BMRB Entry 36174

Name: SOLUTION NMR STRUCTURE OF A 14-MER DOUBLE STRANDED DNA DUPLEX CGCGAAATTTCGCG
Published: 2019-08-06

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PDB ID: 5zld
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36174
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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:

SOLUTION NMR STRUCTURE OF A 14-MER DOUBLE STRANDED DNA DUPLEX CGCGAAATTTCGCG

Deposition date:

2018-03-27

Original release date:

2019-08-06

Authors:

Ganguly, S.; Basu, G.

Citation:

Citation: Ganguly, Sudakshina; Murugan, N Arul; Ghosh, Debasis; Narayanaswamy, Nagarjun; Govindaraju, Thimmaiah; Basu, Gautam. "DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe" Biochemistry 60, 2084-2097 (2021).
PubMed: 34142803

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 4280.792 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):
entity_1: CGCGAAATTTCGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	258

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_A	1
2	entity_B	1

Entities:

Entity 1, entity_A 14 residues - 4280.792 Da.

1

DC

DG

DC

DG

DA

DT

2

DC

DG

DC

DG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3') 300 uM; H2O 90%; D2O, [U-2H], 10%

sample_2: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3') 300 uM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 10 mM; pH: 7.0 .; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 10 mM; pH: 7.0 .; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN v3.0, Bruker Biospin - data analysis

NMR spectrometers:

Bruker AvanceIII 700 MHz