BMRB Entry 17129

Name: Chemical shifts of the 25-mer oligonucleotide encompassing the variable region of a MUC1 DNA aptamer.
Published: 2012-05-22

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17129

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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:

Chemical shifts of the 25-mer oligonucleotide encompassing the variable region of a MUC1 DNA aptamer.

Deposition date:

2010-08-14

Original release date:

2012-05-22

Authors:

Herve du Penhoat, Catherine; Hantz, Edith; Missailidis, Sotiris; Piotto, Martial; Cognet, Jean; Baouendi, Meriem

Citation:

Citation: Baouendi, Meriem; Cognet, Jean; Ferreira, Catia; Missailidis, Sotiris; Coutant, Jerome; Piotto, Martial; Hantz, Edith; Herve du Penhoat, Catherine. "Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR." FEBS J. 279, 479-490 (2012).
PubMed: 22129448

Assembly members:

Assembly members:
25-mer_oligodeoxyribonucleotide, polymer, 25 residues, 8147.2 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
25-mer_oligodeoxyribonucleotide: GCAGTTGATCCTTTGGATAC CCTGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	139
1H chemical shifts	254
31P chemical shifts	25

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	25-mer DNA	1

Entities:

Entity 1, 25-mer DNA 25 residues - 8147.2 Da.

1

DG

DC

DA

DG

DT

DG

DA

DT

DC

2

DC

DT

DG

DA

DT

DA

DC

3

DC

DT

DG

Samples:

sample_2: 25-mer oligodeoxyribonucleotide 1 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 uM; H2O 90%; D2O 10%

sample_1: 25-mer oligodeoxyribonucleotide 2 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 uM; D2O 100%

sample_3: 25-mer oligodeoxyribonucleotide 1 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 uM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: pH: 6.5; pressure: 1 atm; temperature: 264.7 K

sample_conditions_3: pH: 6.5; pressure: 1 atm; temperature: 261.1 K

sample_conditions_4: pH: 6.5; pressure: 1 atm; temperature: 278.0 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P HCOSYINV	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
watergate 1H-1H NOESY	sample_2	isotropic	sample_conditions_4
watergate 1H-1H TOCSY	sample_2	isotropic	sample_conditions_4
watergate 1H-1H NOESY	sample_3	isotropic	sample_conditions_3
g11 1H-1H NOESY	sample_3	isotropic	sample_conditions_2
watergate 1H-1H TOCSY	sample_3	isotropic	sample_conditions_3
2D 1H-31P HSQC_TOCSY	sample_1	isotropic	sample_conditions_1

Software:

PROSA v6.0.2, Guntert - processing

NMRPipe vPC Linux 2004, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN v3.0, Bruker Biospin - collection, processing

XEASY v1.2, Bartels et al. - chemical shift assignment

NMR spectrometers:

Varian UnityPlus 500 MHz
Bruker Avance 500 MHz