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BMRB: 30329


30329
6ALU
Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position
Authors
Gruber, D.R., Shernyukov, A.V., Endutkin, A.V., Bagryanskaya, E.G., Zharkov, D.O., Smirnov, S.L.
Assembly
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')
Entity
1. DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') (polymer, Thiol state: not present), 12 monomers, 3676.411 × 2 Da Detail

XGXXAATTCG CG


Total weight
7352.822 Da
Max. entity weight
3676.411 Da
Source organism
synthetic construct
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 75.0 %, Completeness: 60.9 %, Completeness (bb): 60.3 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H
All60.9 % (53 of 87)60.9 % (53 of 87)
Suger, PO460.3 % (38 of 63)60.3 % (38 of 63)
Nucleobase62.5 % (15 of 24)62.5 % (15 of 24)
Aromatic72.2 % (13 of 18)72.2 % (13 of 18)
Methyl100.0 % (2 of 2)100.0 % (2 of 2)

1. entity 1

XGXXAATTCG CG

Show sample condition
Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*CP*GP*CP*(DG3))-3'), 100% D2O


#NameIsotope labelingTypeConcentration
1DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*CP*GP*CP*(DG3))-3')natural abundance1 mM
2EDTAnatural abundance0.1 mM
3potassium phosphatenatural abundance10 mM
4sodium chloridenatural abundance50 mM

Chem. Shift Complete2
Sequence coverage: 66.7 %, Completeness: 36.2 %, Completeness (bb): 30.2 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H
All36.2 % (63 of 174)36.2 % (63 of 174)
Suger, PO430.2 % (38 of 126)30.2 % (38 of 126)
Nucleobase52.1 % (25 of 48)52.1 % (25 of 48)
Aromatic52.8 % (19 of 36)52.8 % (19 of 36)
Methyl50.0 % (2 of 4)50.0 % (2 of 4)

1. entity 1

XGXXAATTCG CG

Show sample condition
Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 279 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*CP*GP*CP*(DG3))-3'), 100% D2O


#NameIsotope labelingTypeConcentration
1DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*CP*GP*CP*(DG3))-3')natural abundance1 mM
2EDTAnatural abundance0.1 mM
3potassium phosphatenatural abundance10 mM
4sodium chloridenatural abundance50 mM

Release date
2017-08-27
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 3 experiments Detail
nullKeywords DNA, DNA adduct, DNA damage, Drew-Dickerson, lesion, modified DNA, non-canonical, oxidized DNA