Due to their unique properties, fluorocarbon chains represent a useful building block for the construction of supramolecular systems. Perfluoroalkyl chains have a larger cross section and are more rigid than their hydrogenated counterparts. They are considerably more hydrophobic and are lipophobic as well. As a result, when dispersed in water, fluorinated amphiphiles exhibit an enhanced capacity to self-assemble into highly stable and well-defined assemblies such as films, membranes, micelles, vesicles and other stable supramolecular systems [23,24]. The self-assembling behavior of a variety of synthesized single and double chain neutral, zwitterionicor anionic fluorinated phospholipids [25,26,27,28], glycolipid [29,30], glycophospholipids, glycopeptides [31,32] was already explored (Figure 2) [33], to evaluate the impact of the fluorinated chains on the properties of the resulting aggregates. It enhances stability, low permeability to both hydrophilic and lipophilic material and reduces interaction with biological media. These fluorinated amphiphiles possess a considerable potential for the delivery of materials such as drugs, prodrugs, markers, contrast agents and nucleic acids. Recently, new perfluorinated dimerizable polycationic amphiphiles were designed by Vierling et al. to evaluate the ability of the monomer to condense DNA and of the dimer to form stable nanoparticles capable of efficient cell transfection [34]. Although formulation of small-sized cationic monomolecular DNA nanoparticles (<40 nm) with the dimerizable perfluorinated succeeded, spermine-based amphiphiles proved to be poor non-specific transfection agents in vitro. Improvements are still in progress [35,36].

Nucleoside-based lipids commonly named nucleolipids [7] are hybrid molecules composed of a nucleobase, a nucleoside, a nucleotide or an oligonucleotide (either DNA or RNA), and a lipophilic moiety, which might be either simply a single- or double-chained alkyl moiety. Several improved nucleolipids have been reported hereafter (Figure 3) [37,38,39,40,41,42,43,44,45,46,47]. Most nucleolipids have a polar head group at the 5’ position and hydrophobic groups at both the 2’ and 3’ positions, patterned after natural glycerol phospholipids, which are key components of the cellular membrane. Nucleolipids were designed to interact with nucleic acids through hydrogen bonding, π–π stacking, and nucleobase recognition, as well as electrostatic interactions and the hydrophobic effect. Several cationic [12,48,49,50,51] and anionic [52,53] nucleolipids were first investigated as potential agents for the delivery of nucleic acids into cells. Indeed their self-assembled structures into lipoplexes mimic cellular membranes and their cationic properties attract both anionic oligonucleotides and negatively charged cellular membranes. New versions comprising neutral, zwitterionic, and anionic nucleolipids are currently evaluated.

The combination of the self-assembly potential of nucleoside amphiphiles with the hydrophobic character of highly fluorinated chains is of high relevance to prepare new self-assembled structures with tunable physico-chemical properties and functions. To assess whether fluorinated chains can enhance the scope of supramolecular assemblies formed by hybrid fluorocarbon nucleoside amphiphiles, different molecules were synthesized (Figure 4).

The fluorocarbon amphiphile 1 is based on a uridine backbone modified by a phosphocholine moiety at the 5’ position, and two 2H,2H,3H,3H-perfluoroundecanoyl side chains at the 2’ and 3’ positions. One of the goals of the study was to characterize the properties of such new compounds and to compare those results with that observed for the analogous hydrocarbon nucleoamphiphiles. In aqueous solution, fluorocarbon nucleoamphiphiles were surprisingly able to form large vesicular assemblies and unexpected lamellar phases below their T_m, contrary to hydrocarbon analogs that self-assemble into helical structures below their T_m and bilayers above it [54]. These highly hydrophobic fluorocarbon amphiphiles exhibited interesting hybrid microspherical supramolecular assemblies in the presence of thorium that were characterized by Scanning Electron Microscopy (SEM) [55].

Recently, two glycosyl-nucleoside fluorinated amphiphiles (GNFs) were designed to construct new supramolecular hydrogels. Molecules 2 and 3 feature both sugar moieties attached to a thymidine base and a 2H,2H,3H,3H-perfluoroundecanoyl side chain at the 5’ position, linked via triazole bridges resulting from “click” chemistry. The self-assembly and gelation properties of such molecules were investigated. Similarly to their hydrocarbon analogs [56,57] GNFs stabilize hydrogels at low concentrations (0.1% w/w for compound 2). GNFs gelators displayed supramolecular networks of varying morphologies, such as nanofibers and helical springs, which are correlated to the presence of fluorocarbon chains. Moreover, fluorocarbon amphiphile GNF 2 proved to be not toxic for human cells (Huh7) whereas hydrocarbon analogue becomes toxic above 100 µM, demonstrating the greater potential of such fluorocarbon nucleoside amphiphiles for biomedical applications [58].

Recently our group has reported on the synthesis and biological properties of FONs [63]. In previous studies, our group already reported on the synthesis and cellular uptake studies of lipid-oligonucleotide conjugates (LONs) [64,65]. The main purpose of attaching a fluorocarbon chain to a polyanionic oligonucleotide (ONs) was to study how cellular uptake or internalization of ONs are influenced by the nature of the hydrophobic moieties. To address this issue, Godeau et al. have synthesized two FONs featuring C₈F₁₇ and C₆F₁₃ chains using 1,3-dipolar Huisgen’s reaction [66] via a “post synthetic” modification approach. Three different human cell lines were incubated with either FONs or LONs or unconjugated ONs for comparative study of cellular internalization (Figure 5). Moreover, internalization kinetics of FONs, LONs and unconjugated ONs with Huh7 cells were also evaluated. Keeping in mind the hydrophobic and lipophobic properties of fluorocarbon chains, it can be hypothesized that FONs self-assemble outside the cell to form nano aggregates. It is likely that these nanoobjects would be uptaken by the cell via an endocytosis pathway. It is worth mentioning here that to the best of our knowledge, there is no earlier report on oligonucleotide amphiphiles featuring perfluorinated chains.

Various groups have been interested in the synthesis and application of fluorinated oligonucleotide analogues. There are different possible sites for the modification of an oligonucleotide with one or more fluorine atoms for various biological and therapeutical applications. Fluorine atoms have a strong influence on both the electronic and the conformational properties of the nucleic acids’ furanose ring. The 2’-position in the ribose moiety of RNA is prime target for chemical modifications. Extensive research work is going on towards the study of structural properties, biological applications and delivery strategies of oligonucleotides-incorporated with 2’-deoxy-2’fluoronucleotide in combination with other structural modifications [67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84]. Oligonucleotides containing 2’-deoxy-2’fluoronucleosides have been synthesized for regiospecific cleavage of RNA by RNase H [67]. Incorporation of 2’-deoxy-2’-fluoronucleotide into oligonucleotides induces substantial enhancement in their binding affinities to RNA targets [68]. Damha et al. have shown that fluorine-induced sugar pucker in 2’-deoxy-2’fluoro-β-D-ribonucleicacid (2’-F RNA; C3’-endo) and 2’-deoxy-2’fluoro-β-D-arabinonucleicacid (2’-F ANA; C2’/O4’-endo) can improve the activity of siRNA (Figure 6) and enhance its serum stability. They have also provided the evidences for an important role of a pseudohydrogen bond between the F²’ and H⁸ of the nucleobase for 2’-F ANA:RNA duplex stability [72,73,74,75,76,77,78,79,80,81,82,83,84].

On the other side, very interesting and novel studies have been carried out by Erande et al. using 3’-deoxy-3’ribofluoro/xylofluoro uridine incorporated oligonucleotides (2’-5’-strand) [85]. They have shown the effect of incorporation of one or more unit of 3’-deoxy-3’-fluoronucleosides (having either locked or frozen S-type/Ntype sugar conformations) on the stability of isoDNA:RNA duplexes. For the first time, evidences were given that the DNA strand prefers S-type geometry in stable isoDNA:RNA duplexes (Figure 7) [85].

To investigate the forces (hydrogen bonding, base stacking and solvation) which are responsible for stability of the secondary structure of nucleic acids, Engels et al. have synthesized novel nucleic acid analogues in which nucleobases are replaced by their steric mimics, containing one or more fluorine atom. They have utilized fluorobenzene and fluorobenzimidazole derivatives (Figure 8) [86,87]. They have discussed how C–F…H–C hydrogen bonds affect the stability of the secondary structure of nucleic acids in details.

Owing to the favorable NMR properties of fluorine atom (¹⁹F), fluorinated oligonucleotide derivatives provide a sensitive probe for structural study of nucleic acids in the solution state and their interactions with other biological moieties [71,88,89,90,91,92,93,94,95]. Barhate et al. have synthesized nucleosides with perfluorinated tert-butyl group and successfully incorporated it into the oligonucleotide at different positions and demonstrated as a sensitive ¹⁹F NMR probe of nucleic acid conformation [95]. Oligonucleotides, labeled with radioactive isotopes, are new imaging tools to study gene expression at the nucleic acid and protein levels. Due to its positron-emission properties, fluorine-18 (radioactive isotope of fluorine) is widely used for oligonucleotide labeling for in vivo PET (Positron Emission Tomography) imaging. Dollé et al. [96,97,98,99,100]. have developed an original method for labeling oligonucleotides with ¹⁸F in different positions. Several other research groups have also synthesized ¹⁸F labeled oligonucleotide analogues for imaging studies with PET [101,102,103].