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BMRB: 30044


30044
5IZP
Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position
Authors
Gruber, D.R., Hoppins, J.J., Miears, H.L., Kiryutin, A.S., Kasymov, R.D., Yurkovskaya, A.V., Zharkov, D.O., Smirnov, S.L.
Assembly
DNA Dodecamer with 8-oxoguanine at 10th Position
Entity
1. DNA Dodecamer with 8-oxoguanine at 10th Position (polymer, Thiol state: not present), 12 monomers, 3742.364 × 2 Da Detail

CGCGAATTCX CG


Total weight
7484.728 Da
Max. entity weight
3742.364 Da
Source organism
synthetic construct
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 91.7 %, Completeness: 60.8 %, Completeness (bb): 62.5 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H31P
All60.8 % (73 of 120)67.0 % (73 of 109) 0.0 % (0 of 11)
Suger, PO462.5 % (55 of 88)71.4 % (55 of 77) 0.0 % (0 of 11)
Nucleobase56.3 % (18 of 32)56.3 % (18 of 32)
Aromatic72.7 % (16 of 22)72.7 % (16 of 22)
Methyl100.0 % (2 of 2)100.0 % (2 of 2)

1. DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')

CGCGAATTCX CG

Show sample condition
Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 100% D2O


#NameIsotope labelingTypeConcentration
1DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1 mM
2EDTAnatural abundance1 mM
3potassium phosphatenatural abundance10 mM
4sodium chloridenatural abundance50 mM
5D2Onatural abundance100 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 90% H2O/10% D2O


#NameIsotope labelingTypeConcentration
6DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1 mM
7EDTAnatural abundance1 mM
8potassium phosphatenatural abundance10 mM
9sodium chloridenatural abundance50 mM
10H2Onatural abundance90 %
11D2Onatural abundance10 %

Chem. Shift Complete2
Sequence coverage: 50.0 %, Completeness: 32.9 %, Completeness (bb): 34.7 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H31P
All32.9 % (79 of 240)33.5 % (73 of 218)27.3 % (6 of 22)
Suger, PO434.7 % (61 of 176)35.7 % (55 of 154)27.3 % (6 of 22)
Nucleobase28.1 % (18 of 64)28.1 % (18 of 64)
Aromatic36.4 % (16 of 44)36.4 % (16 of 44)
Methyl50.0 % (2 of 4)50.0 % (2 of 4)

1. DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')

CGCGAATTCX CG

Show sample condition
Sample #1

Solvent system 100% D2O, Details 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 100% D2O


#NameIsotope labelingTypeConcentration
1DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1 mM
2EDTAnatural abundance1 mM
3potassium phosphatenatural abundance10 mM
4sodium chloridenatural abundance50 mM
5D2Onatural abundance100 %
Sample #2

Solvent system 90% H2O/10% D2O, Details 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 90% H2O/10% D2O


#NameIsotope labelingTypeConcentration
6DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1 mM
7EDTAnatural abundance1 mM
8potassium phosphatenatural abundance10 mM
9sodium chloridenatural abundance50 mM
10H2Onatural abundance90 %
11D2Onatural abundance10 %

Chem. Shift Complete3
Sequence coverage: 58.3 %, Completeness: 24.7 %, Completeness (bb): 23.1 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H31P
All24.7 % (89 of 360)25.4 % (83 of 327)18.2 % (6 of 33)
Suger, PO423.1 % (61 of 264)23.8 % (55 of 231)18.2 % (6 of 33)
Nucleobase29.2 % (28 of 96)29.2 % (28 of 96)
Aromatic30.3 % (20 of 66)30.3 % (20 of 66)
Methyl33.3 % (2 of 6)33.3 % (2 of 6)

1. DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')

CGCGAATTCX CG

Show sample condition
Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 100% D2O


#NameIsotope labelingTypeConcentration
1DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1 mM
2EDTAnatural abundance1 mM
3potassium phosphatenatural abundance10 mM
4sodium chloridenatural abundance50 mM
5D2Onatural abundance100 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 90% H2O/10% D2O


#NameIsotope labelingTypeConcentration
6DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1 mM
7EDTAnatural abundance1 mM
8potassium phosphatenatural abundance10 mM
9sodium chloridenatural abundance50 mM
10H2Onatural abundance90 %
11D2Onatural abundance10 %

Release date
2016-07-27
Citation
Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation
Gruber, D.R., Toner, J.J., Miears, H.L., Shernyukov, A.V., Kiryutin, A.S., Lomzov, A.A., Endutkin, A.V., Grin, I.R., Petrova, D.V., Kupryushkin, M.S., Yurkovskaya, A.V., Johnson, E.C., Okon, M., Bagryanskaya, E.G., Zharkov, D.O., Smirnov, S.L.
Nucleic Acids Res. (2018), 46, 10827-10839, PubMed 30289469 , DOI 10.1093/nar/gky893 ,
Experiments performed 5 experiments Detail
nullKeywords DNA, DNA adduct, DNA damage, Drew-Dickerson, dodecamer, lesion, modified DNA, non-canonical, oxidized DNA