The present invention relates to methods and systems for the directed evolution of macromolecules. The methods involve increasing the mutation rate of an evolving organism comprising a gene of interest that encodes a gene product lacking a desired activity, whereby a mutated gene of interest is produced that encodes an evolved gene product comprising the desired activity and causing a suppression of mutagenesis. The systems comprise an evolving organism comprising a gene of interest encoding a gene product to be evolved, a host organism, and optionally, a lagoon, a cellstat and/or a suitable growth medium.

Some aspects of the present disclosure provide methods for evolving recombinases to recognize target sequences that differ from the canonical recognition sequences. Some aspects of this disclosure provide evolved recombinases, e.g., recombinases that bind and recombine naturally-occurring target sequences, such as, e.g., target sequences within the human Rosa26 locus. Methods for using such recombinases for genetically engineering nucleic acid molecules in vitro and in vivo are also provided. Some aspects of this disclosure also provide libraries and screening methods for assessing the target site preferences of recombinases, as well as methods for selecting recombinases that bind and recombine a non-canonical target sequence with high specificity.

The invention provides systems, methods, reagents, apparatuses, vectors, and host cells for the continuous evolution of nucleic acids. For example, a lagoon is provided in which a population of viral vectors comprising a gene of interest replicates in a stream of host cells, wherein the viral vectors lack a gene encoding a protein required for the generation of infectious viral particles, and wherein that gene is expressed in the host cells under the control of a conditional promoter, the activity of which depends on a function of the gene of interest to be evolved. Some aspects of this invention provide evolved products obtained from continuous evolution procedures described herein. Kits containing materials for continuous evolution are also provided.

The invention provides systems, methods, reagents, apparatuses, vectors, and host cells for the continuous evolution of nucleic acids. For example, a lagoon is provided in which a population of viral vectors comprising a gene of interest replicates in a stream of host cells, wherein the viral vectors lack a gene encoding a protein required for the generation of infectious viral particles, and wherein that gene is expressed in the host cells under the control of a conditional promoter, the activity of which depends on a function of the gene of interest to be evolved. Some aspects of this invention provide evolved products obtained from continuous evolution procedures described herein. Kits containing materials for continuous evolution are also provided.

Strategies, systems, methods, reagents, and kits for phage-assisted continuous evolution are provided herein. These include strategies, systems, methods, reagents, and kits allowing for stringency modulation to evolve weakly active or inactive biomolecule variants, negative selection of undesired properties, and/or positive selection of desired properties.

The present disclosure relates to genetically engineered phage that bind to cancer cells. The genetically engineered phage can be used to isolate cancer cells, for example, circulating cancer cells, by binding to antigens specifically expressed on the surface of cancer cells. Thus, the present disclosure provides compositions, methods, and kits for improved cancer diagnosis that are useful for improved cancer treatment.

A phage for the specific capture of the SARS-CoV-2 virus, said phage being an M13 phage engineered to display on the P8 protein of its coat either FHKGGYEKTWKLGD sequence peptides or EFTSKAR sequence peptides, said peptides having specific affinity for the Spike S1 protein of the SARS-CoV-2 virus.

The present invention relates to a phage or a composition that comprises it, wherein said phage expresses at least one specific recognition element and is furthermore conjugated with at least 300 molecules of a sonosensitiser. The invention further relates to the use of said phage in a sonodynamic therapy.