BMRBj - BMREntryMaster

Found 1 Document (0.226 seconds)

BMRB: 34445

2'-F-riboguanosine and 2'-F-arabinoguanosine modified G-quadruplex with V-loop and all-syn G-tract

Authors

Haase, L., Weisz, K.

Assembly

F1415

Entity

1. F1415 (polymer, Thiol state: not present), 22 monomers, 7071.443 Da Detail

GGGATGGGAC ACAXXGGACG GG

Formula weight

7071.443 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 90.9 %, Completeness: 59.4 %, Completeness (bb): 53.6 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	59.4 % (111 of 187)	59.4 % (111 of 187)
Suger, PO4	53.6 % (75 of 140)	53.6 % (75 of 140)
Nucleobase	76.6 % (36 of 47)	76.6 % (36 of 47)
Aromatic	87.5 % (35 of 40)	87.5 % (35 of 40)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. entity 1

GGGATGGGAC ACAXXGGACG GG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.4 mM F14A15, 10 mM potassium phosphate buffer at pH 7, i.e. 6.13 mM KH2PO4 and 3.87 mM K2HPO4, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	F14A15	natural abundance		0.4 mM
2	potassium phosphate buffer	natural abundance		10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.4 mM F14A15, 10 mM potassium phosphate buffer at pH 7, i.e. 6.13 mM KH2PO4 and 3.87 mM K2HPO4, 100% D2O.

#	Name	Isotope labeling	Type	Concentration
3	F14A15	natural abundance		0.4 mM
4	potassium phosphate buffer	natural abundance		10 mM

Release date

2019-11-06

Citation

Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions
Haase, L., Weisz, K.
Chem. Commun. (Camb). (2020), 56, 4539-4542, PubMed 32202271 , DOI 10.1039/d0cc01285h , Abstract

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.4 mM F14A15, 10 mM potassium phosphate buffer at pH 7, i.e. 6.13 mM KH2PO4 and 3.87 mM K2HPO4, 90% H2O/10% D2O.

#	Name	Isotope labeling	Type	Concentration
1	F14A15	natural abundance		0.4 mM
2	potassium phosphate buffer	natural abundance		10 mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.4 mM F14A15, 10 mM potassium phosphate buffer at pH 7, i.e. 6.13 mM KH2PO4 and 3.87 mM K2HPO4, 100% D2O.

#	Name	Isotope labeling	Type	Concentration
3	F14A15	natural abundance		0.4 mM
4	potassium phosphate buffer	natural abundance		10 mM

3 2D DQF-COSY

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	F14A15	natural abundance		0.4 mM
4	potassium phosphate buffer	natural abundance		10 mM

4 2D 1H-1H TOCSY

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	F14A15	natural abundance		0.4 mM
4	potassium phosphate buffer	natural abundance		10 mM

5 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	F14A15	natural abundance		0.4 mM
2	potassium phosphate buffer	natural abundance		10 mM

6 2D 19F-1H HOESY

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	F14A15	natural abundance		0.4 mM
2	potassium phosphate buffer	natural abundance		10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34445_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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	14	GF2	2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate)	Assigned chemical shifts
1	15	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Assigned chemical shifts

Content subtype: bmr34445_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	156		100.0 (chain: 1, length: 22)
1	Chemical shift references	chem_shift_reference_1	Warning	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 22, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 129
- ¹³C chemical shifts: 25
- ¹⁹F chemical shifts: 2

Completeness of assignments

Entity_assemble_ID: 1

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
14	GF2
15	GFL

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H21	8.512
1	DG	H22	4.103
1	DG	C8	139.711
2	DG	C8	141.222
3	DG	C8	139.546
4	DA	C2	154.908
4	DA	C8	141.993
5	DT	C6	139.591
6	DG	C8	138.874
7	DG	C8	137.329
8	DG	C8	137.204
9	DA	C8	142.811
10	DC	C6	143.338
11	DA	C8	141.434
12	DC	C6	143.467
13	DA	H61	3.958
13	DA	H62	8.125
13	DA	C2	154.187
13	DA	C8	140.858
16	DG	H21	9.401
16	DG	H22	6.937
16	DG	C8	139.961
17	DG	C8	138.171
18	DA	C2	155.71
18	DA	C8	143.138
19	DC	C6	144.955
20	DG	C8	138.5
21	DG	C8	138.073
22	DG	C8	137.93

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	187	111	59.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	75	53.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	36	76.6

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	1	100.0
¹³C chemical shifts	1	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	19	90.5

Histogram of normalized assigned chemical shifts

Keywords DNA, G-quadruplex, V-loop

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Found 1 Document (0.226 seconds)

BMRB: 34445

Sample #1

Sample #2

Experiments performed 6 experiments Detail

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Chemical shift validation 3 contents Detail