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BMRB: 19278

2M90

Structure of d[GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG] duplex-quadruplex hybrid

Authors

Lim, K., Phan, A.

Assembly

d[GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG] duplex-quadruplex hybrid

Entity

1. d[GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG] duplex-quadruplex hybrid (polymer, Thiol state: not present), 32 monomers, 10181.45 Da Detail

GCGCGAAGCA TTCGCGGGGA GGTGGGGAAG GG

Formula weight

10181.45 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.0 %, Completeness (bb): 82.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	85.0 % (256 of 301)	85.0 % (256 of 301)
Suger, PO4	82.1 % (184 of 224)	82.1 % (184 of 224)
Nucleobase	93.5 % (72 of 77)	93.5 % (72 of 77)
Aromatic	95.3 % (61 of 64)	95.3 % (61 of 64)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA (32-MER)

GCGCGAAGCA TTCGCGGGGA GGTGGGGAAG GG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (32-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (32-MER)	[U-2% 15N]	0.5-2.0 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
9	DNA (32-MER)	[U-100% 2H]		0.5-2.0 mM
10	D2O	natural abundance		100 %

Release date

2013-07-07

Citation

Structural basis of DNA quadruplex-duplex junction formation
Lim, K., Phan, A.
Angew. Chem Int Ed Engl. (2013), 52, 8566-8569, PubMed 23794476 , DOI 10.1002/anie.201302995 , Abstract

Entries sharing articles BMRB: 5 entries Detail

  BMRB: 19276 released on 2013-07-07
    Title Structure of d[CGCGAAGCATTCGCG] hairpin
  BMRB: 19277 released on 2013-07-07
    Title Structure of d[GGTTGGCGCGAAGCATTCGCGGGTTGG] duplex-quadruplex hybrid
  BMRB: 19279 released on 2013-07-07
    Title Structure of d[GGGAAGGGCGCGAAGCATTCGCGAGGTAGG] duplex-quadruplex hybrid
  BMRB: 19280 released on 2013-07-07
    Title Structure of d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid
  BMRB: 19281 released on 2013-07-07
    Title Structure of d[TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT] duplex-quadruplex hybrid

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

2 2D 1H-1H JR NOESY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (32-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

3 2D 1H-1H JR NOESY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (32-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 2D 1H-1H COSY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

7 2D 1H-13C JR HMBC

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (32-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 2D 1H-31P HSQC

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

9 H-D EXCHANGE

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (32-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

10 15N-FILTERED

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (32-MER)	[U-2% 15N]	0.5-2.0 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 D-LABELED

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
9	DNA (32-MER)	[U-100% 2H]		0.5-2.0 mM
10	D2O	natural abundance		100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19278_2m90.nef
Input source #2: Coordindates	2m90.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--------20--------30--
GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG
||||||||||||||||||||||||||||||||
GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	32	0	0	100.0

Content subtype: combined_19278_2m90.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	266		100.0 (chain: A, length: 32)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1151 (1)	noe	100.0 (chain: A, length: 32)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	1 (1)	noe	6.2 (chain: A, length: 32)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	82 (1)	hbond	78.1 (chain: A, length: 32)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	72 (72)	.	75.0 (chain: A, length: 32)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 266
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
18	DG	H21	9.789
18	DG	H22	8.714
21	DG	H21	9.226
21	DG	H22	6.786

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	301	256	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	224	184	82.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	72	93.5

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of restraints: 1151
- Weight of restraints: 1.0 (1151)
- Potential type of restraints: square-well-parabolic (1151)
- Range of distance target values: 2.4, 6.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 6.2%
  - Total number of restraints: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Range of distance target values: 42.1, 42.1 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_2
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 78.1%
    - Total number of restraints: 82
    - Weight of restraints: 1.0 (82)
    - Potential type of restraints: square-well-parabolic (82)
    - Range of distance target values: 2.0, 2.9 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 75.0%
- Total number of restraints: 72
- Total number of restraints per polymer type: 72
- Weight of restraints: 1.0 (72)
- Potential type of restraints: square-well-parabolic (72)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA, duplex, duplex-quadruplex hybrid, quadruplex

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Found 1 Document (0.41 seconds)

BMRB: 19278

Sample #1

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Entries sharing articles BMRB: 5 entries Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 6 contents Detail