Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers

Natural, modified and conjugated carbohydrates in nucleic acids

Storage of genetic information in DNA occurs through a unique ordering of canonical base pairs. However, this would not be possible in the absence of the sugar-phosphate backbone which is essential for duplex formation. While over a hundred nucleobase modifications have been identified (mainly in RNA), Nature is rather conservative when it comes to alterations at the level of the (deoxy)ribose sugar moiety. This trend is not reflected in synthetic analogues of nucleic acids where modifications of the sugar entity is commonplace to improve the properties of DNA and RNA. In this review article, we describe the main incentives behind sugar modifications in nucleic acids and we highlight recent progress in this field with a particular emphasis on therapeutic applications, the development of xeno-nucleic acids (XNAs), and on interrogating nucleic acid etiology. We also describe recent strategies to conjugate carbohydrates and oligosaccharides to oligonucleotides since this represents a particularly powerful strategy to improve the therapeutic index of oligonucleotide drugs. The advent of glycoRNAs combined with progress in nucleic acid and carbohydrate chemistry, protein engineering, and delivery methods will undoubtedly yield more potent sugar-modified nucleic acids for therapeutic, biotechnological, and synthetic biology applications.

The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules

The energy landscape perspective is outlined with particular reference to biomolecules that perform multiple functions. We associate these multifunctional molecules with multifunnel energy landscapes, illustrated by some selected examples, where understanding the organisation of the landscape has provided new insight into function. Conformational selection and induced fit may provide alternative routes to realisation of multifunctionality, exploiting the possibility of environmental control and distinct binding modes.

Stable Hairpin Structures Formed by Xylose-Based Nucleic Acids

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.

Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers

Artificial analogues of the natural nucleic acids have attracted interest as a diverse class of information storage molecules capable of self-replication. In this study, we use the computational potential energy landscape framework to investigate the structural and dynamical properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA), which are derived from their respective RNA and DNA analogues by inversion of a single chiral center in the sugar moiety of the nucleotides. For an octameric XyNA sequence and the analogue dXyNA, we observe facile conformational transitions between a left-handed helix, which is the free energy global minimum, and a ladder-type structure with approximately zero helicity. The competing ensembles are better separated in the dXyNA, making it a more suitable candidate for a molecular switch, whereas the XyNA exhibits additional flexibility. Both energy landscapes exhibit greater frustration than we observe in RNA or DNA, in agreement with the higher degree of optimization expected from the principle of minimal frustration in evolved biomolecules.