December 2019

Bio-Synthesis Newsletter - December 2019

Specific labeling of RNA

5'-adNA-duplex 2HVS-bRNA can be specifically labeled with fluorophors or modified with nonstandard nucleotides as needed for a variety of applications in RNA research. A diverse collection of RNA molecules, short, medium, and long can be prepared using solid-phase chemical synthesis or enzymatic synthesis or a combination of both. RNA probes labeled with fluorophores allow the tracking of RNA in vivo. Methods such as splint ligation, DNA ligase-based ligation, RNA ligase-based ligation, chemical ligation, labeling by hybridization or aptamer-based labeling enable various routes for the study of RNA species in vivo or in vitro. 

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shRNA loop position is critical for Dicer processing

2N82-RNAShort-hairpin RNAs (shRNAs) are used to induce RNAi for discovery and therapeutic purposes. Gu et al. in 2012 reported the design of 30 shRNAs which they used for high throughput small RNA sequencing to establish differential sites of Dicer cleavage. To use Gu et al.’s words “Dicer cleaves precisely when it recognizes a single-stranded RNA sequence either from the loop region or internal bulge at a fixed distance (two nucleotides) relative to the site of cleavage. Otherwise, Dicer cleavage is not precise leading to a range of Dicer cleavage products with variable 5′ start positions.” Their data suggest that Dicer recognizes the loop/bulge structure in shRNAs in addition to the ends of shRNS/pre-miRNAs for accurate processing.

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Carbamylation, a hallmark of aging

HomocitrullineCarbamylation promotes molecular aging through alteration of protein functions such as of long-lived extracellular matrix proteins. The accumulation of carbamylated proteins in tissue appears to be a general hallmark of aging. Carbamylation or homocitrullination is a post-translational modification (PTM) studied for many years in the context of uremia. It involves the non-enzymatic reaction of urea-derived cyanate with free NH2- groups on lysine (K, Lys) residues to yield homocitrulline (Hcit). Carbamylation adds an NHCO group to lysine. Carbamylation of proteins and peptides increases the molecular mass of the modified peptide by a delta mass of 43 mass units which is detected in a mass spectrometer. Homocitrulline can be also analyzed using amino acid analysis. Isocyanic acid (CNOH, ΔM 43) originates from spontaneously dissociating urea forming cyanate and ammonia in aqueous solutions.

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Our genes influence how we process food

Penne_with_eggplant_and_basil_in_yogurt-tomato_sauce Genes influence our metabolism. A recent study showed how mammalian metabolisms react to the food we eat. Genetic differences in mouse models influence metabolic responses to several popular diets. The  search was on for a diet that minimizes or prevents the development of metabolic diseases by enabling a precise genetic and environmental dietary control useful for precision medicine. Four human-comparable mouse diets were designed and tested representatives of those eaten by human populations. Four genetically distinct inbred mouse strains werer studied. The impact of the American diet on metabolic health was compared to three alternative diets, the Mediterranean, the Japanese and the Maasai or ketogenic diet. The study found that individualized diet strategies improved health outcomes in mice much better than a single diet. The findings were that a personalized, or "precision dietetics," approach to dietary recommendations will work much better than the traditional one-size-fits-all diet. 

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