BMRB Entry 25903

Name: Glucose as non natural nucleobase
Published: 2016-08-25

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PDB ID: 2n9f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25903
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:

Glucose as non natural nucleobase

Deposition date:

2015-11-20

Original release date:

2016-08-25

Authors:

Gomez-Pinto, Irene; Vengut-Climent, Empar; Lucas, Ricardo; Avino, Anna; Eritja, Ramon; Gonzalez-Ibanez, Carlos; Morales, Juan Carlos; Penalver, Pablo; Fonseca-Guerra, Celia; Bickelhaupt, Matthias

Citation:

Citation: Vengut-Climent, Empar; Gomez-Pinto, Irene; Lucas, Ricardo; Penalver, Pablo; Avino, Anna; Fonseca-Guerra, Celia; Bickelhaupt, Matthias; Eritja, Ramon; Gonzalez-Ibanez, Carlos; Morales, Juan Carlos. "Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA" Angew. Chem. Int. Ed. Engl. 55, 8643-8647 (2016).
PubMed: 27328804

Assembly members:

Assembly members:
DNA_(5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3'), polymer, 12 residues, 3638.409 Da.
DNA_(5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3'), polymer, 12 residues, 3667.453 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3'): CTAGCGGTCATC
DNA_(5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3'): GATGACXGCTAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	212

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPTPAPGPCPGPGPTPCPAPTPC)-3')	1
2	DNA (5'-D(GPAPTPGPAPCP(GL6)PGPCPTPAPG)-3')	2

Entities:

Entity 1, DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3') 12 residues - 3638.409 Da.

1

DC

DT

DA

DG

DC

DG

DT

DC

DA

2

DT

DC

Entity 2, DNA (5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3') 12 residues - 3667.453 Da.

1

DG

DA

DT

DG

DA

DC

4JA

DG

DC

DT

2

DA

DG

Samples:

sample_1: DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3') 1 mM; DNA (5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3') 1 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 279.6 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Bruker Biospin, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman, Goddard - chemical shift assignment, processing, refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz