BMRB Entry 34836

Name: TINA-conjugated antiparallel DNA triplex
Published: 2024-01-11

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PDB ID: 8pwr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34836
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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:

TINA-conjugated antiparallel DNA triplex

Deposition date:

2023-07-21

Original release date:

2024-01-11

Authors:

Garavis, M.; Edwards, P.; Serrano-Chacon, I.; Doluca, O.; Filichev, V.; Gonzalez, C.

Citation:

Citation: Garavis, M.; Edwards, P.; Serrano-Cachon, I.; Doluca, O.; Filichev, V.; Gonzalez, C.. "Understanding intercalative modulation of G-rich sequence folding: Solution structure of a TINA-conjugated antiparallel DNA triplex" .

Assembly members:

Assembly members:
entity_1, polymer, 7 residues, 2024.348 Da.
entity_2, polymer, 7 residues, 2211.486 Da.
entity_3, polymer, 8 residues, 2636.882 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: TCCTCCT
entity_2: AGGAGGA
entity_3: TGGTGXGT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	213

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	3

Entities:

Entity 1, unit_1 7 residues - 2024.348 Da.

1

DT

DC

DT

DC

DT

Entity 2, unit_2 7 residues - 2211.486 Da.

1

DA

DG

DA

DG

DA

Entity 3, unit_3 8 residues - 2636.882 Da.

1

DT

DG

DT

DG

X0K

DG

DT

Samples:

sample_1: Triplex-TINA 0.5 mM

sample_2: Triplex-TINA 0.5 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 279.6 K

sample_conditions_2: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 300.4 K

Experiments:

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

Software:

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment, peak picking

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

TopSpin, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE 600 MHz
Bruker AVANCE 800 MHz