BMRBj - BMREntryMaster

Found 1 Document (0.443 seconds)

BMRB: 36411

6G7Z

Aptamer enhancing peroxidase activity of myoglobin

Authors

Tsukakoshi, K., Matsugami, A., Khunathai, K., Kanazashi, M., Yamagishi, Y., Nakama, K., Oshikawa, D., Hayashi, F., Kuno, H., Ikebukuro, K.

Assembly

G-quadruplex-forming aptamer

Entity

1. G-quadruplex-forming aptamer (polymer, Thiol state: not present), 16 monomers, 5194.269 Da Detail

GGGTGGGTTG GGAGGG

Formula weight

5194.269 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.2 %, Completeness (bb): 98.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	93.2 % (137 of 147)	93.2 % (137 of 147)
Suger, PO4	98.2 % (110 of 112)	98.2 % (110 of 112)
Nucleobase	77.1 % (27 of 35)	77.1 % (27 of 35)
Aromatic	84.4 % (27 of 32)	84.4 % (27 of 32)
Methyl	0.0 % (0 of 3)	0.0 % (0 of 3)

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

GGGTGGGTTG GGAGGG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), 10 mM Potassium phosphate buffer pH 6.5, 100 uM DSS, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
2	DSS	natural abundance		100 uM
3	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
4	D2O	[U-2H]	solvent	100 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), 10 mM Potassium phosphate buffer pH 6.5, 100 uM NA DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
6	DSS	natural abundance		100 uM
7	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
8	H2O	natural abundance	solvent	95 %
9	D2O	[U-2H]	solvent	5 %

Release date

2021-07-13

Citation

G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol
Tsukakoshi, K., Yamagishi, Y., Kanazashi, M., Nakama, K., Oshikawa, D., Savory, N., Matsugami, A., Hayashi, F., Lee, J., Saito, T., Sode, K., Khunathai, K., Kuno, H., Ikebukuro, K.
Nucleic Acids Res. (2021), 49, 6069-6081, PubMed 34095949 , DOI 10.1093/nar/gkab388 , Abstract

Related entities 1. G-quadruplex-forming aptamer, : 1 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-1H NOESY 500ms

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), 10 mM Potassium phosphate buffer pH 6.5, 100 uM DSS, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
2	DSS	natural abundance		100 uM
3	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
4	D2O	[U-2H]	solvent	100 %

2 2D 1H-1H NOESY 50ms

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
2	DSS	natural abundance		100 uM
3	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
4	D2O	[U-2H]	solvent	100 %

3 2D 1H-1H TOCSY 120ms

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
2	DSS	natural abundance		100 uM
3	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
4	D2O	[U-2H]	solvent	100 %

4 2D DQF-COSY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
2	DSS	natural abundance		100 uM
3	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
4	D2O	[U-2H]	solvent	100 %

5 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
2	DSS	natural abundance		100 uM
3	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
4	D2O	[U-2H]	solvent	100 %

6 2D 1H-1H NOESY 50ms

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), 10 mM Potassium phosphate buffer pH 6.5, 100 uM NA DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
6	DSS	natural abundance		100 uM
7	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
8	H2O	natural abundance	solvent	95 %
9	D2O	[U-2H]	solvent	5 %

7 2D 1H-1H NOESY 250ms

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
6	DSS	natural abundance		100 uM
7	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
8	H2O	natural abundance	solvent	95 %
9	D2O	[U-2H]	solvent	5 %

8 2D JR-HMBC

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
6	DSS	natural abundance		100 uM
7	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
8	H2O	natural abundance	solvent	95 %
9	D2O	[U-2H]	solvent	5 %

9 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D((GUA)PGPGPTPGPGPGPTPTPGPGPGPAPGPGPG)-3')	natural abundance	DNA	1 mM
6	DSS	natural abundance		100 uM
7	Potassium phosphate buffer pH 6.5	natural abundance	buffer	10 mM
8	H2O	natural abundance	solvent	95 %
9	D2O	[U-2H]	solvent	5 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr36411_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr36411_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	220		100.0 (chain: 1, length: 16)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 16, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 153
- ¹³C chemical shifts: 67

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H21	5.575
1	DG	H22	9.837
1	DG	C2'	43.28
1	DG	C4'	88.76
1	DG	C5'	64.49
1	DG	C8	138.84
2	DG	H21	6.687
2	DG	H22	9.142
2	DG	C2'	42.14
2	DG	C4'	87.36
2	DG	C5'	67.81
2	DG	C8	138.27
3	DG	C2'	41.05
3	DG	C4'	85.52
3	DG	C5'	68.75
3	DG	C8	138.11
4	DT	C2'	41.46
4	DT	C4'	87.32
4	DT	C5	14.42
4	DT	C5'	68.24
4	DT	C6	139.95
5	DG	H21	5.663
5	DG	H22	9.934
5	DG	C2'	44.77
5	DG	C4'	87.58
5	DG	C5'	68.53
5	DG	C8	138.33
6	DG	H21	6.301
6	DG	H22	9.339
6	DG	C2'	42.3
6	DG	C4'	87.11
6	DG	C5'	68.66
6	DG	C8	138.43
7	DG	C2'	42.75
7	DG	C4'	87.59
7	DG	C5'	69.11
7	DG	C8	138.04
8	DT	C2'	41.22
8	DT	C4'	87.04
8	DT	C5	14.36
8	DT	C5'	68.44
8	DT	C6	139.98
9	DT	C2'	39.66
9	DT	C4'	86.94
9	DT	C5	14.36
9	DT	C5'	68.77
9	DT	C6	140.7
10	DG	H21	5.504
10	DG	H22	9.804
10	DG	C2'	43.21
10	DG	C4'	86.93
10	DG	C5'	67.62
10	DG	C8	138.43
11	DG	H21	6.625
11	DG	H22	9.181
11	DG	C2'	42.35
11	DG	C4'	87.35
11	DG	C5'	68.66
11	DG	C8	138.04
12	DG	C2'	41.07
12	DG	C4'	85.55
12	DG	C5'	68.63
12	DG	C8	138.18
13	DA	C2'	42.05
13	DA	C4'	87.39
13	DA	C5'	67.2
13	DA	C8	142.7
14	DG	H21	5.648
14	DG	H22	9.778
14	DG	C2'	44.71
14	DG	C4'	87.53
14	DG	C5'	68.66
14	DG	C8	138.4
15	DG	H21	6.051
15	DG	H22	9.348
15	DG	C2'	41.91
15	DG	C4'	87.34
15	DG	C5'	68.72
15	DG	C8	138.32
16	DG	C2'	42.72
16	DG	C4'	88.33
16	DG	C5'	68.68
16	DG	C8	138.05

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	137	93.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	110	98.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	27	77.1

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	0	0.0
¹³C chemical shifts	3	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	12	85.7

Histogram of normalized assigned chemical shifts

Keywords DNA, DNA aptamer parallel G-quadruplex myoglobin peroxidase activity enhancement

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Found 1 Document (0.443 seconds)

BMRB: 36411

Sample #1

Sample #2

Related entities 1. G-quadruplex-forming aptamer, : 1 entities Detail

Experiments performed 9 experiments Detail

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Chemical shift validation 3 contents Detail