At. Daniher et al., MODULATION OF RNASE-H ACTIVITY BY MODIFIED DNA PROBES - MAJOR GROOVE VS MINOR-GROOVE EFFECTS, Bioorganic & medicinal chemistry, 5(6), 1997, pp. 1037-1042
We have previously prepared ribozyme mimics and chemical nucleases-fro
m modified DNA containing pendant bipyridine and terpyridine groups. T
he ability of these modified DNA probes to support RNase H cleavage of
complementary RNA is described. DNA/RNA duplexes were formed using DN
A probes designed to deliver metal complexes via either the major groo
ve or the minor groove of the duplex. The duplexes were treated with E
scherichia coli RNase H. Modifications in the major groove produced th
e same RNA cleavage pattern as unmodified DNA probes. However, minor g
roove substituents inhibited RNA cleavage over a four-base region. Com
parison was made with a DNA probe containing a 2'-OMe modification. Ou
r results support enzyme binding in the minor groove of a DNA/RNA dupl
ex. We do not observe cleavage directly across from the modified nucle
oside. The RNA cleavage efficiency effected by RNase H and a DNA probe
decreases as follows: unmodified DNA greater than or equal to C-5 mod
ified DNA much greater than C2'-modified DNA > Cl'-modified DNA. Resul
ts with 28-mer RNA substrates roughly parallel those obtained with a 1
59-mer RNA target. The differences observed between low and high MW RN
A substrates can be explained by a much higher enzyme-substrate bindin
g constant for the high MW target. (C) 1997 Elsevier Science Ltd.