BMRB: 34579

Synthetic DNA duplex dodecamer

Authors

Lomzov, A.A., Shernuykov, A.V., Sviridov, E.A., Shevelev, G.Y., Bagryanskaya, E.G., Pyshnyi, D.V.

Assembly

DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')

Entity

1. DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), entity 1 (polymer, Thiol state: not present), 10 monomers, 3068.940 Da Detail

CACGCCGCTG

2. DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), entity 2 (polymer, Thiol state: not present), 10 monomers, 3148.988 Da Detail

CAGCGGCGTG

Total weight

6217.9277 Da

Max. entity weight

3148.988 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 78.8 %, Completeness (bb): 71.4 % Detail

Download

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	78.8 % (156 of 198)	78.8 % (156 of 198)
Suger, PO4	71.4 % (100 of 140)	71.4 % (100 of 140)
Nucleobase	96.6 % (56 of 58)	96.6 % (56 of 58)
Aromatic	95.0 % (38 of 40)	95.0 % (38 of 40)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. entity 1

CACGCCGCTG

2. entity 2

CAGCGGCGTG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 288.4 K, pH 7.2, Details 1.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3')	natural abundance		1.1 (±0.05) mM
2	DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')	natural abundance		1.1 (±0.05) mM
3	sodium phosphate	natural abundance		10 (±0.5) mM
4	sodium chloride	natural abundance		100 (±5.0) mM
5	EDTA	natural abundance		200 (±10.0) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.4 K, pH 7.2, Details 1.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3')	natural abundance		1.1 (±0.05) mM
7	DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')	natural abundance		1.1 (±0.05) mM
8	sodium phosphate	natural abundance		10 (±0.5) mM
9	sodium chloride	natural abundance		100 (±5.0) mM
10	EDTA	natural abundance		200 (±10.0) mM

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Release date

2020-12-08

Citation

A Study of a DNA Duplex by Nuclear Magnetic Resonance (NMR) and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements using Triarylmethyl-Based Spin Labels
Lomzov, A.A., Sviridov, E.A., Shernuykov, A.V., Shevelev, G.Y., Pyshnyi, D.V., Bagryanskaya, E.G.
J. Phys. Chem. B (2016), 120, 5125-5133, PubMed 27195671 , DOI 10.1021/acs.jpcb.6b03193 , Abstract

Experiments performed 4 experiments Detail

Chemical shift validation 4 contents Detail