2′-Fluoro-arabinonucleic Acid (FANA): A Versatile Tool for Probing Biomolecular Interactions

Abstract

Conspectus This Account highlights the structural features that render 2′-deoxy-2′-fluoro-arabinonucleic acid (FANA) an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions relevant to chemical biology. The high binding affinity of FANA to DNA and RNA has had implications in therapeutics. FANA can hybridize to complementary RNA, resulting in a predominant A-form helix stabilized by a network of 2′F-H8­(purine) pseudohydrogen bonding interactions. We have shown that FANA/RNA hybrids are substrates of RNase H and Ago2, both implicated in the mechanism of action of antisense oligonucleotides (ASOs) and siRNA, respectvely. This knowledge has helped us study the conformational preferences of ASOs and siRNA as well as crRNA in CRISPR-associated Cas9, thereby revealing structural features crucial to biochemical activity. Additionally, FANA is of particular use in stabilizing noncanonical DNA structures. For instance, we have taken advantage of the anti N-glycosidic bond conformation of FANA monomers to induce a parallel topology in telomeric G-quadruplexes. Subsequent single-molecule FRET studies elucidated the mechanism by which these parallel G-quadruplexes are recognized and extended by telomerase. Similarly, we have utilized FANA to stabilize elusive telomeric i-motifs in the presence of concomitant parallel G-quadruplexes and under physiological conditions, thereby reinforcing their potential relevance to telomere biology. In another study, we adapted microarray technology and used FANA substitutions to enhance the binding affinity of the G-quadruplex thrombin-binding aptamer to its thrombin target. Finally, we discovered that DNA polymerases can synthesize FANA strands from DNA templates. On the basis of this property, other groups demonstrated that FANA, like DNA, can store hereditary information. They did so by engineering polymerases to efficiently transfer genetic information from DNA to FANA and retrieve it back into DNA. Subsequent studies showed that FANA could be evolved to acquire ribozyme-like endonuclease or ligase activity and to form high-affinity aptamers. Overall, the implications of these studies are remarkable because they promise a deeper understanding of human biochemistry for innovative therapeutic avenues. This Account summarizes past achievements and provides an outlook for inspiring the increased use of FANA in biological applications and fostering interdisciplinary collaborations.

Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA

“…[6][7][8][9][10] While prior studies established that bPNA binding to oligo T/U domains can be effective with diverse backbone chemistries such as αpeptide, [11] peptoid, [12] small molecules [13] and polyacrylate, [14][15][16] the aminoethylglycine (AEG) PNA prototype [17] has been shown to be amenable to optimization via backbone, [18][19][20] sidechain [21][22][23][24] and electrostatic [23,25] modifications that greatly enhance nucleic acid hybridization. In addition, optimization strategies have been extensively investigated in sugarphosphate backbones bearing synthetic sugars (XNAs) [26][27][28] that limit backbone conformational freedom through covalent constraints or electronic effects such as locked and unlocked nucleic acids (LNAs, UNAs) [29] and 2'F-arabinose (FANA), [30] respectively, that favor hybridization with DNA.…”

Targeting non-coding RNA family members with artificial endonuclease XNAzymes

“…Analogous “XNAzyme” catalysts can be evolved from a variety of synthetic genetic polymers 62 , including 2′-deoxy-2′-fluoro-β-D-arabino nucleic acid (FANA) 63 , an artificial polymer chemistry capable of stabilising nucleic acid structures and reducing their dependence on Mg 2+ for folding, and offering improved biostability compared with RNA 64 . We recently identified an artificial modular RNA endonuclease, “FR6_1”, comprising a fully-FANA 17 nt catalytic core flanked by substrate-binding arms (Fig.…”

Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms

“…3 c) [ 100 ] and 20-fluoro-arabino nucleic acid (FANA) (Fig. 3 c) [ 101 ]. A novel enzyme 3′–2′ phosphonomethyl-threosyl nucleic acid (tPhoNA) (Fig.…”

“…Apart from that, FANA has been an invaluable tool for therapeutic lead discovery, functional genomics and structural biology. However, given the fact that FANA can stabilize and tune several nucleic structures, the same has also the potential in FANA-based sensors for in-cell experiments [ 101 ]. Several strategies have also been developed for incorporation of ncAA into the proteins; however, there are few of the limiting factors that need to be addressed to achieve the same with ease and in an efficient manner.…”