Preparation of fluorinated RNA nucleotide analogs potentially stable to enzymatic hydrolysis in RNA and DNA polymerase assays

Anton Shakhmin; John-Paul Jones; Inessa Bychinskaya; Mikhail Zibinsky; Keriann Oertell; Myron F Goodman; G K Surya Prakash

doi:10.1016/j.jfluchem.2014.07.019

Preparation of fluorinated RNA nucleotide analogs potentially stable to enzymatic hydrolysis in RNA and DNA polymerase assays

J Fluor Chem. 2014 Oct:167:226-230. doi: 10.1016/j.jfluchem.2014.07.019.

Authors

Anton Shakhmin¹, John-Paul Jones¹, Inessa Bychinskaya¹, Mikhail Zibinsky¹, Keriann Oertell², Myron F Goodman², G K Surya Prakash¹

Affiliations

¹ Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661, United States.
² Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-1661, United States.

Abstract

Analogs of ribonucleotides (RNA) stable to enzymatic hydrolysis were prepared and characterized. Computational investigations revealed that this class of compounds with a modified triphosphate exhibits the correct polarity and minimal steric effects compared to the natural molecule. Non-hydrolysable properties as well as the ability of the modified nucleotide to be recognized by enzymes were probed by performing single-turnover gap filling assays with T7 RNA polymerase and DNA polymerase β.

Keywords: Fluorinated phosphonate; Isostericity and isopolarity; Non-hydrolysable nucleotide analogs; Ribonucleotides; Single-turnover gap filling assay.

Abstract

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