BMRBj - BMREntryMaster

Found 1 Document (0.268 seconds)

BMRB: 34581

DNA duplex with phosphoryl guanidine moiety, Rp-diastereomer

Authors

Lomzov, A.A., Pyshnyi, D.V., Shernuykov, A.V., Apukhtina, V.S.

Assembly

DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')

Entity

1. DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), entity 1 (polymer, Thiol state: not present), 10 monomers, 3068.940 Da Detail

CACGCCGCTG

2. DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), entity 2 (polymer, Thiol state: not present), 10 monomers, 3248.166 Da Detail

CAGCGGCGXG

Total weight

6317.106 Da

Max. entity weight

3248.166 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 95.0 %, Completeness: 73.9 %, Completeness (bb): 80.9 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	73.9 % (153 of 207)	72.9 % (137 of 188)	84.2 % (16 of 19)
Suger, PO4	80.9 % (123 of 152)	80.5 % (107 of 133)	84.2 % (16 of 19)
Nucleobase	54.5 % (30 of 55)	54.5 % (30 of 55)
Aromatic	76.3 % (29 of 38)	76.3 % (29 of 38)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. entity 1

CACGCCGCTG

2. entity 2

CAGCGGCGXG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 303.65 (±0.1) K, pH 7.2, Details 1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1 mM NA-H (DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG), 10 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
2	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
3	sodium phosphate	natural abundance	10 (±0.5) mM
4	sodium chloride	natural abundance	100 (±5.0) mM
5	EDTA	natural abundance	1 (±0.05) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.65 (±0.1) K, pH 7.2, Details 1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1 mM NA-H (DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG), 10 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
7	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
8	sodium phosphate	natural abundance	10 (±0.5) mM
9	sodium chloride	natural abundance	100 (±5.0) mM
10	EDTA	natural abundance	1 (±0.05) mM

Chem. Shift Complete2

Sequence coverage: 85.0 %, Completeness: 50.2 %, Completeness (bb): 47.7 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	50.2 % (208 of 414)	51.1 % (192 of 376)	42.1 % (16 of 38)
Suger, PO4	47.7 % (145 of 304)	48.5 % (129 of 266)	42.1 % (16 of 38)
Nucleobase	57.3 % (63 of 110)	57.3 % (63 of 110)
Aromatic	60.5 % (46 of 76)	60.5 % (46 of 76)
Methyl	50.0 % (1 of 2)	50.0 % (1 of 2)

1. entity 1

CACGCCGCTG

2. entity 2

CAGCGGCGXG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 278.65 (±0.1) K, pH 7.2, Details 1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1 mM NA-H (DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG), 10 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
2	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
3	sodium phosphate	natural abundance	10 (±0.5) mM
4	sodium chloride	natural abundance	100 (±5.0) mM
5	EDTA	natural abundance	1 (±0.05) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278.65 (±0.1) K, pH 7.2, Details 1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1 mM NA-H (DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG), 10 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
7	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
8	sodium phosphate	natural abundance	10 (±0.5) mM
9	sodium chloride	natural abundance	100 (±5.0) mM
10	EDTA	natural abundance	1 (±0.05) mM

Release date

2021-01-05

Citation

DNA duplex with phosphoryl guanidine moiety, Rp-diastereomer
Lomzov, A.A., Pyshnyi, D.V., Shernuykov, A.V., Apukhtina, V.S.

Experiments performed 5 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278.65 (±0.1) K, pH 7.2, Details 1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1 mM NA-H (DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG), 10 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
7	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
8	sodium phosphate	natural abundance	10 (±0.5) mM
9	sodium chloride	natural abundance	100 (±5.0) mM
10	EDTA	natural abundance	1 (±0.05) mM

2 2D 1H-1H NOESY

Instrument

Bruker AVIII - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303.65 (±0.1) K, pH 7.2, Details 1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1 mM NA-H (DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG), 10 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
2	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
3	sodium phosphate	natural abundance	10 (±0.5) mM
4	sodium chloride	natural abundance	100 (±5.0) mM
5	EDTA	natural abundance	1 (±0.05) mM

3 2D 1H-1H TOCSY

Instrument

Bruker AVIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
2	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
3	sodium phosphate	natural abundance	10 (±0.5) mM
4	sodium chloride	natural abundance	100 (±5.0) mM
5	EDTA	natural abundance	1 (±0.05) mM

4 2D 31P-1H HETCOR

Instrument

Bruker AVIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
2	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
3	sodium phosphate	natural abundance	10 (±0.5) mM
4	sodium chloride	natural abundance	100 (±5.0) mM
5	EDTA	natural abundance	1 (±0.05) mM

5 2D 1H-13C HMBC

Instrument

Bruker AVIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPAPCPGPCPCPGPCPTPG)-3')	NA-H	1 (±0.05) mM
2	(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DG)(RGT)(DG)	NA-H	1 (±0.05) mM
3	sodium phosphate	natural abundance	10 (±0.5) mM
4	sodium chloride	natural abundance	100 (±5.0) mM
5	EDTA	natural abundance	1 (±0.05) mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34581_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
2	9	T0N	~{N}-(1,3-dimethylimidazolidin-2-yl)-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy]phosphonamidous acid	Assigned chemical shifts

Content subtype: bmr34581_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	179	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	56	90.0 (chain: 1, length: 10), 90.0 (chain: 2, length: 10)
1	Chemical shift references	chem_shift_reference_1	OK	3	No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 156
  - ³¹P chemical shifts: 17
  - ¹³C chemical shifts: 6
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 90.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 90.0%
- Total number of assignments
  - ¹H chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DA	P	-1.038
3	DC	P	-1.204
4	DG	P	-0.925
5	DC	P	-1.051
7	DG	P	-0.923
8	DC	P	-1.145
9	DT	P	-1.272
10	DG	P	-1.009

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	71	70.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	54	77.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	17	54.8

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Comp_index_ID	Comp_ID
9	T0N

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DA	P	-1.001
3	DG	P	-1.148
4	DC	P	-1.201
5	DG	P	-1.117
6	DG	P	-1.057
7	DC	P	-1.126
8	DG	P	-1.282
10	DG	P	-1.207

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	66	75.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	53	84.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	13	54.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	30	29.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	11	15.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	19	61.3

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	2	40.0

Comp_index_ID	Comp_ID
9	T0N

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	25	28.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	11	17.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	14	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	3	42.9

Keywords DNA, PGO, duplex, phosphoryl guanidine oligonucleotide

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Found 1 Document (0.268 seconds)

BMRB: 34581

Sample #1

Sample #2

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

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Sample

Chemical shift validation 5 contents Detail