BMRBj - BMREntryMaster

Found 1 Document (0.761 seconds)

BMRB: 30254

5UZF

Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNA structure

Authors

Sathyamoorthy, B., Shi, H., Xue, Y., Al-Hashimi, H.M.

Assembly

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

Entity

1. DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*AP*AP*AP*AP*AP*TP*CP*G)-3'), entity 1 (polymer, Thiol state: not present), 12 monomers, 3722.359 Da Detail

CGATTTTTTG GC

2. DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*AP*AP*AP*AP*AP*TP*CP*G)-3'), entity 2 (polymer, Thiol state: not present), 12 monomers, 3727.405 Da Detail

GCCAAAAAAT CG

Total weight

7449.7637 Da

Max. entity weight

3727.405 Da

Source organism

synthetic construct

Exptl. method

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 65.8 %, Completeness (bb): 60.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	65.8 % (169 of 257)	63.1 % (147 of 233)	91.7 % (22 of 24)
Suger, PO4	60.4 % (116 of 192)	56.0 % (94 of 168)	91.7 % (22 of 24)
Nucleobase	81.5 % (53 of 65)	81.5 % (53 of 65)
Aromatic	95.8 % (46 of 48)	95.8 % (46 of 48)
Methyl	100.0 % (7 of 7)	100.0 % (7 of 7)

1. entity 1

CGATTTTTTG GC

2. entity 2

GCCAAAAAAT CG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*GP*CP*CP*AP*AP*AP*AP*AP*AP*TP*CP*G)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.25 (±0.25) mM
7	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.25 (±0.25) mM
8	sodium phosphate buffer	natural abundance		15 mM
9	sodium chloride	natural abundance		25 mM
10	EDTA	natural abundance		0.1 mM

Release date

2017-03-26

Citation

Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A
Sathyamoorthy, B., Shi, H., Zhou, H., Xue, Y., Rangadurai, A., Merriman, D.K., Al-Hashimi, H.M.
Nucleic Acids Res. (2017), 45, 5586-5601, PubMed 28369571 , DOI 10.1093/nar/gkx186 , Abstract

Experiments performed 9 experiments Detail

1 2D 1H-15N SOFAST-HMQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

2 2D 1H-13C SOFAST-HMQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

3 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

5 2D 1H-1H TOCSY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

6 2D DQF-COSY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

7 2D 1H-31P HSQC

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

8 2D 1H-13C TROSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.5 (±0.5) mM
2	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.5 (±0.5) mM
3	sodium phosphate buffer	natural abundance		15 mM
4	sodium chloride	natural abundance		25 mM
5	EDTA	natural abundance		0.1 mM

9 2D 1H-13C TROSY

Instrument

Varian INOVA - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 3.5 mM DNA (5'-D(*GP*CP*CP*AP*AP*AP*AP*AP*AP*TP*CP*G)-3'), 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	DNA (5'-D(CPGPAPTPTPTPTPTPTPGPGPC)-3')	natural abundance		3.25 (±0.25) mM
7	DNA (5'-D(GPCPCPAPAPAPAPAPAPTPCPG)-3')	natural abundance		3.25 (±0.25) mM
8	sodium phosphate buffer	natural abundance		15 mM
9	sodium chloride	natural abundance		25 mM
10	EDTA	natural abundance		0.1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_30254_5uzf.nef
Input source #2: Coordindates	5uzf.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--
CGATTTTTTGGC
||||||||||||
CGATTTTTTGGC

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

------20----
GCCAAAAAATCG
||||||||||||
GCCAAAAAATCG
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	12	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_30254_5uzf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	294		100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	251 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	OK	67 (67)	.	83.3 (chain: A, length: 12), 83.3 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 147
- ¹³C chemical shifts: 115
- ¹⁵N chemical shifts: 10
- 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)
1	DC	C1'	87.9
1	DC	C2'	40.0
1	DC	C4'	88.3
1	DC	C5	99.8
1	DC	C6	143.1
2	DG	C1'	84.0
2	DG	C2'	39.9
2	DG	C4'	87.4
2	DG	C8	138.2
2	DG	N1	147.3
2	DG	P	-0.39
3	DA	C1'	85.0
3	DA	C2	155.0
3	DA	C2'	41.3
3	DA	C4'	87.8
3	DA	C8	141.5
3	DA	P	-0.45
4	DT	C1'	84.8
4	DT	C2'	39.1
4	DT	C4'	85.4
4	DT	C6	138.4
4	DT	C7	14.0
4	DT	N3	159.3
4	DT	P	-0.85
5	DT	C1'	85.3
5	DT	C2'	39.0
5	DT	C4'	85.9
5	DT	C6	140.2
5	DT	C7	14.4
5	DT	N3	159.9
5	DT	P	-0.78
6	DT	C1'	85.2
6	DT	C2'	39.0
6	DT	C4'	86.0
6	DT	C6	140.3
6	DT	C7	14.4
6	DT	N3	159.9
6	DT	P	-0.84
7	DT	C1'	85.2
7	DT	C2'	39.0
7	DT	C4'	86.0
7	DT	C6	140.2
7	DT	C7	14.4
7	DT	N3	159.6
7	DT	P	-0.73
8	DT	C1'	85.2
8	DT	C2'	38.8
8	DT	C4'	85.8
8	DT	C6	140.2
8	DT	C7	14.5
8	DT	N3	159.4
8	DT	P	-0.7
9	DT	C1'	85.0
9	DT	C2'	39.1
9	DT	C4'	85.3
9	DT	C6	139.6
9	DT	C7	14.6
9	DT	N3	159.1
9	DT	P	-0.7
10	DG	C1'	84.1
10	DG	C2'	40.2
10	DG	C4'	87.7
10	DG	C8	138.5
10	DG	N1	147.2
10	DG	P	-0.48
11	DG	C1'	84.9
11	DG	C2'	41.1
11	DG	C4'	86.9
11	DG	C8	137.5
11	DG	N1	147.4
11	DG	P	-0.22
12	DC	C1'	86.5
12	DC	C2'	41.6
12	DC	C4'	86.6
12	DC	C5	98.5
12	DC	C6	143.2
12	DC	P	-0.41

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	76	64.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	46	54.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	30	88.2

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	6	100.0

Aromatic group atoms

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

Entity_assemble_ID: B

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	DG	C1'	85.3
13	DG	C2'	40.3
13	DG	C4'	89.1
13	DG	C8	138.8
14	DC	C1'	86.7
14	DC	C2'	39.7
14	DC	C4'	86.1
14	DC	C5	98.9
14	DC	C6	142.8
14	DC	P	-0.61
15	DC	C1'	86.3
15	DC	C2'	39.3
15	DC	C4'	85.7
15	DC	C5	99.0
15	DC	C6	143.2
15	DC	P	-0.54
16	DA	C1'	84.5
16	DA	C2	154.2
16	DA	C2'	40.1
16	DA	C4'	87.1
16	DA	C8	141.5
16	DA	P	-0.24
17	DA	C1'	84.0
17	DA	C2	153.7
17	DA	C2'	40.8
17	DA	C4'	87.1
17	DA	C8	140.9
17	DA	P	-0.62
18	DA	C1'	84.2
18	DA	C2	153.5
18	DA	C2'	41.3
18	DA	C4'	87.1
18	DA	C8	140.9
18	DA	P	-0.64
19	DA	C1'	84.2
19	DA	C2	153.4
19	DA	C2'	41.7
19	DA	C4'	87.0
19	DA	C8	140.8
19	DA	P	-0.74
20	DA	C1'	84.0
20	DA	C2	153.3
20	DA	C2'	41.9
20	DA	C4'	86.8
20	DA	C8	140.7
20	DA	P	-0.78
21	DA	C1'	84.6
21	DA	C2	154.5
21	DA	C2'	41.9
21	DA	C4'	86.8
21	DA	C8	141.0
21	DA	P	-0.7
22	DT	C1'	84.9
22	DT	C2'	39.5
22	DT	C4'	85.1
22	DT	C6	138.5
22	DT	C7	13.9
22	DT	N3	159.3
22	DT	P	-0.76
23	DC	C1'	86.4
23	DC	C2'	39.5
23	DC	C4'	85.5
23	DC	C5	98.7
23	DC	C6	143.8
23	DC	P	-0.58
24	DG	C1'	84.7
24	DG	C2'	41.9
24	DG	C4'	88.1
24	DG	C8	139.3
24	DG	P	-0.21

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	115	71	61.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	48	57.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	23	74.2

Methyl group atoms

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

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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 251
- Weight of restraints: 1.0 (251)
- Potential type of restraints: square-well-parabolic (251)
- Range of distance target values: 2.15, 5.36 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 83.3%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 83.3%
- Total number of restraints: 67
- Potential type of restraints: square-well-parabolic (67)
- Range of observed RDC values: -9.6, 36.7 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
    None

Keywords DNA, DNA structure and dynamics, Damage recognition and repair, Hoogsteen base pairs, N1-methyladenine