Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers

Abstract

Xeno nucleic acids (XNAs) are analogues of DNA and RNA that have a non‐ribose artificial scaffold. XNAs are possible prebiotic genetic carriers as well as alternative genetic systems in artificial life. In addition, XNA oligomers can be used as biological tools. Acyclic XNAs, which do not have cyclic scaffolds, are attractive due to facile their synthesis and remarkably high nuclease resistance. To maximize the performance of XNAs, a negatively charged backbone is preferable to provide sufficient water solubility; however, acyclic XNAs containing polyanionic backbones suffer from high entropy cost upon duplex formation, because of the high flexibility of the acyclic nature. Herein, we review the relationships between the structure and duplex hybridization properties of various acyclic XNA oligomers with polyanion backbones.

Tuning Exciton Coupling of Merocyanine Nucleoside Dimers by RNA, DNA and GNA Double Helix Conformations

“…The enhanced fluorescence emission intensity of BAM upon incorporation into RNA oligonucleotides and its spectral overlap with 2-aminopurine makes BAM a promising fluorescent pyrimidine nucleobase analogue for probing RNA structures and dynamics, comparable to fluorescent cytidine analogues. [34] Moreover, our experiments manifest the value of GNA as simple, programmable and predictable xenobiotic nucleic acid (XNA) [35] for engineering exciton coupling and transport. The demonstrated control over exciton coupling by the helical supramolecular environment provides a starting point for the elucidation of the photodynamic nature of larger BAM aggregates in nucleic acids, and may stimulate their use for photonic and fluorescent nucleic acid nanoarchitectures.…”

Functional Xeno Nucleic Acids for Biomedical Application

“…So far, both XNAzymes refer to a type of DNAzymes/ribozymes containing XNAs, which could function as a nuclease, or a ligase in degradation reactions [49] . Holliger and colleagues [50] reported the original four XNAzymes(FANAzyme, ANAzyme, substrates [12] .…”

“…Chemical modification is a vital method to develop useful nucleic acid with additional properties [12][13][14] . So far, it has been used to synthesize and investigate nucleic acid analogues with modifications at nucleotide backbone, bases and sugar [15] .…”

“…Nucleobase modification can regulate the strength and specificity of base-pairing, and phosphodiester backbone modification can improve pharmacokinetic properties and nuclease resistance. Sugar moiety modification has beneficial effects on various properties of natural nucleic acid, including duplex-forming ability, nuclease resistance, and toxicity in cells and animals [12] . Xeno nucleic acids(XNAs) first appeared in 2009 in a theoretical paper on nucleic acid polymers [16] .…”

“…It refers to the nucleic acids that differ from deoxyribose and ribose in chemical backbone motif. By comparison with natural DNA and RNA, XNAs possess desirable biological properties for biomedical application, such as increased biological stability, enhanced binding affinity, improved tissue specificity, and reduced immune responses [12,17] . In recent years, numerous works have used XNA to improve the performance of FNAs, and functional xeno nucleic acids have been applied to varied biomedical fields.…”