Chimeric RNA Oligonucleotides Incorporating Triazole-Linked Trinucleotides: Synthesis and Function as mRNA in Cell-Free Translation Reactions

Access to capped RNAs by chemical ligation

A distinctive feature of eukaryotic mRNAs is the presence of a cap structure at the 5' end. The typical cap consists of 7-methylguanosine linked to the first transcribed nucleotide through a 5',5'-triphosphate bridge. It plays a key role in many processes in eukaryotic cells, including splicing, intracellular transport, initiation of translation and turnover. Synthetic capped oligonucleotides have served as useful tools for elucidating these physiological processes. In addition, cap mimics with artificial modifications are of interest for the design of mRNA-based therapeutics and vaccines. While the short cap mimics can be obtained by chemical synthesis, the preparation of capped analogs of mRNA length is still challenging and requires templated enzymatic ligation of synthetic RNA fragments. To increase the availability of capped mRNA analogs, we present here a practical and non-templated approach based on the use of click ligation resulting in RNAs bearing a single triazole linkage within the oligo-phosphate backbone. Capped RNA fragments with up to 81 nucleotides in length have thus been obtained in nanomolar yields and are in demand for biochemical, spectroscopic or structural studies.

Genome-wide analysis of NPR1-like genes in citrus species and expression analysis in response to citrus canker (Xanthomonas axonopodis pv. citri)

Citrus fruits, revered for their nutritional value, face significant threats from diseases like citrus canker, particularly impacting global citrus cultivation, notably in Pakistan. This study delves into the critical role of NPR1-like genes, the true receptors for salicylic acid (SA), in the defense mechanisms of citrus against Xanthomonas axonopodis pv. citri (Xcc). By conducting a comprehensive genome-wide analysis and phylogenetic study, the evolutionary dynamics of Citrus limon genes across diverse citrus cultivars are elucidated. Structural predictions unveil conserved domains, such as the BTB domain and ankyrin repeat domains, crucial for the defense mechanism. Motif analysis reveals essential conserved patterns, while cis-regulatory elements indicate their involvement in transcription, growth, response to phytohormones, and stress. The predominantly cytoplasmic and nuclear localization of NPR1-like genes underscores their pivotal role in conferring resistance to various citrus species. Analysis of the Ks/Ka ratio indicates a purifying selection of NPR1-like genes, emphasizing their importance in different species. Synteny and chromosomal mapping provide insights into duplication events and orthologous links among citrus species. Notably, Xac infection stimulates the expression of NPR1-like genes, revealing their responsiveness to pathogenic challenges. Interestingly, qRT-PCR profiling post-Xac infection reveals cultivar-specific alterations in expression within susceptible and resistant citrus varieties. Beyond genetic factors, physiological parameters like peroxidase, total soluble protein, and secondary metabolites respond to SA-dependent PR genes, influencing plant characteristics. Examining the impact of defense genes (NPR1) and plant characteristics on disease resistance in citrus, this study marks the inaugural investigation into the correlation between NPR1-associated genes and various plant traits in both susceptible and resistant citrus varieties to citrus bacterial canker.

Triazole-linked Nucleic Acids: Synthesis, Therapeutics and Synthetic Biology Applications

This article covers the triazole-linked nucleic acids where the triazole linkage (TL) replaces the natural phosphate backbone. The replacement is done at either a few selected linkages or all the phosphate linkages. Two triazole linkages, the four-atom TL1 and the six-atom TL2, have been discussed in detail. These triazole-modified oligonucleotides have found a wide range of applications, from therapeutics to synthetic biology. For example, the triazole-linked oligonucleotides have been used in the antisense oligonucleotide (ASO), small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology as therapeutic agents. Due to the ease of the synthesis and a wide range of biocompatibility, the triazole linkage TL2 has been used to assemble a functional 300-mer DNA from alkyne- and azide-functionalized 100-mer oligonucleotides as well as an epigenetically modified variant of a 335 base-pair gene from ten short oligonucleotides. These outcomes highlight the potential of triazole-linked nucleic acids and open the doors for other TL designs and artificial backbones to fully exploit the vast potential of artificial nucleic acids in therapeutics, synthetic biology and biotechnology.

Azide-modified Nucleosides as Versatile Tools for Bioorthogonal Labeling and Functionalization

Azide-modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide-alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide-modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide-alkyne cycloadditions for labelling and functionalization.

1,2,3-Triazole-based sequence-defined oligomers and polymers

This review offers a summary on the advances in the construction of 1,2,3-triazole-based sequence-defined oligomers and polymers through MAAC-based ISG or IEG strategies.

Gene Expression of 4'-Thioguanine DNA via 4'-Thiocytosine RNA

DNA and RNA nucleotides are ubiquitous molecules that store and transmit genetic information. The emergence of synthetic elements that fulfill the function of DNA and RNA provides an alternative gene expression system. Herein, we demonstrate the gene expression of 4'-thioguanine DNA (d^SG DNA) via 4'-thiocytosine RNA (d^SC RNA) to give green fluorescent protein (GFPuv) in a single test tube. In replication, transcription, and translation, DNA/RNA polymerases and Escherichia coli (E. coli) ribosome can tolerate the replacement of O4' with S4' in the nucleotide, despite the fact that sulfur has a larger atomic radius than oxygen. Additionally, d^SG DNA and d^SC RNA acted as alternative genetic polymers to natural DNA and RNA for protein synthesis in artificial cells comprising a reconstituted E. coli gene expression machinery. This work involved simple experiments that are widely used in molecular biology, but which underscore the feasibility of life control by substances other than DNA/RNA nucleotides.

Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation

Circular RNA without a stop codon enables rolling circle translation. we carried out one-pot chemical synthesis of circular RNA from RNA fragments. The synthesized circular RNAs acted as translation templates, despite the presence of unnatural phosphoramidate linkages.

Nucleic Acid Aptamer: A Novel Potential Diagnostic and Therapeutic Tool for Leukemia

Leukemia immunotherapy has been dominant via using synthetic antibodies to target cluster of differentiation (CD) molecules, nevertheless inevitable cytotoxicity and immunogenicity would limit its development. Recently, increasing reports have focused on nucleic acid aptamers, a class of high-affinity nucleic acid ligands. Aptamers purportedly serve as “chemical antibodies”, have negligible cytotoxicity and low immunogenicity, and would be widely applied for the therapy and diagnosis of various diseases, especially leukemia. In the preclinical applications, nucleic acid aptamers have displayed the augmented specificity and selectivity via recognizing targets on leukemia cells based on unique three-dimensional conformations. As small molecules with nucleic acid characteristics, aptamers need to be chemically modified to resist nuclease degradation, renal clearance and improve binding affinities. Moreover, aptamers can be linked with neoteric detection techniques to enhance sensitivity and selectivity of diagnosis and therapy. In this review, we summarized aptamers’ preparation, chemical modification and conjugation, and discussed the application of aptamers in diagnosis and treatment of leukemia through highly specifically recognizing target molecules. Significantly, the application prospect of aptamers in fusion genes would be introduced.

Duplex-forming Oligonucleotide of Triazole-linked RNA

An oligonucleotide of triazole-linked RNA (^TL RNA) was synthesized by performing consecutive copper-catalyzed azide-alkyne cycloaddition reactions for elongation. The reaction conditions that had been optimized for the synthesis of 3-mer ^TL RNA were found to be inappropriate for longer oligonucleotides, and the conditions were reoptimized for the solid-phase synthesis of an 11-mer ^TL RNA oligonucleotide. Duplex formation of the 11-mer ^TL RNA oligonucleotide was examined with the complementary oligonucleotide of natural RNA to reveal the effects of the 2'-OH groups on the duplex stability.

Locked nucleic acid (LNA) enhances binding affinity of triazole-linked DNA towards RNA

LNA improves the RNA-binding affinity and enzymatic stability of triazole-linked DNA.

Oligonucleotides containing internal triazole–3′-LNA linkages bind to complementary RNA with similar affinity and specificity to unmodified oligonucleotides, and significantly better than oligonucleotides containing triazole alone. In contrast LNA on the 5′-side of the triazole does not stabilise duplexes. Triazole–LNA confers great resistance towards enzymatic degradation relative to LNA alone.