BMRB Entry 25723

Name: Universal Base oligonucleotide structure
Published: 2016-09-06

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PDB ID: 2n5o
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25723
MolProbity Validation Chart

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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:

Universal Base oligonucleotide structure

Deposition date:

2015-07-23

Original release date:

2016-09-06

Authors:

Spring-Connell, Alexander; Evich, Marina; Seela, Frank; Germann, Markus

Citation:

Citation: Spring-Connell, Alexander; Evich, Marina; Debelak, Harald; Seela, Frank; Germann, Markus. "Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog" Nucleic Acids Res. 44, 8576-8587 (2016).
PubMed: 27566150

Assembly members:

Assembly members:
DNA_(5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3'), polymer, 9 residues, 2423.621 Da.
DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), polymer, 9 residues, 2715.821 Da.

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):
DNA_(5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3'): ATGGXGCTC
DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'): GAGCTCCAT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	136
31P chemical shifts	16

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(APTPGPGP(UB)PGPCPTP*C)-3')	1
2	DNA (5'-D(GPAPGPCPTPCPCPAP*T)-3')	2

Entities:

Entity 1, DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') 9 residues - 2423.621 Da.

1

DA

DT

DG

4EN

DG

DC

DT

DC

Entity 2, DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 9 residues - 2715.821 Da.

1

DG

DA

DG

DC

DT

DC

DA

DT

Samples:

D2O_sample: DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') 1 mM; DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM; D2O, 100% deuterium, 100%; sodium chloride 100 mM; sodium phosphate 10 mM

H2O_sample: DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') 1 mM; DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM; sodium chloride 100 mM; sodium phosphate 10 mM; D2O, 100% deuterium, 10%; H2O 90%

D2O_conditions: ionic strength: 100 mM; pH*: 6.36; pressure: 1 atm; temperature: 294 K

H2O_conditions: pH: 6.79

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY 75 ms	D2O_sample	isotropic	D2O_conditions
2D 1H-1H NOESY 150 ms	D2O_sample	isotropic	D2O_conditions
2D 1H-1H NOESY 250 ms	D2O_sample	isotropic	D2O_conditions
2D Low Flip COSY	D2O_sample	isotropic	D2O_conditions
2D 1H-13C HSQC	D2O_sample	isotropic	D2O_conditions
2D 1H-1H constant time NOESY	D2O_sample	isotropic	D2O_conditions
2D 1H-1H TOCSY	D2O_sample	isotropic	D2O_conditions
2D 1H-31P CORR	D2O_sample	isotropic	D2O_conditions
1D 1H	D2O_sample	isotropic	D2O_conditions
1D 1H 1-1 jump and return	H2O_sample	isotropic	H2O_conditions
1D 31P	D2O_sample	isotropic	D2O_conditions
2D 1H-1H NOESY 1-1 jump and return	H2O_sample	isotropic	H2O_conditions

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

SPARKY, Goddard - chemical shift assignment, peak picking

xwinnmr, Bruker Biospin - collection

CORMA, Thomas James - data analysis, refinement

MARDIGRAS, Thomas James - data analysis, refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 500 MHz