BMRB: 34025

G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2

Authors

Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.

Assembly

DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')

Entity

1. DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), entity 1 (polymer, Thiol state: not present), 19 monomers, 6133.889 Da Detail

TAGGGAGGGT AGGGAGGGT

2. DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), entity 6XM (non-polymer), 510.627 × 2 Da

Total weight

7155.143 Da

Max. entity weight

6133.889 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.7 %, Completeness: 67.2 %, Completeness (bb): 61.7 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	67.2 % (117 of 174)	67.2 % (117 of 174)
Suger, PO4	61.7 % (82 of 133)	61.7 % (82 of 133)
Nucleobase	85.4 % (35 of 41)	85.4 % (35 of 41)
Aromatic	84.2 % (32 of 38)	84.2 % (32 of 38)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. entity 1

TAGGGAGGGT AGGGAGGGT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DAOTA-M2	natural abundance		0.4 mM
2	DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')	natural abundance		0.2 mM
3	potassium chloride	natural abundance		100 mM
4	potassium phosphate	natural abundance		20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 10 mM LITHIUM CACODYLATE, 0.4 mM DAOTA-M2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
5	DAOTA-M2	natural abundance		0.4 mM
6	DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')	natural abundance		0.2 mM
7	LITHIUM CACODYLATE	natural abundance		10 mM
8	potassium chloride	natural abundance		100 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2, 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	DAOTA-M2	natural abundance		0.4 mM
10	DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')	natural abundance		0.2 mM
11	potassium chloride	natural abundance		100 mM
12	potassium phosphate	natural abundance		20 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 0.2 mM U-8% 15N, U-8 %13C DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	DAOTA-M2	natural abundance		0.4 mM
14	DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')	U-8% 15N, U-8 %13C		0.2 mM
15	potassium chloride	natural abundance		100 mM
16	potassium phosphate	natural abundance		20 mM

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Release date

2016-09-08

Citation

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex
Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.
Angew. Chem Int Ed Engl. (2016), 55, 12508-12511, PubMed 27577037 , DOI 10.1002/anie.201606877 , Abstract

Experiments performed 9 experiments Detail