Search

Query history

Search help 
Download

Found 1 Document (2.29 seconds)

BMRB: 30250


30250
5UZ1
Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd position and 8-oxoguanine at the 10th position
Authors
Gruber, D.R., Hoppins, J.J., Miears, H.L., Endutkin, A.V., Zharkov, D.O., Smirnov, S.L.
Assembly
DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')
Entity
1. DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') (polymer, Thiol state: not present), 12 monomers, 3756.391 × 2 Da Detail

CGXGAATTCX CG


Total weight
7512.782 Da
Max. entity weight
3756.391 Da
Source organism
synthetic construct
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 66.7 %, Completeness: 10.2 %, Completeness (bb): 0.0 % Detail
Download

Polymer type: polydeoxyribonucleotide

Total1H
All10.2 % (10 of 98)10.2 % (10 of 98)
Suger, PO4 0.0 % (0 of 70) 0.0 % (0 of 70)
Nucleobase35.7 % (10 of 28)35.7 % (10 of 28)
Aromatic30.0 % (6 of 20)30.0 % (6 of 20)
Methyl 0.0 % (0 of 2) 0.0 % (0 of 2)

1. entity 1

CGXGAATTCX 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 chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 100% D2O


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

Chem. Shift Complete2
Sequence coverage: 83.3 %, Completeness: 34.2 %, Completeness (bb): 28.6 % Detail
Download

Polymer type: polydeoxyribonucleotide

Total1H
All34.2 % (67 of 196)34.2 % (67 of 196)
Suger, PO428.6 % (40 of 140)28.6 % (40 of 140)
Nucleobase48.2 % (27 of 56)48.2 % (27 of 56)
Aromatic52.5 % (21 of 40)52.5 % (21 of 40)
Methyl50.0 % (2 of 4)50.0 % (2 of 4)

1. entity 1

CGXGAATTCX 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 chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 100% D2O


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

Release date
2017-05-22
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 8-oxoguanine, CpG site, DNA, Drew-Dickerson, epigenetics, methylated DNA, modified DNA, non-canonical, oxidized DNA