Abstract: Methods of measuring multiple enzyme activities in parallel in a sequencing-based assay to characterize enzyme activities in individual mammalian cells. In preferred implementations, the methods involve forming microfluidic droplets containing oligonucleotide functionalized microbeads and single mammalian cells, lysing the cells, and allowing enzyme activity on enzyme substrates present in the oligonucleotides, isolating the individual microbeads, and determining the enzymatic activity to quantitate and evaluate the enzymatic activity or capacity of the cells.

Abstract: Genomic DNA contains embedded ribonucleotides (rNMPs) that are incorporated during DNA replication and repair, or formed during DNA damage. The modifications have been linked to genome instability and disease, but no method currently exists to profile their locations genome-wide. rNMP incorporation has been extensively studied in recent years; however, locating sites of rNMP incorporation in genomic DNA has not yet been possible. Disclosed herein is a unique method for mapping rNMPs in genomic DNA that exploits the unique ligation mechanism of Arabidopsis thaliana tRNA ligase (AtRNL), normally involved in tRNA maturation. As disclosed herein AtRNL captures 2?,3?-cyclic phosphate or 2?-phosphate termini of DNA derived from alkaline cleavage of a DNA oligonucleotide (oligo) at an embedded rNMP, ligating the 2?-phosphate end to the 5?-phosphate terminus of the same DNA molecule and producing a ssDNA circle containing an embedded rNMP.

Abstract: Compositions and methods are provided to make, isolate, characterize and use regulatable, catalytically active nucleic acids (RCANA). The present invention is directed to RCANA that transduce molecular recognition into catalysis. Also, RCANAs according to the invention can be used as regulatory elements to control the expression of one or more genes in a metabolic pathway. RCANAs can also be used as regulated selectable markers to create a selective pressure favoring (or disfavoring) production of a targeted bioproduct.

Abstract: Compositions and methods are provided to make, isolate, characterize and use regulatable, catalytically active nucleic acids (RCANA). RCANA may be used for regulating gene expression and in assays to detect the presence of ligands or to detect activation by an effector of an RCANA bound to a solid support such as a chip or multi-well plate. Also disclosed are compositions and methods for automating the selection procedures of the present invention.