BMRB Entry 52101

Name: dGrU-RNA-DNA-Hybrid-R1rho
Published: 2024-01-04

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52101

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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:

dGrU-RNA-DNA-Hybrid-R1rho

Deposition date:

2023-08-25

Original release date:

2024-01-04

Authors:

Szekely, Or; Rangadurai, Atul; Gu, Stephanie; Manghrani, Akanksha; Guseva, Serafima; Al-Hashimi, Hashim

Citation:

Citation: Szekely, Or; Rangadurai, Atul; Gu, Stephanie; Manghrani, Akanksha; Guseva, Serafima; Al-Hashimi, Hashim. "NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G.T/U in RNA:DNA hybrids: Implications for the fidelity of transcription and CRISPR/Cas9 gene editing" .
PubMed: 37662220

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, Formula weight is not available
entity_2, polymer, 12 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available 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: CTGACGGATCGC
entity_2: GCGAUUCGUCAG

Data sets:

heteronucl_T1rho_relaxation

Data type

Count

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA strand	1
2	RNA strand	2

Entities:

Entity 1, DNA strand 12 residues - Formula weight is not available

G7 is [U-13C; U-15N] labeled

1

DC

DT

DG

DA

DC

DG

DA

DT

DC

2

DG

DC

Entity 2, RNA strand 12 residues - Formula weight is not available

U18 is [15N-N3] labeled

1

G

C

G

A

U

C

G

U

C

2

A

G

Samples:

sample_1: dGrU, RNA strand, [15N-N3]-rU18, 0.8 mM; dGrU, DNA strand, [U-13C; U-15N]-dG7, 0.8 mM; Sodium Phosphate 15 mM; NaCl 25 mM; EDTA 0.1 mM

sample_2: dGrU, RNA strand, [15N-N3]-rU18, 0.8 mM; dGrU, DNA strand, [U-13C; U-15N]-dG7, 0.8 mM; Sodium Phosphate 15 mM; NaCl 25 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 51 mM; pH: 7.4; pressure: 1 atm; temperature: 298.2 K

sample_conditions_2: ionic strength: 51 mM; pH: 7.8; pressure: 1 atm; temperature: 298.2 K

Experiments:

Name	Sample	Sample state	Sample conditions
T1rho/R1rho relaxation	sample_1	isotropic	sample_conditions_1
T1rho/R1rho relaxation	sample_2	isotropic	sample_conditions_2

Software:

NMRPipe v10.6 Revision 2020.007.13.34 - processing

NMR spectrometers:

Bruker AVANCE III 700 MHz