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BMRB: 34438

Guanine-rich oligonucleotide with 5'- and 3'-GC ends form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pair

Authors

Pavc, D., Wang, B., Spindler, L., Drevensek-Olenik, I., Plavec, J., Sket, P.

Assembly

GCnCG

Entity

1. GCnCG (polymer, Thiol state: not present), 14 monomers, 4514.849 × 2 Da Detail

GCGGAGGGGA GGCG

Total weight

9029.698 Da

Max. entity weight

4514.849 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.4 %, Completeness (bb): 96.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	94.4 % (136 of 144)	94.6 % (123 of 130)	92.9 % (13 of 14)
Suger, PO4	96.4 % (108 of 112)	96.9 % (95 of 98)	92.9 % (13 of 14)
Nucleobase	87.5 % (28 of 32)	87.5 % (28 of 32)
Aromatic	92.9 % (26 of 28)	92.9 % (26 of 28)

1. entity 1

GCGGAGGGGA GGCG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM 8% 13C, 8% 15N GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	GCnCG	[8% 13C; 8% 15N]	1 mM
2	sodium chloride	natural abundance	175 mM
3	sodium phosphate buffer	natural abundance	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	GCnCG	natural abundance	1 mM
5	sodium chloride	natural abundance	175 mM
6	sodium phosphate buffer	natural abundance	10 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCnCG	natural abundance	1 mM
8	sodium chloride	natural abundance	175 mM
9	sodium phosphate buffer	natural abundance	10 mM

Release date

2020-07-13

Citation

GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly
Pavc, D., Wang, B., Spindler, L., Drevensek-Olenik, I., Plavec, J., Sket, P.
Nucleic Acids Res. (2020), 48, 2749-2761, PubMed 31996902 , DOI 10.1093/nar/gkaa058 , Abstract

Experiments performed 8 experiments Detail

1 2D NOESY

Instrument

Agilent Agilent Technologies VNMRS 800 MHz NMR spectrometer - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	GCnCG	natural abundance	1 mM
5	sodium chloride	natural abundance	175 mM
6	sodium phosphate buffer	natural abundance	10 mM

2 2D NOESY

Instrument

Agilent Agilent Technologies DD2 600 MHz NMR spectrometer - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	GCnCG	natural abundance	1 mM
5	sodium chloride	natural abundance	175 mM
6	sodium phosphate buffer	natural abundance	10 mM

3 2D NOESY

Instrument

Agilent Agilent Technologies VNMRS 800 MHz NMR spectrometer - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCnCG	natural abundance	1 mM
8	sodium chloride	natural abundance	175 mM
9	sodium phosphate buffer	natural abundance	10 mM

4 2D NOESY

Instrument

Agilent Agilent Technologies DD2 600 MHz NMR spectrometer - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCnCG	natural abundance	1 mM
8	sodium chloride	natural abundance	175 mM
9	sodium phosphate buffer	natural abundance	10 mM

5 2D TOCSY

Instrument

Agilent Agilent Technologies DD2 600 MHz NMR spectrometer - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCnCG	natural abundance	1 mM
8	sodium chloride	natural abundance	175 mM
9	sodium phosphate buffer	natural abundance	10 mM

6 2D DQF-COSY

Instrument

Agilent Agilent Technologies DD2 600 MHz NMR spectrometer - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	GCnCG	natural abundance	1 mM
5	sodium chloride	natural abundance	175 mM
6	sodium phosphate buffer	natural abundance	10 mM

7 2D 1H-31P COSY

Instrument

Agilent Agilent Technologies DD2 600 MHz NMR spectrometer - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCnCG	natural abundance	1 mM
8	sodium chloride	natural abundance	175 mM
9	sodium phosphate buffer	natural abundance	10 mM

8 2D 1H-13C HSQC aromatic

Instrument

Agilent Agilent Technologies DD2 600 MHz NMR spectrometer - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1 mM 8% 13C, 8% 15N GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	GCnCG	[8% 13C; 8% 15N]	1 mM
2	sodium chloride	natural abundance	175 mM
3	sodium phosphate buffer	natural abundance	10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34438_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: bmr34438_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	145		100.0 (chain: 1, length: 14)
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: 14, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 132
- ³¹P chemical shifts: 13

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	8.925
1	DG	H22	5.978
2	DC	P	-0.99
3	DG	P	-1.32
4	DG	P	-0.604
5	DA	P	-1.025
6	DG	H22	6.729
6	DG	P	-0.785
7	DG	H21	10.156
7	DG	H22	6.27
7	DG	P	-0.407
8	DG	H21	9.3
8	DG	H22	8.357
8	DG	P	-1.124
9	DG	P	-1.083
10	DA	P	0.487
11	DG	H21	9.011
11	DG	H22	5.537
11	DG	P	0.279
12	DG	P	-0.521
13	DC	P	-0.522
14	DG	P	-0.696

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	130	123	94.6

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	95	96.9

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	28	87.5

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	14	14	100.0

Histogram of normalized assigned chemical shifts

Keywords 5'- and 3'-GC ends, A(GGGG)A hexad, DNA, G-quadruplex, GCGC-quartet

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Found 1 Document (0.798 seconds)

BMRB: 34438

Sample #1

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Sample #3

Experiments performed 8 experiments Detail

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Chemical shift validation 3 contents Detail