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BMRB: 18640

2LWO

Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion

Authors

Zalianyak, T., de los Santos, C., Lukin, M., Attaluri, S., Johnson, F.

Assembly

Duplex DNA Containing a b-Carba-Fapy-dG Lesion

Entity

1. 11 mer oligonucleotide-B (polymer, Thiol state: not present), 11 monomers, 3413.201 Da Detail

CGTACXCATG C

2. 11 mer oligonucleotide-D (polymer, Thiol state: not present), 11 monomers, 3437.182 Da Detail

GCATGCGTAC G

Total weight

6850.383 Da

Max. entity weight

3437.182 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 64.7 %, Completeness (bb): 67.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	64.7 % (134 of 207)	64.7 % (134 of 207)
Suger, PO4	67.3 % (99 of 147)	67.3 % (99 of 147)
Nucleobase	58.3 % (35 of 60)	58.3 % (35 of 60)
Aromatic	73.8 % (31 of 42)	73.8 % (31 of 42)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. 11 mer oligonucleotide-B

CGTACXCATG C

2. 11 mer oligonucleotide-D

GCATGCGTAC G

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.0 ~ 0.0 mM
2	11_mer_oligonucleotide-D	natural abundance		0.0 ~ 0.0 mM
3	phosphate buffer	natural abundance		25 mM
4	NaCl	natural abundance		50 mM
5	EDTA	natural abundance		0.5 mM
6	D2O	natural abundance		100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	11_mer_oligonucleotide-B	natural abundance		1.5 mM
8	11_mer_oligonucleotide-D	natural abundance		1.5 mM
9	phosphate buffer	natural abundance		25 mM
10	NaCl	natural abundance		50 mM
11	EDTA	natural abundance		0.5 mM
12	D2O	natural abundance		10 %
13	H2O	natural abundance		90 %

Release date

2013-02-17

Citation

Solution structure of duplex DNA containing a β-carba-Fapy-dG lesion
Lukin, M., Zalianyak, T., Attaluri, S., Johnson, F., de los Santos, C.
Chem. Res. Toxicol. (2012), 25, 2423-2431, PubMed 22897814 , DOI 10.1021/tx300290b , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 18638 released on 2013-02-17
    Title Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion
  BMRB: 18639 released on 2013-02-17
    Title Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.0 ~ 0.0 mM
2	11_mer_oligonucleotide-D	natural abundance		0.0 ~ 0.0 mM
3	phosphate buffer	natural abundance		25 mM
4	NaCl	natural abundance		50 mM
5	EDTA	natural abundance		0.5 mM
6	D2O	natural abundance		100 %

2 2D 1H-1H COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.0 ~ 0.0 mM
2	11_mer_oligonucleotide-D	natural abundance		0.0 ~ 0.0 mM
3	phosphate buffer	natural abundance		25 mM
4	NaCl	natural abundance		50 mM
5	EDTA	natural abundance		0.5 mM
6	D2O	natural abundance		100 %

3 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.0 ~ 0.0 mM
2	11_mer_oligonucleotide-D	natural abundance		0.0 ~ 0.0 mM
3	phosphate buffer	natural abundance		25 mM
4	NaCl	natural abundance		50 mM
5	EDTA	natural abundance		0.5 mM
6	D2O	natural abundance		100 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.0 ~ 0.0 mM
2	11_mer_oligonucleotide-D	natural abundance		0.0 ~ 0.0 mM
3	phosphate buffer	natural abundance		25 mM
4	NaCl	natural abundance		50 mM
5	EDTA	natural abundance		0.5 mM
6	D2O	natural abundance		100 %

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.0 ~ 0.0 mM
2	11_mer_oligonucleotide-D	natural abundance		0.0 ~ 0.0 mM
3	phosphate buffer	natural abundance		25 mM
4	NaCl	natural abundance		50 mM
5	EDTA	natural abundance		0.5 mM
6	D2O	natural abundance		100 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	11_mer_oligonucleotide-B	natural abundance		1.5 mM
8	11_mer_oligonucleotide-D	natural abundance		1.5 mM
9	phosphate buffer	natural abundance		25 mM
10	NaCl	natural abundance		50 mM
11	EDTA	natural abundance		0.5 mM
12	D2O	natural abundance		10 %
13	H2O	natural abundance		90 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18640_2lwo.nef
Input source #2: Coordindates	2lwo.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:6:DC:O3'	1:7:LWM:P1	unknown	unknown	n/a
1:7:LWM:O3'	1:8:DC:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	6	LWM	[(1R,2S,4R)-4-{[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl dihydrogen phosphate	Assigned chemical shifts, Coordinates

Sequence alignments

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

-------------10-
....GCGTACXCATGC
    ||||||      
GCATGCGTACG-.-.-
--------10- - -

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
B	B	12	0	0	100.0
D	D	11	0	0	100.0

Content subtype: combined_18640_2lwo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	142		91.7 (chain: B, length: 12), 100.0 (chain: D, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	400 (1)	noe	83.3 (chain: B, length: 12), 100.0 (chain: D, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 91.7%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 142
- Completeness of assignments
  - Entity_assemble_ID: B
  - Entity_assemble_ID: D
- Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 83.3%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 400
- Weight of restraints: 1.0 (400)
- Potential type of restraints: square-well-parabolic (400)
- Range of distance target values: 1.53, 7.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: B
  - Chain_ID: D
- Distance restraints on contact map

Keywords DNA, Fapy-dG lesion, NMR, Oxidative damage