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

Citation
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
Citations number
33
Categorie Soggetti
Chemistry & Analysis","Organic Chemistry/Polymer Science
Journal title
TETRAHEDRON
ISSN journal
00404020 → ACNP
Volume
55
Issue
5
Year of publication
1999
Pages
1505 - 1516
Database
ISI
SICI code
0040-4020(19990129)55:5<1505:HKAIAR>2.0.ZU;2-Y
Abstract
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.