2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

• DOI: 10.1021/bi052322r
• Publication Date: 2006-03-28T05:21:38Z
• Authors: Feng Li; Sanjay Sarkhel; Christopher J. Wilds; Zdzislaw Wawrzak; Thazha P. Prakash; Muthiah Manoharan; Martin Egli
• Keywords: RNase H; Binding affinities; Affinities

2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic (ANA) paired to RNA are substrates of RNase H. The conformation the natural DNA/RNA hybrid appears be neither A-form nor B-form. Consistent with this, conformations FANA ANA were found intermediate between A- B-forms. However, opposite is preferred by H over ANA, affinity considerably exceeds that ANA. By investigating conformational boundaries residues in crystal structures B-form DNA duplexes at atomic resolution, we demonstrate display subtle differences. structural data provide insight into requirements catalytic site They also allow conclusions regard relative importance stereoelectronic effects hydration as modulators affinity.