BMRB: 34054

Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

Authors

Kocman, V., Plavec, J.

Assembly

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

Entity

1. DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') (polymer, Thiol state: not present), 15 monomers, 4828.056 × 4 Da Detail

GCGAGGGAGC GAGGG

Total weight

19312.225 Da

Max. entity weight

4828.056 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 66.2 %, Completeness (bb): 59.0 % Detail

Download

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	66.2 % (92 of 139)	66.2 % (92 of 139)
Suger, PO4	59.0 % (62 of 105)	59.0 % (62 of 105)
Nucleobase	88.2 % (30 of 34)	88.2 % (30 of 34)
Aromatic	86.7 % (26 of 30)	86.7 % (26 of 30)

1. entity 1

GCGAGGGAGC GAGGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6, Details 1.0 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')	natural abundance		1.0 mM
2	sodium chloride	natural abundance		150 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6, Details 1 mM residue specific 15N and 13C DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')	residue specific 15N and 13C		1 mM
4	sodium chloride	natural abundance		150 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6, Details 1 mM D8 residue specific labeled DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')	D8 residue specific labeled		1 mM
6	sodium chloride	natural abundance		150 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6, Details 1 mM uniformly labeled with D8 DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
7	DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')	uniformly labeled with D8		1 mM
8	sodium chloride	natural abundance		150 mM

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Release date

2017-05-21

Citation

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions
Kocman, V., Plavec, J.
Nat. Commun. (2017), 8, 15355-15355, PubMed 28513602 , DOI 10.1038/ncomms15355 , Abstract

Related entities 1. DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), : 29 entities Detail

Experiments performed 6 experiments Detail