Xylonucleic acid: synthesis, structure, and orthogonal pairing properties

Mohitosh Maiti; Munmun Maiti; Christine Knies; Shrinivas Dumbre; Eveline Lescrinier; Helmut Rosemeyer; Arnout Ceulemans; Piet Herdewijn

doi:10.1093/nar/gkv719

Xylonucleic acid: synthesis, structure, and orthogonal pairing properties

Nucleic Acids Res. 2015 Sep 3;43(15):7189-200. doi: 10.1093/nar/gkv719. Epub 2015 Jul 14.

Authors

Mohitosh Maiti¹, Munmun Maiti¹, Christine Knies², Shrinivas Dumbre¹, Eveline Lescrinier¹, Helmut Rosemeyer², Arnout Ceulemans³, Piet Herdewijn⁴

Affiliations

¹ Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
² Organic Materials Chemistry and Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastrasse. 7, D-49069 Osnabrück, Germany.
³ Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
⁴ Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium Piet.Herdewijn@rega.kuleuven.be.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Pairing
DNA / chemistry
Models, Molecular
Nucleic Acid Conformation
Nucleic Acid Denaturation
Nucleic Acids / chemical synthesis
Nucleic Acids / chemistry*
RNA / chemistry
Xylose / chemistry*

Substances

Nucleic Acids
RNA
DNA
Xylose