Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.
RNase H1 cleaves the RNA strand of RNA:DNA hybrids. Replacement of RNA 2'-hydroxyls by fluorine (FRNA) is commonly used to stabilize aptamers and siRNAs. However, FRNA:DNA hybrids fail to elicit RNase H activity. The underlying reasons are unclear, as 2'-OH groups are not directly involved in cleavage. We determined the crystal structure of Bacillus halodurans RNase H bound to a FRNA:DNA hybrid. The structure points to dynamic (slippage of the FRNA:DNA hybrid relative to the enzyme), geometric (different curvatures of FRNA:DNA and RNA:DNA hybrids), and electronic reasons (Mg(2+) absent from the active site of the FRNA:DNA complex) for the loss of RNaseH activity.
Department of Biochemistry, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States.
Pradeep S
PS
Pallan
Department of Medicinal Chemistry, Ionis Pharmaceuticals Inc. , Carlsbad, California 92010, United States.
Thazha P
TP
Prakash
Department of Biochemistry, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States.
Arnie R
AR
de Leon
Department of Biochemistry, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States.
Martin
M
Egli
D001407:Bacillus / Q000201:enzymology*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D005461:Fluorine / Q000737:chemistry*; D018716:Molecular Mimicry; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry*; D016914:Ribonuclease H / Q000737:chemistry*
D005461:Fluorine; D012313:RNA; D004247:DNA; D016914:Ribonuclease H