1ho6
From Proteopedia
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CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM
Overview
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 A, 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.
About this Structure
1HO6 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids., Denisov AY, Noronha AM, Wilds CJ, Trempe JF, Pon RT, Gehring K, Damha MJ, Nucleic Acids Res. 2001 Nov 1;29(21):4284-93. PMID:11691916
Page seeded by OCA on Sun Nov 25 02:50:02 2007
