BMRB Entry 34280

Name: Tc-DNA/DNA duplex
Published: 2018-06-07

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PDB ID: 6gpi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34280
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Tc-DNA/DNA duplex

Deposition date:

2018-06-05

Original release date:

2018-06-07

Authors:

Istrate, A.; Johannsen, S.; Istrate, A.; Sigel, R.; Leumann, C.

Citation:

Citation: Istrate, A.; Johannsen, S.; Istrate, A.; Sigel, R.; Leumann, C.. "NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance" Nucleic Acids Res. 47, 4872-4882 (2019).
PubMed: 30916334

Assembly members:

Assembly members:
entity_1, polymer, 10 residues, 3352.575 Da.
entity_2, polymer, 10 residues, 3094.042 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: XXXXXXXXAX
entity_2: GTAAGCCGAG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	59
1H chemical shifts	234

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 10 residues - 3352.575 Da.

1

F7H

EAN

TCJ

F4Q

TCJ

EAN

TCY

TCJ

Entity 2, entity_2 10 residues - 3094.042 Da.

1

DG

DT

DA

DG

DC

DG

DA

DG

Samples:

sample_1: tc-DNA/DNA 0.5 mM; tc-DNA/DNA 0.5 mM; NaCl 50 mM; NaH2PO4 10 mM

sample_2: tc-DNA/DNA 0.5 mM; tc-DNA/DNA 0.5 mM; NaCl 50 mM; NaH2PO4 10 mM

sample_conditions_1: pH: 7.05; pressure: 1 atm; temperature: 298 K

sample_conditions_2: pH: 7.05; pressure: 1 atm; temperature: 283 K

sample_conditions_3: pH: 7.05; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

GROMOS, van Gunsteren and Berendsen - refinement

SPARKY, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker AvanceII 700 MHz