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BMRB: 17887

2LIB

DNA sequence context conceals alpha anomeric lesion

Authors

Johnson, C.N., Spring, A.M., Cunningham, R.P., Germann, M.W.

Assembly

alpha anomeric lesion

Entity

1. DNA (5'-D(*GP*TP*CP*CP*ADA*GP*GP*AP*CP*G)-3') (polymer, Thiol state: not present), 10 monomers, 3132.989 Da Detail

GTCCXGGACG

2. DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3') (polymer, Thiol state: not present), 10 monomers, 3083.951 Da Detail

CGTCCTGGAC

Total weight

6216.94 Da

Max. entity weight

3132.989 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.0 %, Completeness: 87.0 %, Completeness (bb): 92.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	87.0 % (180 of 207)	86.7 % (163 of 188)	89.5 % (17 of 19)
Suger, PO4	92.1 % (140 of 152)	92.5 % (123 of 133)	89.5 % (17 of 19)
Nucleobase	72.7 % (40 of 55)	72.7 % (40 of 55)
Aromatic	97.4 % (37 of 38)	97.4 % (37 of 38)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA (5'-D(*GP*TP*CP*CP*ADA*GP*GP*AP*CP*G)-3')

GTCCXGGACG

2. DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')

CGTCCTGGAC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
1	DNA_chain_1	natural abundance	0.75 mM
2	DNA_chain_2	natural abundance	0.75 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	DSS	natural abundance	0.2 uM
7	EDTA	natural abundance	2 mM
8	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
9	DNA_chain_1	natural abundance	0.75 mM
10	DNA_chain_2	natural abundance	0.75 mM
11	sodium phosphate	natural abundance	10 mM
12	sodium chloride	natural abundance	50 mM
13	D2O	natural abundance	100 %
14	DSS	natural abundance	0.2 uM
15	EDTA	natural abundance	2 mM

Release date

2012-01-17

Citation

DNA sequence context conceals α-anomeric lesions
Johnson, C.N., Spring, A.M., Desai, S., Cunningham, R.P., Germann, M.W.
J. Mol. Biol. (2012), 416, 425-437, PubMed 22227386 , DOI 10.1016/j.jmb.2011.12.051 , Abstract

Experiments performed 12 experiments Detail

1 1-1 jump return

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.65

#	Name	Isotope labeling	Concentration
1	DNA_chain_1	natural abundance	0.75 mM
2	DNA_chain_2	natural abundance	0.75 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	DSS	natural abundance	0.2 uM
7	EDTA	natural abundance	2 mM
8	H2O	natural abundance	90 %

2 1D NOE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.65

#	Name	Isotope labeling	Concentration
1	DNA_chain_1	natural abundance	0.75 mM
2	DNA_chain_2	natural abundance	0.75 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	DSS	natural abundance	0.2 uM
7	EDTA	natural abundance	2 mM
8	H2O	natural abundance	90 %

3 1-1 NOESY 2D 150 ms

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.65

#	Name	Isotope labeling	Concentration
1	DNA_chain_1	natural abundance	0.75 mM
2	DNA_chain_2	natural abundance	0.75 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	DSS	natural abundance	0.2 uM
7	EDTA	natural abundance	2 mM
8	H2O	natural abundance	90 %

4 Low Flip COSY