7BFS | pdb_00007bfs

deoxyxylose nucleic acid hairpin

• PDB DOI: https://doi.org/10.2210/pdb7BFS/pdb
• BMRB: 34587
• NAKB: 7BFS

• Classification: DNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-04 Released: 2021-01-27 
• Deposition Author(s): Mattelaer, C.-A., Mohitosh, M., Smets, L., Maiti, M., Schepers, G., Mattelaer, H.-P., Rosemeyer, H., Herdewijn, P., Lescrinier, E.
• Funding Organization(s): KU Leuven, Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

Stable Hairpin Structures Formed by Xylose-Based Nucleic Acids.

Mattelaer, C.A., Maiti, M., Smets, L., Maiti, M., Schepers, G., Mattelaer, H.P., Rosemeyer, H., Herdewijn, P., Lescrinier, E.

(2021) Chembiochem 22: 1638-1645

• PubMed: 33427360 
• DOI: https://doi.org/10.1002/cbic.202000803
• Primary Citation Related Structures: 
  7BFS, 7BFX


• PubMed Abstract: 
  

  Xenobiology explores synthetic nucleic acid polymers as alternative carriers of genetic information to expand the central dogma. The xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA), containing 3' epimers of riboses and deoxyriboses, are considered to be potential candidates for an orthogonal system. In this study, thermal and spectroscopic analyses show that XyNA and dXyNA form stable hairpins. The dXyNA hairpin structure determined by NMR spectroscopy contains a flexible loop that locks the stem into a stable ladder-like duplex with marginal right-handed helicity. The reduced flexibility of the dXyNA duplex observed in the stem of the hairpin demonstrates that folding of dXyNA yields more stable structures described so far.

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Organizational Affiliation: 
• Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium.
Research Centre for Operations Management, Faculty of Economics and Business, KU Leuven, Naamsestraat 69, 3000, Leuven, Belgium.
Present address: Membrane Separations, Adsorption, Catalysis, and Spectroscopy for Sustainable Solutions (cMACS), KU Leuven (Arenberg), Celestijnenlaan 200f, Box 2454, 3001, Leuven, Belgium.
Organische Materialchemie (OMC), Universität Osnabrück, Institut für Chemie neuer Materialien, Barbarastraße 7, 49076, Osnabrück, Germany.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content 

• Total Structure Weight: 6.06 kDa 
• Atom Count: 401 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')	A	20	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Mattelaer, C.-A., Mohitosh, M., Smets, L., Maiti, M., Schepers, G., Mattelaer, H.-P., Rosemeyer, H., Herdewijn, P., Lescrinier, E.

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Funding Organization	Location	Grant Number
KU Leuven	Belgium	C14/29/102
Research Foundation - Flanders (FWO)	Belgium	1S23217N

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2021-05-12
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references