I. Synthesis, bio-conjugation, electronic and spectral properties
of phenanthroline analogs
II. Phenanthroline cleavage of RNA
Research Advisor: Charles M. Thompson, Ph.D.
Phenanthroline was used as a targeted chemical nuclease, to help elucidate the regions of rRNA which are near-neighbors of the stem-loop structure centering at nucleotide 790 in the 16S rRNA of the E. coli 30S ribosomal subunit. Using phenanthroline covalently attached to a DNA oligomer complementary to nucleotides 787-795, nucleotides 582-584, 693-694, 787-790 and 795-797 were cleaved robustly and must lie within about 15Å of the tethered site at the 5'-end of the DNA oligomer, which is adjacent to nucleotide 795 of 16S rRNA.
Using phenanthroline-copper, covalently attached to a DNA oligomer
complementary to nucleotides in the decoding region (1396-1403) it was
determined that nucleotides 923- 929, 1391-1396 and 1190-1192 are within
approximately 15 of an adjacent position to nucleotide 1403 in inactive
subunits. Additionally, cleavage of these proximal sites is removed
or greatly attenuated upon activation of the subunits, while in the active
state only cleavages (1404-1405) immediately proximal to the 5' end of
the hybridized probe are present. These results suggest dynamic
interactions within the 30S ribosomal subunit which may allow the discrete
structural changes that allow the binding of tRNA in active subunits to
Further studies of targeted scission using the phenanthroline-DNA probe showed an increase in cleavage efficiency in the presence of exogenous hydrogen peroxide. These conditions provided evidence that the oP-Cu cleavage reaction can be tuned to produce a mild or robust cleavage reaction, a unique property never demonstrated with an organo- metallic chemical nuclease.