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Found 1 Document (0.277 seconds)

BMRB: 34328

Dodecamer DNA containing the synthetic base pair P-Z

Authors

Padroni, G., Reichenbach, L.F., Parkinson, J.A., Burley, G.A.

Assembly

DNA (5'-*(DC5)P*GP*AP*TP*(P)P*TP*AP*(Z)P*AP*TP*CP*(DG3))-3')

Entity

1. DNA (5'-*(DC5)P*GP*AP*TP*(P)P*TP*AP*(Z)P*AP*TP*CP*(DG3))-3') (polymer, Thiol state: not present), 12 monomers, 3769.386 × 2 Da Detail

CGATXTAXAT CG

Total weight

7538.772 Da

Max. entity weight

3769.386 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.3 %, Completeness: 81.3 %, Completeness (bb): 86.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	81.3 % (87 of 107)	80.4 % (78 of 97)	90.0 % (9 of 10)
Suger, PO4	86.3 % (69 of 80)	85.7 % (60 of 70)	90.0 % (9 of 10)
Nucleobase	66.7 % (18 of 27)	66.7 % (18 of 27)
Aromatic	75.0 % (15 of 20)	75.0 % (15 of 20)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. entity 1

CGATXTAXAT CG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.3 mM ZP-DNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	ZP-DNA	natural abundance		1.3 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.3 mM ZP-DNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	ZP-DNA	natural abundance		1.3 mM

Release date

2019-06-02

Citation

Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components
Padroni, G., Withers, J.M., Taladriz-Sender, A., Reichenbach, L.F., Parkinson, J.A., Burley, G.A.
J. Am. Chem. Soc. (2019), 141, 9555-9563, PubMed 31117639 , DOI 10.1021/jacs.8b12444 , Abstract

Experiments performed 6 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34328_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
1	5	DP	[(2~{R},3~{S},5~{R})-5-(2-azanyl-4-oxidanylidene-imidazo[1,2-a][1,3,5]triazin-8-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate	Assigned chemical shifts
1	8	DZ	[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{H}-pyridin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate	Assigned chemical shifts

Content subtype: bmr34328_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	181		100.0 (chain: 1, length: 12)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 12, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 98
- ¹³C chemical shifts: 72
- ³¹P chemical shifts: 11

Completeness of assignments

Entity_assemble_ID: 1

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
5	DP
8	DZ

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DC	C1'	85.219
1	DC	C2'	37.246
1	DC	C3'	75.171
1	DC	C4'	85.576
1	DC	C5'	61.011
1	DC	C6	140.456
2	DG	C1'	81.342
2	DG	C2'	37.387
2	DG	C3'	76.921
2	DG	C4'	84.657
2	DG	C5'	65.568
2	DG	C8	135.586
2	DG	P	-1.078
3	DA	C1'	82.354
3	DA	C2	152.266
3	DA	C2'	38.534
3	DA	C3'	76.716
3	DA	C4'	84.886
3	DA	C5'	65.891
3	DA	C8	138.623
3	DA	P	-1.065
4	DT	C1'	82.231
4	DT	C2'	36.871
4	DT	C3'	73.929
4	DT	C4'	82.525
4	DT	C5'	63.92
4	DT	C6	135.718
4	DT	C7	11.321
4	DT	P	-1.404
6	DT	C1'	82.593
6	DT	C2'	36.436
6	DT	C3'	75.083
6	DT	C4'	83.185
6	DT	C6	136.535
6	DT	C7	11.526
6	DT	P	-1.598
7	DA	C1'	82.251
7	DA	C2	151.942
7	DA	C2'	37.301
7	DA	C3'	77.029
7	DA	C4'	84.789
7	DA	C5'	65.587
7	DA	C8	139.043
7	DA	P	-1.257
9	DA	C1'	82.735
9	DA	C2	151.438
9	DA	C2'	38.621
9	DA	C3'	76.09
9	DA	C4'	84.598
9	DA	C8	139.161
9	DA	P	-0.801
10	DT	C1'	82.491
10	DT	C2'	36.636
10	DT	C3'	74.071
10	DT	C4'	82.623
10	DT	C6	135.889
10	DT	C7	11.294
10	DT	P	-1.497
11	DC	C1'	83.821
11	DC	C2'	36.583
11	DC	C3'	74.193
11	DC	C4'	82.813
11	DC	C6	141.107
11	DC	P	-1.258
12	DG	C1'	82.075
12	DG	C2'	39.159
12	DG	C3'	70.795
12	DG	C4'	85.287
12	DG	C8	136.554
12	DG	P	-0.893

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	78	80.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	60	85.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	18	66.7

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0
¹³C chemical shifts	3	3	100.0

Aromatic group atoms

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

Histogram of normalized assigned chemical shifts

Keywords DNA, P, Z, synthetic base pair

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Found 1 Document (0.277 seconds)

BMRB: 34328

Sample #1

Sample #2

Experiments performed 6 experiments Detail

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Chemical shift validation 3 contents Detail