Several future challenges must be addressed for DNA
enzymes that 3′-phosphorylate oligonucleotide substrates.
Such DNA enzymes may have the greatest practical utility for
3′-32P-radiolabeling, which for DNA is presently accomplished
using an α-32P-dNTP and terminal deoxytransferase (TdT), but
often with product heterogeneity because TdT can attach more
than one successive 32P-nucleotide to the 3′-terminus. A DNA
enzyme for 3′-32P-radiolabeling would preferably use commercially
available γ-32P-ATP or GTP as the phosphoryl donor with
low Km value, rather than the pppRNA required by 3′Kin1. Our
ongoing efforts toward deoxyribozymes for peptide side chain
phosphorylation support the expectation that such reactivity
with a small-molecule phosphoryl donor such as ATP or GTP
should be achievable.32,33 3′-Phosphorylation of RNA rather
than DNA is also a valuable objective. For all of these
applications, the most general substrate sequence scope is
desired, either from an individual DNA enzyme or collectively
from a set of DNA enzymes. Such generality has been achieved
with RNA-cleaving deoxyribozymes49−51 and RNA ligase
deoxyribozymes52,53 and seems likely for DNA-hydrolyzing
deoxyribozymes as well,45,54 suggesting the viability of general
DNA-catalyzed oligonucleotide 3′-phosphorylation.