2N4J | pdb_00002n4j

Solution structure of a self complementary Xylonucleic Acid duplex

• PDB DOI: https://doi.org/10.2210/pdb2N4J/pdb
• BMRB: 25669
• NAKB: 2N4J

• Classification: UNKNOWN FUNCTION
• Mutation(s): No 


• Deposited: 2015-06-19 Released: 2015-07-29 
• Deposition Author(s): Maiti, M., Lescrinier, E., Herdewijn, P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Xylonucleic acid: synthesis, structure, and orthogonal pairing properties.

Maiti, M., Maiti, M., Knies, C., Dumbre, S., Lescrinier, E., Rosemeyer, H., Ceulemans, A., Herdewijn, P.

(2015) Nucleic Acids Res 43: 7189-7200

• PubMed: 26175047 
• DOI: https://doi.org/10.1093/nar/gkv719
• Primary Citation Related Structures: 
  2N4J


• PubMed Abstract: 
  

  There is a common interest for studying xeno-nucleic acid systems in the fields of synthetic biology and the origin of life, in particular, those with an engineered backbone and possessing novel properties. Along this line, we have investigated xylonucleic acid (XyloNA) containing a potentially prebiotic xylose sugar (a 3'-epimer of ribose) in its backbone. Herein, we report for the first time the synthesis of four XyloNA nucleotide building blocks and the assembly of XyloNA oligonucleotides containing all the natural nucleobases. A detailed investigation of pairing and structural properties of XyloNAs in comparison to DNA/RNA has been performed by thermal UV-melting, CD, and solution state NMR spectroscopic studies. XyloNA has been shown to be an orthogonal self-pairing system which adopts a slightly right-handed extended helical geometry. Our study on one hand, provides understanding for superior structure-function (-pairing) properties of DNA/RNA over XyloNA for selection as an informational polymer in the prebiotic context, while on the other hand, finds potential of XyloNA as an orthogonal genetic system for application in synthetic biology.

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Organizational Affiliation: 
• Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
Organic Materials Chemistry and Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastrasse. 7, D-49069 Osnabrück, Germany.
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.05 kDa 
• Atom Count: 334 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
XNA (5'-R(*(8XG)P*(8XU)P*(8XG)P*(8XU)P*(8XA)P*(8XC)P*(8XA)P*(8XC))-3')	A, B	8	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Maiti, M., Lescrinier, E., Herdewijn, P.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references