¹⁹F NMR of RNA. The Structural and Chemical Aspects of 5-Fluoro-cytidine and-uridine Labelling of Oligoribonucleotides

15N-Enriched 5-Fluorocytosine as a Probe for Examining Unusual DNA Structures

“…At the same time, it was reported that unprotected FdC could be successfully incorporated into synthetic oligonucleotides (12), however, recent attempts to incorporate unprotected 5-fluorocytidine into synthetic RNA report low yields (13). Alternatively, 5-fluorocytidine is reported to be incorporated successfully into synthetic RNA via the 4-O-methyl substituted 5-fluorouridine phosphoramidite, followed by ammonolysis (13).…”

“…Alternatively, it was reported that FC residues could be generated in synthetic oligonucleotides by incorporation of 4-substituted FdU derivatives and post-synthetic displacement of 4-O-(2,4,6-trimethylphenyl), 4-O-methylthio, or 4-O-triazole groups (9)(10)(11). At the same time, it was reported that unprotected FdC could be successfully incorporated into synthetic oligonucleotides (12), however, recent attempts to incorporate unprotected 5-fluorocytidine into synthetic RNA report low yields (13). Alternatively, 5-fluorocytidine is reported to be incorporated successfully into synthetic RNA via the 4-O-methyl substituted 5-fluorouridine phosphoramidite, followed by ammonolysis (13).…”

19F-Site-Specific-Labeled Nucleotides for Nucleic Acid Structural Analysis by NMR

“…Here, we describe a combination of RNA-labeling techniques as well as NMR methods and applications to a well-established model system, the human immunodeficiency virus (HIV) transactivation response element (TAR) (Fischer et al, 1996;Fischer, Gdaniec, Olejniczak, Bielecki, & Adamiak, 1999;Hennig et al, 2006Hennig et al, , 2007Huang, Varani, & Drobny, 2010; Olejniczak et al, 2002;Olsen et al, 2005;Scott et al, 2004). The Tat (transcription activator)-TAR complex formation provides an essential gene regulatory function for HIV (Marciniak, Calnan, Frankel, & Sharp, 1990;Seelamgari et al, 2004).…”

A General Approach for the Identification of Site‐Specific RNA Binders by 19F NMR Spectroscopy: Proof of Concept

“…With respect to nucleic acids, these properties have been exploited to some extent for studies on metal-ion binding, [22] hairpin-duplex transitions, [23] hammerhead ribozyme folding, [24] DNA methylation, [25] and oligonucleotide hybridization. [26,27] Most of these 19 F NMR studies on nucleic acids utilize nucleotides that have been modified with fluorine at the nucleobase, [28][29][30][31][32] but a few reports also document ribose 2'-F labeling. [27,33] Of particular interest here is that the introduction of a fluorine in the 2'-position favors ribose C3'-endo conformation.…”