BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 25906

Title: Glucose as a nuclease mimic in DNA   PubMed: 27328804

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

Data sets:
Data typeCount
1H chemical shifts235

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3')1
2DNA (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   DGDADTDGDADCDTDGDCDT
2   DADG

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   DCDTDADGDC4JADGDTDCDA
2   DTDC

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_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

Related Database Links: