BMRB Entry 25906
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25906
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Title: Glucose as a nuclease mimic in DNA PubMed: 27328804
Deposition date: 2015-11-25 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; Muro, Alicia; Penalver, Pablo; Fonseca-Guerra, Celia; Bickelhaupt, Matthias
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).
Assembly members:
DNA_(5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3'), polymer, 12 residues, 3702.458 Da.
DNA_(5'-D(*CP*TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3'), polymer, 12 residues, 3578.391 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3'): GATGACTGCTAG
DNA_(5'-D(*CP*TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3'): CTAGCXGTCATC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 235 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3') | 1 |
| 2 | DNA (5'-D(*CP*TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3') | 2 |
Entities:
Entity 1, DNA (5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3') 12 residues - 3702.458 Da.
| 1 | DG | DA | DT | DG | DA | DC | DT | DG | DC | DT | ||||
| 2 | DA | DG |
Entity 2, DNA (5'-D(*CP*TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3') 12 residues - 3578.391 Da.
| 1 | DC | DT | DA | DG | DC | 4JA | DG | DT | DC | DA | ||||
| 2 | DT | DC |
Samples:
sample_1: DNA (5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3') 1 mM; DNA (5'-D(*CP*TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3') 1 mM; SUGAR 1 mM; Potassium phosphate 10 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