BMRB: 30251

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd and 9th 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*(DMC)P*(8OG)P*CP*G)-3')

Entity

1. DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3') (polymer, Thiol state: not present), 12 monomers, 3770.418 × 2 Da Detail

CGXGAATTXX CG

Total weight

7540.836 Da

Max. entity weight

3770.418 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 58.3 %, Completeness: 9.2 %, Completeness (bb): 0.0 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	9.2 % (8 of 87)	9.2 % (8 of 87)
Suger, PO4	0.0 % (0 of 63)	0.0 % (0 of 63)
Nucleobase	33.3 % (8 of 24)	33.3 % (8 of 24)
Aromatic	33.3 % (6 of 18)	33.3 % (6 of 18)
Methyl	0.0 % (0 of 2)	0.0 % (0 of 2)

1. entity 1

CGXGAATTXX CG

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, 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*(DMC)P*(8OG)P*CP*G)-3'), 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3')	natural abundance		1 mM
2	EDTA	natural abundance		0.1 mM
3	potassium chloride	natural abundance		10 mM
4	sodium chloride	natural abundance		50 mM

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Chem. Shift Complete2

Sequence coverage: 75.0 %, Completeness: 33.9 %, Completeness (bb): 28.6 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	33.9 % (59 of 174)	33.9 % (59 of 174)
Suger, PO4	28.6 % (36 of 126)	28.6 % (36 of 126)
Nucleobase	47.9 % (23 of 48)	47.9 % (23 of 48)
Aromatic	52.8 % (19 of 36)	52.8 % (19 of 36)
Methyl	50.0 % (2 of 4)	50.0 % (2 of 4)

1. entity 1

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

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3')	natural abundance		1 mM
2	EDTA	natural abundance		0.1 mM
3	potassium chloride	natural abundance		10 mM
4	sodium chloride	natural abundance		50 mM

Hide sample codition

Release date

2017-03-20

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 , Abstract

Experiments performed 3 experiments Detail