A Caged Ligatable DNA Strand Break

One general solution to the problem of generating sticky ends of any length or sequence would be to cage the end by incorporating it into a hairpin loop with a photocleavable precursor to a 5'-phosphate and a 3'-hydroxyl. This strategy would also have the advantage of substantially reducing the length of the intermediate DNA molecules required in a synthesis. Though there have been several reports of photochemically triggered DNA strand breaks, there have been no examples of methods for directly phototriggering the simultaneous formation of 3'hydroxyl and 5'-phosphate termini. Herein, we report the design and synthesis od the first building block that can be used to site-specifically introduce such a caged break into oligonucleotides, and further demonstrate that the break can be enzymatically ligated. Such a caged ligatable strand break could be used to produce sticky ends of any desired length or sequence, in a structure-independent manner.