N. Puri et J. Chattopadhyaya, How kinetically accessible is an RNA target for hybridization with an antisense oligo? A lesson from an RNA target which is as small as a 20mer, TETRAHEDRON, 55(5), 1999, pp. 1505-1516
A 20 mer RNA (1), characterized as a duplex with two A.A mismatch basepairs
and four tandem G.U wobble basepairs, was targeted at the first A.A intern
al loop by nonameric 5'-Polyarene DNA-conjugates. For comparison, its DNA c
ounterpart (10), which was found to form a hairpin with one A.A mismatch an
d a four nucleotide loop, was targeted at the single stranded loop starting
from the A.A internal loop. The secondary structure of the duplex RNA (1)
could not be disrupted by the DNA-conjugates while the hairpin DNA (10) was
found to hybridize successfully, thereby showing the intrinsic ability of
RNA (compared to DNA counterpart) to fold into a tertiary structure that is
kinetically difficult to access for heteroduplex formation by an antisense
ODN. (C) 1999 Elsevier Science Ltd. All rights reserved.