Synthesis and hydrolytic stability of cyclic phosphatidic acids: implications for synthetic- and proto-cell studies

Cyclic phosphatidic acids (cPAs) are bioactive compounds with therapuetic potential, but are in short supply. We describe a robust synthesis of cPAs employing an efficient cyclophosphorylation procedure and report on their hydrolytic properties - which should facilitate the study of their biological properties and as plausible proto- and synthetic-cell components.

Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids

Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.

Replacement of oxygen with sulfur on the furanose ring of cyclic dinucleotides enhances the immunostimulatory effect via STING activation

Cyclic dinucleotides (CDNs) are secondary messengers composed of two purine nucleotides linked via two phosphodiester linkages: c-di-GMP, c-di-AMP, 3',3'-cGAMP, and 2',3'-cGAMP. CDNs activate the stimulator of interferon genes (STING) and trigger immune responses in mammalian species. CDNs are thus fascinating molecules as drug candidates, and chemically stable CDN analogues that act as STING agonists are highly desired at present. We herein report the practical synthesis of 4'-thiomodified c-di-AMP analogues, which have sulfur atoms at the 4'-position on the furanose ring instead of oxygen atoms, using simple phosphoramidite chemistry. The resulting 4'-thiomodified c-di-AMP analogues acted as potent STING agonists with long-term activity. Our results show that replacing O4' on CDNs with sulfur can lead to enhanced immunostimulatory effects via STING activation.

A Green Approach for Organic Transformations Using Microwave Reactor

Microwave-assisted organic transformation (MAOR) is presently gaining wide popularity in the field of organic synthesis. The conventional heating technique is gradually being removed from the laboratory and a novel microwave heating technique established to be used in both academia and industry. As compared to the classical organic methodology, the green technology tools have several advantages like dramatically reduced reaction times, improved yields, site selectivity, and the increased product purities with simplification of work-up procedures. In the current study, we have briefly described the overview of recent developments and applications of microwave irradiation in organic transformation with schematic compiling of the organic reactions, bioactive heterocyclic compounds, and so on. This review also presents a critical analysis of the various advantages of microwave irradiation in organic synthesis/transformation compared to the classical or conventional heating. So, we believe that our current study of the green microwave heating technique will be highly beneficial for the researchers from both academia and industry in their near future.

Chimeric XNA: An Unconventional Design for Orthogonal Informational Systems

The paradigm of homogenous-sugar-backbone of RNA and DNA has reliably guided the construction of many functional and useful xeno nucleic acid (XNA) systems to date. Deviations from this monotonous and canonical design, in many cases, results in oligonucleotide systems that lack base pairing with themselves, or with RNA or DNA. Here we show that nucleotides of two such compromised XNA systems can be combined with RNA and DNA in specific patterns to produce chimeric-backbone oligonucleotides, which in certain cases demonstrate base pairing properties comparable to-or stronger than-canonical systems, while also altering the conventional Watson-Crick pairing behavior. The unorthodox pairing properties generated from these chimeric sugar-backbone oligonucleotides suggest a counterintuitive approach of creating modules consisting of non-base pairing XNAs with RNA/DNA in a set pattern. This strategy has the potential to increase the diversity of unconventional nucleic acids leading to orthogonal backbone-sequence-controlled informational systems.

Sensing the impact of environment on small molecule differentiation of RNA sequences

Using pattern recognition of RNA with small molecules (PRRSM) with fluorescent RNA chemosensors and aminoglycosides, we reveal the impact of changing environmental conditions on the differentiation of a range of RNA structures as well as the ability to predict different sequence/size compositions of five canonical RNA motifs.

Small Molecule-Based Pattern Recognition To Classify RNA Structure

Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes. Complete (100%) predictive ability for this RNA training set was achieved by incorporating two exhaustively guanidinylated aminoglycosides into the receptor library. The PCA was then externally validated using biologically relevant RNA constructs. In bulge-stem-loop constructs of HIV-1 transactivation response element (TAR) RNA, we achieved nucleotide-specific classification of two independent secondary structure motifs. Furthermore, examination of cheminformatic parameters and PCA loading factors revealed trends in aminoglycoside:RNA recognition, including the importance of shape-based discrimination, and suggested the potential for size and sequence discrimination within RNA structural motifs. These studies present a new approach to classifying RNA structure and provide direct evidence that RNA topology, in addition to sequence, is critical for the molecular recognition of RNA.