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Found 1 Document (0.375 seconds)

BMRB: 19159

2M6W

Solution NMR structure of the d(GGGGTTGGGGTTTTGGGGAAGGGG) quadruplex in sodium conditions

Authors

Karsisiotis, A., Webba da Silva, M.

Assembly

d(GGGGTTGGGGTTTTGGGGAAGGGG) quadruplex

Entity

1. d(GGGGTTGGGGTTTTGGGGAAGGGG) quadruplex (polymer, Thiol state: not present), 24 monomers, 7736.877 Da Detail

GGGGTTGGGG TTTTGGGGAA GGGG

Formula weight

7736.877 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 87.0 %, Completeness (bb): 94.8 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	87.0 % (214 of 246)	86.5 % (192 of 222)	91.7 % (22 of 24)
Suger, PO4	94.8 % (182 of 192)	95.2 % (160 of 168)	91.7 % (22 of 24)
Nucleobase	59.3 % (32 of 54)	59.3 % (32 of 54)
Aromatic	54.2 % (26 of 48)	54.2 % (26 of 48)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

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

GGGGTTGGGG TTTTGGGGAA GGGG

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
2	sodium phosphate	natural abundance		20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 81.1 %, Completeness (bb): 83.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	81.1 % (399 of 492)	84.9 % (377 of 444)	45.8 % (22 of 48)
Suger, PO4	83.3 % (320 of 384)	88.7 % (298 of 336)	45.8 % (22 of 48)
Nucleobase	73.1 % (79 of 108)	73.1 % (79 of 108)
Aromatic	69.8 % (67 of 96)	69.8 % (67 of 96)
Methyl	100.0 % (12 of 12)	100.0 % (12 of 12)

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

GGGGTTGGGG TTTTGGGGAA GGGG

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
2	sodium phosphate	natural abundance		20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

Release date

2014-04-15

Citation

DNA quadruplex folding formalism--a tutorial on quadruplex topologies
Karsisiotis, A., Webba da Silva, C.
Methods (2013), 64, 28-35, PubMed 23791747 , DOI 10.1016/j.ymeth.2013.06.004 , Abstract

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
2	sodium phosphate	natural abundance		20 mM

2 2D 1H-1H NOESY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

3 2D 1H-1H TOCSY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

4 2D DQF-COSY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

5 2D [1H-13C] H1(C5)H8 JR HMBC

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
2	sodium phosphate	natural abundance		20 mM

6 2D [1H-31P]-HSQC

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPGPTPTPGPGPGPGPTPTPTPTPGPGPGPGPAPAPGPGPGPG)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19159_2m6w.nef
Input source #2: Coordindates	2m6w.cif
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

Sequence alignments

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

--------10--------20----
GGGGTTGGGGTTTTGGGGAAGGGG
||||||||||||||||||||||||
GGGGTTGGGGTTTTGGGGAAGGGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	24	0	0	100.0

Content subtype: combined_19159_2m6w.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_non_exchangeable_protons_293K	Warning	214		100.0 (chain: A, length: 24)
2	Assigned chemical shifts	assigned_chem_shift_list_non_exchangeable_protons_278K	Warning	212		100.0 (chain: A, length: 24)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	379 (1)	noe	95.8 (chain: A, length: 24)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	645 (1)	noe	100.0 (chain: A, length: 24)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_non_exchangeable_protons_293K

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 192
- ³¹P chemical shifts: 22

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	P	-4.016
3	DG	P	-3.425
4	DG	P	-4.171
5	DT	P	-3.762
6	DT	P	-5.209
7	DG	P	-3.824
8	DG	P	-4.27
9	DG	P	-3.889
10	DG	P	-3.996
11	DT	P	-4.529
12	DT	P	-4.337
13	DT	P	-3.866
14	DT	P	-5.343
15	DG	P	-3.984
17	DG	P	-4.057
18	DG	P	-3.73
19	DA	P	-2.153
20	DA	P	-3.229
21	DG	P	-2.888
22	DG	P	-3.579
23	DG	P	-3.915
24	DG	P	-3.777

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	192	86.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	160	95.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	32	59.3

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0

Histogram of normalized assigned chemical shifts

Saveframe: assigned_chem_shift_list_non_exchangeable_protons_278K

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 212

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H21	10.904
1	DG	H22	6.087
2	DG	H21	9.691
3	DG	H21	9.685
3	DG	H22	6.766
4	DG	H21	9.314
4	DG	H22	7.046
7	DG	H21	10.056
7	DG	H22	6.305
9	DG	H21	9.699
9	DG	H22	6.834
10	DG	H21	9.955
15	DG	H21	9.696
15	DG	H22	7.509
16	DG	H21	9.263
16	DG	H22	6.378
17	DG	H21	8.626
17	DG	H22	6.364
18	DG	H21	9.684
21	DG	H21	9.685
21	DG	H22	6.182
22	DG	H21	9.38
22	DG	H22	6.397
23	DG	H21	8.577
23	DG	H22	6.668
24	DG	H21	9.697
24	DG	H22	6.835

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	185	83.3

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	138	82.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	47	87.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	18	90.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 95.8%
- Total number of restraints: 379
- Weight of restraints: 1.0 (379)
- Potential type of restraints: square-well-parabolic (379)
- Range of distance target values: 3.0, 8.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 100.0%
  - Total number of restraints: 645
  - Weight of restraints: 1.0 (645)
  - Potential type of restraints: square-well-parabolic (645)
  - Range of distance target values: 2.3, 6.65 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords Folding Topology, G-Quadruplex

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Found 1 Document (0.375 seconds)

BMRB: 19159

Sample #1

Sample #2

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

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NMR combined restraints 5 contents Detail