Single-stranded nucleic acid template-mediated recombination and nucleic acid fragment isolation

A method of isolating nucleic acid fragments from a set of nucleic acid fragments, the method comprising:

• hybridizing at least two sets of nucleic acids, wherein a first set of nucleic acids comprises single-stranded nucleic acid templates and a second set of nucleic acids comprises at least one set of nucleic acid fragments;
• separating the hybridized nucleic acids from unhybridized nucleic acids by at least one first separation technique;
• and
• denaturing the separated hybridized nucleic acids to yield the single-stranded nucleic acid templates and isolated nucleic acid fragments.

A method of generating chimeric nucleic acids, the method comprising:

• hybridizing a first plurality of first parental single-stranded nucleic acids and a second plurality of second parental single-stranded nucleic acids, wherein the hybridized first and second parental single-stranded nucleic acids comprise at least one nonhybridized region of sequence diversity;
• nicking at least one strand in the at least one nonhybridized region of sequence diversity;
• cleaving the at least one nicked strand in the at least one nonhybridized region of sequence diversity to provide at least one sequence gap between hybridized regions;
• and,
• elongating, ligating, or both, the at least one sequence gap between the hybridized regions to generate chimeric progeny nucleic acids.

A method of recombining a set of nucleic acid fragments, the method comprising:

• providing a set of at least partially double-stranded nucleic acids that encode a polypeptide of interest or portion thereof;
• contacting the set of at least partially double-stranded nucleic acids with an exonuclease that selectively degrades one strand of the at least partially double-stranded nucleic acids to provide a set of single-stranded nucleic acid templates;
• hybridizing the set of single-stranded nucleic acid templates with a second set of nucleic acids comprising at least one set of nucleic acid fragments;
• and,
• elongating, ligating, or both, sequence gaps between the hybridized nucleic acid fragments to generate at least substantially full-length chimeric nucleic acid sequences that correspond to the single-stranded nucleic acid templates, thereby recombining the set of nucleic acid fragments.