THE DIHEDRAL ANGLE RESTRAINTS AND HYDROGEN BONDS OF THE GGGG TETRADS WERE MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES WERE USED AS RESTRAINTS AND NON-EXCHANGEABLE PROTON DISTANCE RESTRAINTS WITH THE SCALE FACTOR OF 0.1 RELATIVE TO THE INTENSITY RESTRAINTS. SOFT PLANARITY RESTRAINTS MAINTAINED DURING RELAXATION REFINEMENTS WERE SWITCHED OFF BEFORE THE FINAL STEPS OF MINIMIZATION. THE RELAXATION PATHWAYS WERE CALCULATED USING CUTOFF 4.5 ANGSTROM AND 7.91 NS ISOTROPIC CORRELATION TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.07 A.	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,BACK-CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	3 (closest to the average, fewest violations)

Additional NMR Experimental Information
Details	SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A,8BR-G,DU,5BR-DU, 2,6A, I, 5ME-C ANALOGS AND SITE-SPECIFIC OR UNIFORMLY 13C AND 15N LABELED SAMPLES HAVE BEEN USED

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.1	BRUNGER, A.T. et al.
2	collection	VNMR	6.0	VARIAN
3	processing	Felix	2000	MSI
4	data analysis	Insight II	2000	MSI

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.