BMRB Entry 34596

Name: Solution structure of DNA duplex containing a 7,8-dihydro-8-oxo-1,N6-ethenoadenine base modification that induces exclusively A-&gt;T transversions in Escherichia coli
Published: 2022-02-25

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PDB ID: 7nbp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34596
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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:

Solution structure of DNA duplex containing a 7,8-dihydro-8-oxo-1,N6-ethenoadenine base modification that induces exclusively A->T transversions in Escherichia coli

Deposition date:

2021-01-27

Original release date:

2022-02-25

Authors:

Aralov, A.; Gubina, N.; Cabrero, C.; Tsvetkov, V.; Turaev, A.; Fedeles, B.; Croy, R.; Isaakova, E.; Melnik, D.; Dukova, S.; Khrulev, A.; Varizhuk, A.; Gonzalez, C.; Zatsepin, T.; Essigmann, J.

Citation:

Citation: Aralov, Andrey; Gubina, Nina; Cabrero, Cristina; Tsvetkov, Vladimir; Turaev, Anton; Fedeles, Bogdan; Croy, Robert; Isaakova, Ekaterina; Melnik, Denis; Dukova, Svetlana; Ryazantsev, Dmitriy; Khrulev, Alexei; Varizhuk, Anna; Gonzalez, Carlos; Zatsepin, Timofei; Essigmann, John. "7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A\u2192T transversions in Escherichia coli" Nucleic Acids Res. 50, 3056-3069 (2022).
PubMed: 35234900

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 2763.845 Da.
entity_2, polymer, 9 residues, 2739.824 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTACXCATG
entity_2: CATGAGTAC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	146

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

Entities:

Entity 1, unit_1 9 residues - 2763.845 Da.

1

DG

DT

DA

DC

U7T

DC

DA

DT

DG

Entity 2, unit_2 9 residues - 2739.824 Da.

1

DC

DA

DT

DG

DA

DG

DT

DA

DC

Samples:

sample_1: DNA (5'-D(*GP*TP*AP*CP*(EDA)P*CP*AP*TP*G)-3') 0.5 M; DNA (5'-D(*CP*AP*TP*GP*AP*GP*TP*AP*C)-3') 0.5 M; sodium phosphate 25 mM; sodium chloride 100 mM; DSS 0.5 % v/v

sample_conditions_1: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 276 K

sample_conditions_2: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 278 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_1	isotropic	sample_conditions_2

Software:

TopSpin, Bruker Biospin - collection, processing

NMRFAM-SPARKY, Goddard & Kneller - chemical shift assignment

Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

MOLMOL, Koradi, Billeter and Wuthrich - data analysis

3DNA, Lu & Olson - data analysis

NMR spectrometers:

Bruker AVANCE 600 MHz