Capping DNA with DNA

Twelve classes of deoxyribozymes that promote an ATP-dependent "self-capping" reaction were isolated by in vitro selection from a random-sequence pool of DNA. Each deoxyribozyme catalyzes the transfer of the AMP moiety of ATP to its 5'-terminal phosphate group, thereby forming a 5',5'-pyrophosphate linkage. An identical DNA adenylate structure is generated by the T4 DNA Ligase during enzymatic DNA ligation. A 41-nucleotide class I deoxyribozyme requires Cu2+ as a cofactor and adopts a structure that recognizes both the adenine and triphosphate moieties of ATP or dATP, The catalytic efficiency for this DNA, measured at 10(4) M(-1.)min(-1) using either ATP or dATP as substrate, is similar to other catalytic nucleic acids that use small substrates. Chemical probing and site-directed mutagenesis implicate the formation of guanine quartets as critical components of the active structure, The observation of ATP-dependent "'self-charging" by DNA suggests that DNA could be made to perform the reactions typically associated with DNA cloning, but without the assistance of protein enzymes.