1HOQ

CHIMERIC RNA/DNA HAIRPIN

Summary for 1HOQ

• Entry DOI: 10.2210/pdb1hoq/pdb
• Related: 1FC8 1HO6
• Descriptor: DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*GP*GP*TP*CP*C)-3') (1 entity in total)
• Functional Keywords: hairpin, dna, rna
• Total number of polymer chains: 1
• Total formula weight: 3718.38

Authors

Denisov, A.Y.,Gehring, K. (deposition date: 2000-12-11, release date: 2001-11-07, Last modification date: 2024-05-22)

Primary citation

Denisov, A.Y.,Noronha, A.M.,Wilds, C.J.,Trempe, J.F.,Pon, R.T.,Gehring, K.,Damha, M.J.
Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.
Nucleic Acids Res., 29:4284-4293, 2001

PubMed Abstract: 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.

PubMed: 11691916
DOI: 10.1093/nar/29.21.4284

Experimental method

SOLUTION NMR