1G5D

NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	NOESY	2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer	D2O	10 mM sodium phosphate buffer	6.8	ambient	293
2	PE-COSY	2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer	D2O	10 mM sodium phosphate buffer	6.8	ambient	293
3	watergate-NOESY	2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer	10% D2O, 90% H2O	10 mM sodium phosphate buffer	6.8	ambient	278
4	31P-HCOSY	3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer	D2O	10 mM sodium phosphate buffer	6.8	ambient	298
5	31P-decoupled-PE-COSY	3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer	D2O	10 mM sodium phosphate buffer	6.8	ambient	298
6	31P-decoupled-J-scaled-DQCOSY	3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer	D2O	10 mM sodium phosphate buffer	6.8	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Home-built	home-built	750
2	Home-built	home-built	600

NMR Refinement
Method	Details	Software
molecular dynamics	The structure is based on 475 NOE-derived distance constraints and 101 dihedral angle restraints.	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	10
Conformers Submitted Total Number	10

Additional NMR Experimental Information
Details	The abasic site deoxyribose 1H-1H coupling constants and the DNA 31P-H3' coupling constants were experimentally determined. This information was used in the modeling protocol.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR	3.851	Brunger
2	processing	Felix	95.0	MSI
3	data analysis	Felix	95.0	MSI
4	refinement	X-PLOR	3.851	Brunger