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Nucleic Acids Research, 2001, Vol. 29, No. 21 4284-4293
© 2001 Oxford University Press

Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids

Alexei Yu. Denisov1, Anne M. Noronha2, Christopher J. Wilds2, Jean-François Trempe1, Richard T. Pon3, Kalle Gehring1,2 and Masad J. Damha2,*

1Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal, QC H3G 1Y6, Canada, 2Department of Chemistry, Otto Maas Chemistry Building, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 2K6, Canada and 3University Core DNA Services, University of Calgary, Calgary, AB T2N 4N1, Canada

Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a ‘rigid’ O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 ± 0.5 Å, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.

* To whom correspondence should be addressed. Tel: +1 514 398 7552; Fax: +1 514 398 3797; Email: masad.damha{at}mcgill.ca


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