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BMRB: 25915

2N9Q

Photoswitchable G-quadruplex

Authors

Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.PN., Slavov, C., Jonker, H.RA., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.

Assembly

Photoswitchable G-quadruplex

Entity

1. DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3') (polymer, Thiol state: not present), 5 monomers, 1639.076 × 4 Da Detail

GGXGG

2. Photoswitchable G-quadruplex, entity K (non-polymer), 39.098 × 3 Da

Total weight

6673.598 Da

Max. entity weight

1639.076 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 80.0 %, Completeness: 100.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	100.0 % (36 of 36)	100.0 % (36 of 36)
Suger, PO4	100.0 % (28 of 28)	100.0 % (28 of 28)
Nucleobase	100.0 % (8 of 8)	100.0 % (8 of 8)
Aromatic	100.0 % (8 of 8)	100.0 % (8 of 8)

1. DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')

GGXGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(GPGP(AZW)PGP*G)-3')	natural abundance	550 uM
2	Tris-HCl	natural abundance	25 mM
3	KCl	natural abundance	50 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
4	DNA (5'-D(GPGP(AZW)PGP*G)-3')	natural abundance	550 uM
5	Tris-HCl	natural abundance	25 mM
6	KCl	natural abundance	50 mM

Release date

2016-02-14

Citation

Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif
Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.PN., Slavov, C., Jonker, H.RA., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.
Angew. Chem Int Ed Engl. (2016), 55, 2738-2742, PubMed 26805928 , DOI 10.1002/anie.201510269 , Abstract

Experiments performed 6 experiments Detail

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_25915_2n9q.nef
Input source #2: Coordindates	2n9q.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
3:4:DG:O6	5:3:K:K	unknown	unknown	n/a
4:4:DG:O6	5:3:K:K	unknown	unknown	n/a
1:2:DG:O6	5:1:K:K	unknown	unknown	n/a
2:4:DG:O6	5:1:K:K	unknown	unknown	n/a
2:2:DG:O6	5:1:K:K	unknown	unknown	n/a
1:4:DG:O6	5:1:K:K	unknown	unknown	n/a
4:2:DG:O6	5:3:K:K	unknown	unknown	n/a
3:1:DG:O6	5:3:K:K	unknown	unknown	n/a
1:1:DG:O6	5:2:K:K	unknown	unknown	n/a
2:1:DG:O6	5:1:K:K	unknown	unknown	n/a
4:1:DG:O6	5:2:K:K	unknown	unknown	n/a
1:1:DG:O6	5:1:K:K	unknown	unknown	n/a
4:1:DG:O6	5:3:K:K	unknown	unknown	n/a
2:1:DG:O6	5:2:K:K	unknown	unknown	n/a
3:2:DG:O6	5:3:K:K	unknown	unknown	n/a
3:1:DG:O6	5:2:K:K	unknown	unknown	n/a
1:5:DG:O6	5:2:K:K	unknown	unknown	n/a
4:5:DG:O6	5:2:K:K	unknown	unknown	n/a
2:5:DG:O6	5:2:K:K	unknown	unknown	n/a
3:5:DG:O6	5:2:K:K	unknown	unknown	n/a
2:5:DG:O6	5:1:K:K	unknown	unknown	n/a
4:5:DG:O6	5:3:K:K	unknown	unknown	n/a
1:5:DG:O6	5:1:K:K	unknown	unknown	n/a
3:5:DG:O6	5:3:K:K	unknown	unknown	n/a
1:2:DG:O3'	1:3:AZW:P	unknown	unknown	n/a
2:2:DG:O3'	2:3:AZW:P	unknown	unknown	n/a
3:2:DG:O3'	3:3:AZW:P	unknown	unknown	n/a
4:2:DG:O3'	4:3:AZW:P	unknown	unknown	n/a
1:3:AZW:O3'	1:4:DG:P	unknown	unknown	n/a
2:3:AZW:O3'	2:4:DG:P	unknown	unknown	n/a
3:3:AZW:O3'	3:4:DG:P	unknown	unknown	n/a
4:3:AZW:O3'	4:4:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	AZW	4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate	Coordinates
B	3	AZW	4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate	Assigned chemical shifts, Coordinates
C	3	AZW	4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate	Coordinates
D	3	AZW	4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate	Coordinates
E	1	K	POTASSIUM ION	None
E	2	K	POTASSIUM ION	None
E	3	K	POTASSIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-----
GGXGG
|||||
GGXGG

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-----
GGXGG
|||||
GGXGG

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

-----
GGXGG
|||||
GGXGG

Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D

-----
GGXGG
|||||
GGXGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	5	100.0
B	B	5	100.0
C	C	5	100.0
D	D	5	100.0

Content subtype: combined_25915_2n9q.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	32		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	82		100.0 (chain: B, length: 5)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: B, Chain length: 5, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 48
- ¹³C chemical shifts: 34

Completeness of assignments

Entity_assemble_ID: B

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
3	AZW

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	C1'	86.53
1	DG	C2'	34.25
1	DG	C3'	78.5
1	DG	C4'	87.42
1	DG	C5'	62.72
1	DG	C8	138.01
2	DG	C1'	80.96
2	DG	C2'	37.01
2	DG	C3'	77.36
2	DG	C4'	84.7
2	DG	C5'	65.69
2	DG	C8	136.08
4	DG	C1'	86.75
4	DG	C2'	32.64
4	DG	C3'	77.64
4	DG	C4'	86.2
4	DG	C5'	67.54
4	DG	C8	139.01
5	DG	C1'	80.92
5	DG	C2'	38.98
5	DG	C3'	69.36
5	DG	C4'	84.53
5	DG	C5'	63.89
5	DG	C8	136.13

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	36	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords azobenzene, photoswitch, quadruplex

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Found 1 Document (0.4 seconds)

BMRB: 25915

Sample #1

Sample #2

Experiments performed 6 experiments Detail

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NMR combined restraints 2 contents Detail