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BMRB: 34436

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

Authors

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

Assembly

GCn

Entity

1. GCn (polymer, Thiol state: not present), 12 monomers, 3896.462 × 2 Da Detail

GCGGAGGGGA GG

Total weight

7792.924 Da

Max. entity weight

3896.462 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.5 %, Completeness (bb): 99.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	97.5 % (119 of 122)	98.2 % (108 of 110)	91.7 % (11 of 12)
Suger, PO4	99.0 % (95 of 96)	100.0 % (84 of 84)	91.7 % (11 of 12)
Nucleobase	92.3 % (24 of 26)	92.3 % (24 of 26)
Aromatic	91.7 % (22 of 24)	91.7 % (22 of 24)

1. entity 1

GCGGAGGGGA GG

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 GCN, 100 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	GCN	[8% 13C; 8% 15N]	1 mM
2	sodium chloride	natural abundance	100 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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	GCN	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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCN	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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	GCN	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	GCN	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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCN	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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCN	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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCN	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	GCN	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 GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O

#	Name	Isotope labeling	Concentration
7	GCN	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 GCN, 100 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	GCN	[8% 13C; 8% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate buffer	natural abundance	10 mM

Chemical shift validation 3 contents Detail

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	126		100.0 (chain: 1, length: 12)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H21	8.976
1	DG	H22	5.932
2	DC	P	-1.011
3	DG	P	-1.345
4	DG	P	-0.614
5	DA	P	-1.07
6	DG	P	-0.864
7	DG	H21	10.192
7	DG	P	-0.305
8	DG	H21	9.484
8	DG	H22	8.341
8	DG	P	-1.169
9	DG	P	-1.108
10	DA	P	0.422
11	DG	H21	9.108
11	DG	H22	5.609
11	DG	P	0.2
12	DG	P	-0.445

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	110	108	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	84	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	24	92.3

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

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

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34436_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

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Found 1 Document (0.57 seconds)

BMRB: 34436

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Experiments performed 8 experiments Detail

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Chemical shift validation 3 contents Detail