Regio-Selective Chemical-Enzymatic Synthesis of Pyrimidine Nucleotides Facilitates RNA Structure and Dynamics Studies

Isotope labeling has revolutionized NMR studies of small nucleic acids, but to extend this technology to larger RNAs, site‐specific labeling tools to expedite NMR structural and dynamics studies are required. Using enzymes from the pentose phosphate pathway, we coupled chemically synthesized uracil nucleobase with specifically 13C‐labeled ribose to synthesize both UTP and CTP in nearly quantitative yields. This chemoenzymatic method affords a cost‐effective preparation of labels that are unattainable by current methods. The methodology generates versatile 13C and 15N labeling patterns which, when employed with relaxation‐optimized NMR spectroscopy, effectively mitigate problems of rapid relaxation that result in low resolution and sensitivity. The methodology is demonstrated with RNAs of various sizes, complexity, and function: the exon splicing silencer 3 (27 nt), iron responsive element (29 nt), Pro‐tRNA (76 nt), and HIV‐1 core encapsidation signal (155 nt). Chemoenzymatic creations: Using a cost‐effective chemoenzymatic method, we coupled a specifically 13C,15N‐labeled uracil nucleobase with specifically 13C‐labeled ribose to synthesize both UTP and CTP in nearly quantitative yields. The methodology generates versatile 13C and 15N labeling patterns that can expedite NMR structure and dynamics studies for RNAs of various sizes and complexity.