2N9F

Glucose as non natural nucleobase

• PDB DOI: https://doi.org/10.2210/pdb2N9F/pdb
• NAKB: 2N9F
• BMRB: 25903

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-11-20 Released: 2016-08-31 
• Deposition Author(s): Gomez-Pinto, I., Vengut-Climent, E., Lucas, R., Avino, A., Eritja, R., Gonzalez-Ibanez, C., Morales, J., Penalver, P., Fonseca-Guerra, C., Bickelhaupt, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA.

Vengut-Climent, E., Gomez-Pinto, I., Lucas, R., Penalver, P., Avino, A., Fonseca Guerra, C., Bickelhaupt, F.M., Eritja, R., Gonzalez, C., Morales, J.C.

(2016) Angew Chem Int Ed Engl 55: 8643-8647

• PubMed: 27328804 
• DOI: https://doi.org/10.1002/anie.201603510
• Primary Citation of Related Structures:  
  2N9F, 2N9H


• PubMed Abstract: 
  

  Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair.

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Organizational Affiliation: 

Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Américo Vespucio 49, 41092, Sevilla, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.34 kDa 
• Atom Count: 486 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3')	A	12	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*TP*GP*AP*CP*(4JA)P*GP*CP*TP*AP*G)-3')	B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Gomez-Pinto, I., Vengut-Climent, E., Lucas, R., Avino, A., Eritja, R., Gonzalez-Ibanez, C., Morales, J., Penalver, P., Fonseca-Guerra, C., Bickelhaupt, M.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2023-06-14
  Changes: Database references, Other, Structure summary
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references