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BMRB: 30151


30151
5L2G
Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position
Authors
Miears, H.L., Hoppins, J.J., Gruber, D.R., Kasymov, R.D., Johnson, E.C., Zharkov, D.O., Smirnov, S.L.
Assembly
DNA (5'-D(*CP*GP*(5CM)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
Entity
1. DNA (5'-D(*CP*GP*(5CM)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') (polymer, Thiol state: not present), 12 monomers, 3740.391 × 2 Da Detail

CGCGAATTXG CG


Total weight
7480.782 Da
Max. entity weight
3740.391 Da
Source organism
synthetic construct
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 75.0 %, Completeness: 9.3 %, Completeness (bb): 0.0 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H
All 9.3 % (10 of 107) 9.3 % (10 of 107)
Suger, PO4 0.0 % (0 of 77) 0.0 % (0 of 77)
Nucleobase33.3 % (10 of 30)33.3 % (10 of 30)
Aromatic31.8 % (7 of 22)31.8 % (7 of 22)
Methyl 0.0 % (0 of 2) 0.0 % (0 of 2)

1. entity 1

CGCGAATTXG CG

Show sample condition
Sample

Solvent system 100% D2O, Pressure 1 null, Temperature 278 K, pH 6.8, Details 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3'), 100% D2O


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

Chem. Shift Complete2
Sequence coverage: 91.7 %, Completeness: 37.4 %, Completeness (bb): 33.8 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H
All37.4 % (80 of 214)37.4 % (80 of 214)
Suger, PO433.8 % (52 of 154)33.8 % (52 of 154)
Nucleobase46.7 % (28 of 60)46.7 % (28 of 60)
Aromatic52.3 % (23 of 44)52.3 % (23 of 44)
Methyl50.0 % (2 of 4)50.0 % (2 of 4)

1. entity 1

CGCGAATTXG CG

Show sample condition
Sample

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


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

Release date
2016-11-10
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 4 experiments Detail
nullKeywords CpG site, DNA, Drew-Dickerson, epigenetics, methylated DNA, modified DNA, non-canonical