RNA sequence to structure analysis from comprehensive pairwise mutagenesis of multiple self-cleaving ribozymes.

Self-cleaving ribozymes are RNA molecules that catalyze the cleavage of their own phosphodiester backbones. These ribozymes are found in all domains of life and are also a tool for biotechnical and synthetic biology applications. Self-cleaving ribozymes are also an important model of sequence-to-function relationships for RNA because their small size simplifies synthesis of genetic variants and self-cleaving activity is an accessible readout of the functional consequence of the mutation.

Predicting higher-order mutational effects in an RNA enzyme by machine learning of high-throughput experimental data.

Ribozymes are RNA molecules that catalyze biochemical reactions. Self-cleaving ribozymes are a common naturally occurring class of ribozymes that catalyze site-specific cleavage of their own phosphodiester backbone. In addition to their natural functions, self-cleaving ribozymes have been used to engineer control of gene expression because they can be designed to alter RNA processing and stability.

Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes.

Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems.

Silver-Catalyzed Enantioselective Propargylic C-H Bond Amination through Rational Ligand Design.

Asymmetric C-H amination via nitrene transfer is a powerful tool to prepare enantioenriched amine precursors from abundant C-H bonds. Herein, we report a regio- and enantioselective synthesis of γ-alkynyl γ-aminoalcohols via a silver-catalyzed propargylic C-H amination. The protocol was enabled by a new bis(oxazoline) (BOX) ligand designed via a rapid structure-activity relationship (SAR) analysis.

Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments.

In vitro selection combined with high-throughput sequencing is a powerful experimental approach with broad application in the engineering and characterization of RNA molecules. Diverse pools of starting sequences used for selection are often flanked by fixed sequences used as primer binding sites. These low diversity regions often lead to data loss from complications with Illumina image processing algorithms.

Solvent-free synthesis of soluble, near-IR absorbing titanyl phthalocyanine derivatives.

Solvent-free synthesis of a series of alkylthio-substituted titanyl phthalocyanine (TiOPc) derivatives starting from the corresponding phthalonitriles (Pn) is reported. This methodology eliminates the formation of the unmetalated phthalocyanine (H2Pc), a side product that makes purification difficult. The alkylthio groups on the reported derivatives enhance solubility in common organic solvents and shift the absorption to the near-IR region.