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