Abstract: The invention includes a method for recombining and, optionally, cloning nucleic acids without the use of restriction enzymes or DNA ligase. The method involves recombining an insert and a recipient nucleic acid using custom designed complementary regions to anneal strands from the nucleic acids. The complementary regions on double stranded nucleic acids are exposed by limited digestion of the ends of the nucleic acids. After annealing the digested ends, single stranded gaps on the hybridized nucleic acid are closed to yield a double stranded nucleic acid which may, optionally, be cloned into a microorganism. The invention also includes kits for recombining and, optionally, cloning nucleic acids using the methods of the invention. The invention further includes recombinant nucleic acids prepared using the methods of the invention.