CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.

Small self-cleaving ribozymes are catalytic RNAs that cleave their phosphodiester backbone rapidly and site-specifically, without the assistance of proteins. Their catalytic properties make them ideal targets for applications in RNA pharmaceuticals and bioengineering. Consequently, computational pipelines that predict or design thousands of self-cleaving ribozyme candidates have been developed.

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally.

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally.

Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity.

Small nucleolytic ribozymes are RNAs that cleave their own phosphodiester backbone. While proteinaceous enzymes are regulated by a variety of known mechanisms, methods of regulation for ribozymes remain unclear. Twister is one ribozyme class for which many structural and catalytic properties have been elucidated.

The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.

We examined the complex network of interactions among RNA, the metabolome, and divalent Mg under conditions that mimic the cytoplasm. We determined Mg binding constants for the top 15 metabolites, comprising 80% of the metabolome by concentration at physiological pH and monovalent ion concentrations. These data were used to inform the development of an artificial cytoplasm that mimics conditions, which we term "Eco80".

Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc155.

The annotation of six cluster N phages (Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob) reveals regions of genomic diversity, particularly within the central region of the genome. The genome of Kevin1 includes two orphams (genes with no similarity to other phage genes), with one predicted to encode an AAA-ATPase.

Semantic distance norms computed from an electronic dictionary (WordNet).

WordNet, an electronic dictionary (or lexical database), is a valuable resource for computational and cognitive scientists. Recent work on the computing of semantic distances among nodes (synsets) in WordNet has made it possible to build a large database of semantic distances for use in selecting word pairs for psychological research. The database now contains nearly 50,000 pairs of words that have values for semantic distance, associative strength, and similarity based on co-occurrence.