## 4 Glycol and Butyl Nucleic Acids (GNA and BuNA)
A GNA nucleoside analog containing 1\(H\)-imidazol-[4,5-7][1,10]phenanthroline (P, **23a**, Chart 6) as a nucleobase was found to form a base pair within a DNA duplex 5\({}^{\prime}\)-d(GAGGGTPTGAAAG)-3\({}^{\prime}\)/3\({}^{\prime}\)-d(CTCCAPACTTTC)-5\({}^{\prime}\), which was able to coordinate a Cu\({}^{+}\) cation, with a marked increase in Tm (+23 \({}^{\circ}\)C) [51]. Unmodified duplexes with A:T or G:C base pairs in place of the P:P base pair did not respond to the presence of this cation. Importantly, this probe was insensitive to Cu\({}^{2+}\) cations for geometric reasons, leading to some repulsion effects. This differentiation can be used to tune a duplex dissociation/association process by changes in the redox state of the copper cation. The same authors reported that the addition of 2 equivalents of Zn\({}^{2+}\) to a duplex:  
5\({}^{\prime}\)-d(AAAAAAAAPAATTTTTPAATATTT)-3\({}^{\prime}\)  
3\({}^{\prime}\)-d(  
Apart from the acyclic structure, GNA nucleotides differ from DNA and RNA units in the number of atoms present in the backbone units. There are 5 atoms in GNA (O3\({}^{\prime}\)-C3\({}^{\prime}\)-C2\({}^{\prime}\)-O2\({}^{\prime}\)-P) and six atoms in natural nucleotides (O5\({}^{\prime}\)-C5\({}^{\prime}\)-C4\({}^{\prime}\)-C3-O3\({}^{\prime}\)-P). It has been suggested that the difference in linker length is one reason why GNA oligomers do not hybridize with DNA. Therefore, it was tempting to make a homolog of GNA with six atoms in the backbone, and this was carried out with the synthesis of Butyl Nucleic Acids (BuNA, **25**, Chart 8) [56]. In the first attempt, the carboxyl groups of (S)-malic acid were reduced to yield the corresponding triol, in which two hydroxyl groups were protected using benzaldehyde dimethyl acetal. Then, the nucleobases were substituted for the third hydroxyl under the conditions of a Mitsunobu reaction. By this synthetic route, the intermediates bearing uracil, thymine and adenine were obtained in 40-60% yield, but the further workup was successful only for the uracil derivative, so the relevant scheme is not shown. The BuNA derivatives of Ade, Thy, Gua and Cyt were obtained starting from aspartic acid (**26**, Scheme 5), which was subjected to NH\({}_{2}\)\(\longrightarrow\)Br conversion (using an HNO\({}_{2}\)/HBr mixture), followed by a reduction of the carboxyl groups and epoxide ring closure. The resulting epoxy alcohol **27** was tritylated with DMT-Cl and reacted with thymine, benzolyated cytosine, adenine or 2-amino-6-chloropurine. It should be noted that starting from one enantiomer of aspartic acid, only single enantiomers of BuNA nucleosides were obtained. Finally, after the protection of adenine and the conversion of 2-amino-6-chloropurine into guanine, the corresponding phosphoramidite monomers were obtained in good yield. Ten fully modified (eight of them with a DNA nucleoside at the 3\({}^{\prime}\)-end) and eight partially modified oligomers were synthesized. It was found that (S)-butyl nucleic acids (BuNA) form duplexes with their complementary strands, but the observed thermal stability was lower than that for corresponding DNA duplexes. Thus, increasing the backbone length by one carbon atom resulted in a decrease in the melting temperature of (S)-BuNA duplexes compared to GNA duplexes. Moreover, the CD spectra showed that (S)-BuNA duplexes adopt the A-like conformation and form a left-handed helical structure. The incorporation of (S)-BuNA nucleotides into DNA strands resulted in destabilized duplexes. The primer extension studies on fully modified (S)-BuNA strands and (S)-BuNA-substituted DNA were carried out using the polymerases Bst, Bsu, Taq and Therminator. No extension was observed with fully modified primers, but when (S)-BuNA-substituted DNA strands were used, full extension of the modified primers was observed.