BMRB Entry 30730

Name: Tandem UU:GA mismatch within an RNA helix
Published: 2020-08-31

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30730

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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: Tandem UU:GA mismatch within an RNA helix PubMed: 32786414

Deposition date: 2020-02-28 Original release date: 2020-08-31

Authors: Nikonowicz, E.; Chang, A.

Citation: Chang, A.; Chen, L.; Song, L.; Zhang, S.; Nikonowicz, E.. "2-Amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA)" Biochemistry ., .-. (2020).

Assembly members:
entity_1, polymer, 28 residues, 8963.334 Da.

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

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGGCUGUGAUGCUUCGGCAU AUCAGCCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	215
15N chemical shifts	51
1H chemical shifts	239

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 28 residues - 8963.334 Da.

1

G

C

U

G

U

G

A

U

2

G

C

U

C

G

C

A

U

3

A

U

C

A

G

C

Samples:

sample_1: RNA 1.5 mM

sample_2: RNA, [U-99% 13C; U-99% 15N], 1.3 mM

sample_3: RNA, [U-99% 13C; U-99% 15N], 0.25 mM

sample_4: RNA, [U-99% 13C; U-99% 15N], 1.4 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 299 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 285 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C ct-HSQC	sample_3	anisotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_2
2D 1H-13C ctep-HSQC	sample_2	isotropic	sample_conditions_1
2d H(CN)C	sample_2	isotropic	sample_conditions_1
2D H(N)CO	sample_4	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_2

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

Felix, Accelrys Software Inc. - chemical shift assignment, peak picking

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz