BMRB Entry 19280

Name: Structure of d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid
Published: 2013-07-08

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PDB ID: 2m92
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19280
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid

Deposition date:

2013-05-30

Original release date:

2013-07-08

Authors:

Lim, Kah Wai; Phan, Anh Tuan

Citation:

Citation: Lim, Kah Wai; Phan, Anh Tuan. "Structural basis of DNA quadruplex-duplex junction formation." Angew. Chem. Int. Ed. Engl. 52, 8566-8569 (2013).
PubMed: 23794476

Assembly members:

Assembly members:
DNA_(34-MER), polymer, 34 residues, 10702.922 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(34-MER): AGGGTGGGTGCTGGGGCGCG AAGCATTCGCGAGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	263

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (34-MER)	1

Entities:

Entity 1, DNA (34-MER) 34 residues - 10702.922 Da.

1

DA

DG

DT

DG

DT

DG

2

DC

DT

DG

DC

DG

DC

DG

3

DA

DG

DC

DA

DT

DC

DG

DC

4

DG

DA

DG

Samples:

DNA-1: DNA (34-MER) 0.5-2.0 mM; H2O 90%; D2O 10%

DNA-2: DNA (34-MER) 0.5-2.0 mM

DNA-3: DNA (34-MER), [U-2% 15N], 0.5-2.0 mM

DNA-4: DNA (34-MER), [U-100% 2H], 0.5-2.0 mM

sample_conditions_1: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	DNA-2	isotropic	sample_conditions_1
2D 1H-1H JR NOESY	DNA-1	isotropic	sample_conditions_1
2D 1H-1H JR NOESY	DNA-1	isotropic	sample_conditions_2
2D 1H-1H COSY	DNA-2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	DNA-2	isotropic	sample_conditions_1
2D 1H-13C HSQC	DNA-2	isotropic	sample_conditions_1
2D 1H-13C JR HMBC	DNA-1	isotropic	sample_conditions_1
H-D EXCHANGE	DNA-2	isotropic	sample_conditions_1
15N-FILTERED	DNA-3	isotropic	sample_conditions_1
15N-FILTERED	DNA-3	isotropic	sample_conditions_2
D-LABELED	DNA-4	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - processing

FELIX v2007, Felix NMR, Inc. - peak picking

X-PLOR NIH v2.29, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 400 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz