BMRB: 30116

Structural impact of single ribonucleotides in DNA

Authors

Evich, M., Spring-Connell, A.M., Storici, F., Germann, M.W.

Assembly

DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')

Entity

1. DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), entity 1 (polymer, Thiol state: not present), 9 monomers, 2834.795 Da Detail

ATCCGGTAG

2. DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), entity 2 (polymer, Thiol state: not present), 9 monomers, 2778.771 Da Detail

CTACCGGAT

Total weight

5613.566 Da

Max. entity weight

2834.795 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 50.0 %, Completeness: 70.4 %, Completeness (bb): 73.6 % Detail

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Polymer type: polydeoxyribonucleotide/polyribonucleotide hybrid

	Total	1H	31P
All	70.4 % (69 of 98)	68.5 % (61 of 89)	88.9 % (8 of 9)
Suger, PO4	73.6 % (53 of 72)	71.4 % (45 of 63)	88.9 % (8 of 9)
Nucleobase	61.5 % (16 of 26)	61.5 % (16 of 26)
Aromatic	77.8 % (14 of 18)	77.8 % (14 of 18)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

2. entity 2

CTACCGGAT

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 294 K, pH 6.6, Details 1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	D2O	100% deuterium		100 %
2	DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')	natural abundance		1 mM
3	DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3')	natural abundance		1 mM
4	sodium chloride	natural abundance		100 mM
5	sodium phosphate	natural abundance		10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 294 K, pH 6.6, Details 1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 10 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	D2O	100% deuterium		10 %
7	DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')	natural abundance		1 mM
8	DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3')	natural abundance		1 mM
9	sodium chloride	natural abundance		100 mM
10	sodium phosphate	natural abundance		10 mM

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Release date

2016-08-21

Citation

Structural impact of single ribonucleotides in DNA
Evich, M., Spring-Connell, A.M., Storici, F., Germann, M.W.
Chembiochem. (2016), 17, 1968-1977, PubMed 27504600 , DOI 10.1002/cbic.201600385 , Abstract

Experiments performed 10 experiments Detail