BMRB Entry 34906

Name: An i-motif/B-DNA aptamer with high affinity for influenza A virus
Published: 2025-02-04

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PDB ID: 8s4n
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34906
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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:

An i-motif/B-DNA aptamer with high affinity for influenza A virus

Deposition date:

2024-02-21

Original release date:

2025-02-04

Authors:

Tsvetkov, V.; Mir, B.; Alieva, R.; Arutyunyan, A.; Oleynikov, I.; Novikov, R.; Boravleva, E.; Kamzeeva, P.; Zatsepin, T.; Aralov, A.; Gonzalez, C.; Zavyalova, E.

Citation:

Citation: Tsvetkov, V.; Mir, B.; Alieva, R.; Arutyunyan, A.; Oleynikov, I.; Novikov, R.; Boravleva, E.; Kamzeeva, P.; Zatsepin, T.; Aralov, A.; Gonzalez, C.; Zavyalova, E.. "Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus" Nucleic Acids Res. 53, gkae1282-gkae1282 (2025).
PubMed: 39777463

Assembly members:

Assembly members:
entity_1, polymer, 43 residues, 12884.235 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGCTCACGCXXXGTDTTCCC DCCCCCDCCCGTDTTXXXCC GTGAGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	196

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 43 residues - 12884.235 Da.

1

DC

DG

DC

DT

DC

DA

DC

DG

DC

DNR

2

DNR

DG

DT

DC

3

DC

DG

DT

4

DT

DNR

DC

DG

DT

DG

DA

5

DG

DC

DG

Samples:

sample_1: DNA (43-MER) 800 uM; sodium phosphate 10 mM; DSS 0.5 v/v

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 6; 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

Sparky, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

MOLMOL, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Bruker AVANCE 600 MHz