BMRB: 19440

NMR structure of DNA duplex

Authors

Brzezinska, J., Gdaniec, Z., Popenda, L., Markiewicz, W.T.

Assembly

N-[4,9,13-triazatridecan-1-yl]-2-deoxycytidine modified duplex DNA

Entity

1. DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') (polymer, Thiol state: not present), 8 monomers, 2521.587 Da Detail

GTCGGCTG

2. DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') (polymer, Thiol state: not present), 8 monomers, 2459.567 Da Detail

CAGCCGAC

Total weight

4981.154 Da

Max. entity weight

2521.587 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 86.2 %, Completeness (bb): 98.4 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H	31P
All	86.2 % (150 of 174)	86.1 % (136 of 158)	87.5 % (14 of 16)
Suger, PO4	98.4 % (126 of 128)	100.0 % (112 of 112)	87.5 % (14 of 16)
Nucleobase	52.2 % (24 of 46)	52.2 % (24 of 46)
Aromatic	75.0 % (24 of 32)	75.0 % (24 of 32)
Methyl	0.0 % (0 of 2)	0.0 % (0 of 2)

1. DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')

GTCGGCTG

2. DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')

CAGCCGAC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')	natural abundance		0.5 mM
2	DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')	natural abundance		0.5 mM
3	D2O	[U-100% 2H]		100 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		10 mM
6	EDTA	natural abundance		0.1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')	natural abundance		0.5 mM
8	DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')	natural abundance		0.5 mM
9	D2O	[U-100% 2H]		10 %
10	H2O	natural abundance		90 %
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.1 mM

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Chem. Shift Complete2

Sequence coverage: 75.0 %, Completeness: 48.9 %, Completeness (bb): 49.2 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H	31P
All	48.9 % (170 of 348)	49.4 % (156 of 316)	43.8 % (14 of 32)
Suger, PO4	49.2 % (126 of 256)	50.0 % (112 of 224)	43.8 % (14 of 32)
Nucleobase	47.8 % (44 of 92)	47.8 % (44 of 92)
Aromatic	46.9 % (30 of 64)	46.9 % (30 of 64)
Methyl	50.0 % (2 of 4)	50.0 % (2 of 4)

1. DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')

GTCGGCTG

2. DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')

CAGCCGAC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')	natural abundance		0.5 mM
2	DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')	natural abundance		0.5 mM
3	D2O	[U-100% 2H]		100 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		10 mM
6	EDTA	natural abundance		0.1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')	natural abundance		0.5 mM
8	DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')	natural abundance		0.5 mM
9	D2O	[U-100% 2H]		10 %
10	H2O	natural abundance		90 %
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.1 mM

Hide sample codition

Release date

2014-01-22

Citation

Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine
Brzezinska, J., Gdaniec, Z., Popenda, L., Markiewicz, W.T.
Biochim. Biophys. Acta (2014), 1840, 1163-1170, PubMed 24361616 , DOI 10.1016/j.bbagen.2013.12.008 , Abstract

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 6 experiments Detail