The disclosure provides methods for the concurrent assessment of large numbers of genome engineering proteins, including CRISPR nucleases and base editors. Specifically, the disclosure provides methods of providing a plurality of individual discrete samples comprising populations of cells, wherein each population of cells overexpresses both (i) a single genome engineering protein or a variant thereof and (ii) a reporter protein, lysing the cells to release the proteins; normalizing levels of the genome engineering proteins or variants thereof; allowing the genome engineering proteins or variants thereof to combine with a guide RNA under conditions sufficient to form ribonucleoprotein complexes in each sample; contacting each sample with a plurality of analysis substrates, determining levels of each of the analysis substrate in each sample at a plurality of times; and calculating rate of depletion or enrichment of each of the analysis substrates from each sample.

The present invention provides a heat-resistant DNA polymerase mutant with high amplification activity. Particularly, the present invention uses protein directed evolution technology to construct a random mutation library for the polymerase active domain of Taq enzyme, and gradually adds screening pressure, so that unsuitable mutations will be eliminated naturally, and mutations with dominant traits will gradually accumulate. Finally, a series of amino acid sites and their mutations that are critical to Taq enzyme amplification and polymerization performance will be selected, and a Taq enzyme mutant with high amplification activity will be obtained.

The invention relates to a method for selecting a sequence set from a library of expressed nucleic acid sequences, wherein cells are provided, each cell comprises an expressed nucleic acid sequence expressed as a target protein. The cells are encapsulated by treating them with a cationic polysaccharide and subsequently treating them with an anionic polysaccharide, yielding encapsulated cells, perforating the membrane of the encapsulated cells, yielding solubilized compartments, contacting them with a ligand to said target protein, the ligand bearing a detectable label, and selecting a subset of solubilized compartments as a function of detectable label and isolating the expressed nucleic acid sequences from the selection as a selected sequence set.

This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are a method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.

Provided herein are lasso peptides libraries, and particularly phage display libraries of lasso peptides. Also provided herein are related methods and systems for producing the libraries and for screening the libraries to identify candidate lasso peptides having desirable properties.

Some aspects of this disclosure relate to systems, apparatuses, compositions (e.g., isolated nucleic acids and vectors), and methods for improving the stability and/or solubility of proteins evolved using phage-assisted continuous evolution (PACE). In some embodiments, vectors described herein comprise nucleic acids encoding selection systems (e.g., positive and/or negative selection systems) that link expression of genes required for production of infectious phage particles to a desirable physiochemical (e.g., stability or solubility) and/or desired function of an evolved protein.

Provided herein are methods for identifying pairs of protein binding partners, mutations of which may inform the discovery of pharmaceutically useful small molecules. The methods disclosed herein may allow for the adaptation of the native protein degradation system to modulate specific disease targets at the protein level, in particular, for targets that have long been considered undruggable.

Described herein are compositions defective SARS-CoV-2 constructs and particles that can interfere with or block infection of uninfected cells and methods for generating such defective SARS-CoV-2 constructs and particles. The compositions and methods described herein are useful for treatment of SARS-CoV-2 infections.

Provided herein are systems and methods for screening desirable biological variants using a high-throughput integrated system. The integrated system may be configured to input a plurality of parameters from functional studies of biological variants under applied conditions, in conjunction with integrated libraries of biological variants, and filter the inputs to produce desirable biological variants based on an input performance requirement. The system may output optimized strains, molecules, or novel molecules expected to have a desirable functional characteristic. Accordingly, the methods and systems disclosed herein enable multi-parametric studies of biological diversity and conditional diversity in systems biology.

The present disclosure relates to a method of protein structure and amino acid residue interaction prediction based on saturation suppressor mutagenesis screening of a protein of interest. The method of the instant disclosure can be adapted for multi-protein complexes, and is useful where crystal structure of a protein of interest is not available.