2L5K | pdb_00002l5k

Solution structure of truncated 23-mer DNA MUC1 aptamer

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	2 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	100% D2O	50	6.5	ambient	298
2	2D 1H-13C HSQC	2 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	100% D2O	50	6.5	ambient	298
3	2D 1H-31P COSY	2 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	100% D2O	50	6.5	ambient	298
4	2D DQF-COSY	2 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	100% D2O	50	6.5	ambient	298
5	2D 1H-1H TOCSY	2 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	100% D2O	50	6.5	ambient	298
6	2D 1H-1H NOESY	2 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	100% D2O	50	6.5	ambient	298
7	2D 1H-1H TOCSY	1 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 5 uM sodium azide, 50 mM sodium chloride	90% H2O/10% D2O	50	6.5	ambient	298
8	2D 1H-1H NOESY	1 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 5 uM sodium azide, 50 mM sodium chloride	90% H2O/10% D2O	50	6.5	ambient	298
9	2D 1H-1H TOCSY	1 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	90% H2O/10% D2O	50	6.5	1 atm	264.5
10	2D 1H-1H NOESY	1 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide	90% H2O/10% D2O	50	6.5	1 atm	264.5

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	UNITYPLUS	500
2	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
simulated annealing, bioplymer chain elasticity	100 structures were calculated with DYANA and the 20 structures with the smallest residual target function have been refined by energy minimization with AMBER before being deposited., A model with the NMR-defined torsion angles was constructed with the BCE method and AMBER energy refined. It contains 2 bridging water molecules (coordinates available upon request to J. Cognet).	DYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	DYANA	1.5	Guntert, Braun and Wuthrich
2	processing	PROSA	6.0.2	Guntert
3	chemical shift assignment	XEASY	1.2	Bartels et al.
4	peak picking	XEASY	1.2	Bartels et al.
5	processing	NMRPipe	1998	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	geometry optimization	Amber	8	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
7	structure solution	Smol	1	(SMOL) Pakleza, Santini, Cognet