BMRB Entry 34502

Name: LNA modified G-quadruplex with flipped G-tract and central tetrad
Published: 2020-08-31

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PDB ID: 6yep
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34502
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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:

LNA modified G-quadruplex with flipped G-tract and central tetrad

Deposition date:

2020-03-25

Original release date:

2020-08-31

Authors:

Weisz, K.; Haase, L.

Citation:

Citation: Haase, Linn; Weisz, Klaus. "Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design" Nucleic Acids Res. 48, 10555-10566 (2020).
PubMed: 32890406

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 7000.501 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: GGGATGGGACACAGXGGACG GG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	24
1H chemical shifts	125

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 22 residues - 7000.501 Da.

1

DG

DA

DT

DG

DA

DC

2

DA

DC

DA

DG

LCG

DG

DA

DC

DG

3

DG

Samples:

sample_1: L15 0.4 mM

sample_2: L15 0.4 mM

sample_conditions_1: ionic strength: 15 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v4.0.4, Bruker Biospin - processing

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment

X-PLOR NIH v2.49, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE NEO 600 MHz