SERS combined with PCR as a potent tool for detecting mutations: a case study of tomato plants

Conventional methods of detecting economically essential mutations have several disadvantages. Even though fluorescence-based methods are still the best option, Surface-Enhanced Raman Spectroscopy (SERS) may soon emerge as an alternative to the current techniques for detecting these mutations, because of its ability to detect molecular vibrational signatures. We were able to identify and develop a PCR-based SERS assay that can relentlessly differentiate between different types of indels, and SNPs as demonstrated in the case of tomato genome related to tomato yellow leaf curl virus and root-knot nematodes, diseases that are economically significant to the global agriculture industry and where the selection of resistant crops is the best solution. This tri-primer assay utilizes mutation-specific forward primers and SERS probes tagged with FAM and Cy3 dyes, specific for each allele of a particular gene (Ty-3 and Mi-1). The unique Raman spectral features of these dyes enabled to perform of multiplexing, which made it possible to detect not only the indel type but also the zygosity in a single experiment. Moreover, this technique successfully differentiated between two different SNP-based alleles. Therefore, due to its efficient multiplexing capability and lack of the need for quenchers, it has the potential to become a powerful onsite and offsite screening tool in the not-too-distant future.

New HSV-1 Anti-Viral 1'-Homocarbocyclic Nucleoside Analogs with an Optically Active Substituted Bicyclo[2.2.1]Heptane Fragment as a Glycoside Moiety

New 1′-homocarbanucleoside analogs with an optically active substituted bicyclo[2.2.1]heptane skeleton as sugar moiety were synthesized. The pyrimidine analogs with uracil, 5-fluorouracil, thymine and cytosine and key intermediate with 6-chloropurine (5) as nucleobases were synthesized by a selective Mitsunobu reaction on the primary hydroxymethyl group in the presence of 5-endo-hydroxyl group. Adenine and 6-substituted adenine homonucleosides were obtained by the substitution of the 6-chlorine atom of the key intermediate 5 with ammonia and selected amines, and 6-methoxy- and 6-ethoxy substituted purine homonucleosides by reaction with the corresponding alkoxides. No derivatives appeared active against entero, yellow fever, chikungunya, and adeno type 1viruses. Two compounds (6j and 6d) had lower IC₅₀ (15 ± 2 and 21 ± 4 µM) and compound 6f had an identical value of IC₅₀ (28 ± 4 µM) to that of acyclovir, suggesting that the bicyclo[2.2.1]heptane skeleton could be further studied to find a candidate for sugar moiety of the nucleosides.

Novel homologated-apio adenosine derivatives as A3 adenosine receptor agonists: design, synthesis and molecular docking studies

A series of homologated-apio adenosine derivatives including homologated-apio IB-MECA and Cl-IB-MECA have been designed and synthesized successfully. The molecular modelling and docking studies of the compounds have been explored as A₃AR agonists.