## 4 Glycol and Butyl Nucleic Acids (GNA and BuNA)  
Structurally simple and synthetically relatively easily accessible acyclic glycol nucleic acids (GNA; **19**, Chart 5, B=Thy or Ade, a dinucleotide is shown) were obtained by [PERSON] and coworkers in 2004 and reported in 2005 [34]. Note that unlike FNA and UNA, a GNA scaffold contains stereogenic centers (marked with the asterisks in **19**) and GNA units can exist in \(R\) and \(S\) forms. Fortunately, the enantiomerically pure substrates, i.e., (\(S\))-(\(-\))-glycidol (**20**, Chart 5) and (\(R\))-(+)-glycidol (**21**), are commercially available. After dimethoxytritylation, the DMT derivatives were successfully ring-opened with the unprotected thymine and adenine. The adenine derivative was benzoylated at the exocyclic amino group, and the product and thymine derivative were converted into the final phosphoridities, which were further used in the solid-phase synthesis of 7 oligomers, each 18-nt in length. Their sequences allowed the study of the formation of antiparallel and parallel duplexes. It was found that uniformly modified GNA oligomers form highly stable (Tm = 63 \({}^{\circ}\)C) antiparallel helical duplex structures according to the Watson-Crick base-pairing scheme. This stability significantly exceeds the thermal stability of the analogous DNA duplex. The recorded melting curves showed a characteristic sigmoidal shape, while the curves of the oligomers intended to form a parallel duplex showed no transition. Notably, a single mismatch in the middle of the sequence significantly reduced the stability of the duplex (Tm = 55 \({}^{\circ}\)C). It was found that (\(S\))-GNA and its Watson-Crick-paired (\(R\))-GNA counterpart neither hybridize with each other nor form stable duplexes with DNA. However, initial results showed that (\(S\))-GNA 2\({}^{\prime}\)-ATTTTAAATAAATAATT-3\({}^{\prime}\) (and not (\(R\))-GNA) associates with RNA (Tm = 35 \({}^{\circ}\)C). The GNA derivatives of cytosine, guanine and uracil were prepared in a similar manner, although to obtain the guanine derivative, the reaction of 2-amino-6-chloropurinehad to be used, followed by hydrolysis with 1N HCl [35]. The ring opening yields of 49-61% were only satisfactory. The crystal structures of the glycol nucleosides confirmed the formation of the desired regioisomers. The syntheses of the corresponding phospho-ramidite monomers were rather routine and it was shown that GNA oligonucleotides can be synthesized in high yield under the conditions of solid-phase synthesis. Analysis of the thermal stability of a GNA/GNA duplex formed by 3\({}^{\prime}\)-CACATTATTGTTGTGA-2\({}^{\prime}\) with 2\({}^{\prime}\)-GTGTAATAACAACAT-3\({}^{\prime}\) revealed a Tm of 71 \({}^{\circ}\)C compared to 46 \({}^{\circ}\)C for a normal DNA duplex of the same sequence. The CD spectrum recorded for this duplex showed greatly increased CD signals at around 205, 220, and 275 nm, supporting the formation of a helical duplex. Based on long-term observations, it was found that the widely used amide protecting groups in the monomers used for solid-phase synthesis of GNA lead to the formation of by-products, resulting in lower final yields than expected. In addition, the GNA-G phosphoramidite is unstable and decomposes slowly, even at \(-\)20 \({}^{\circ}\)C. To alleviate these problems, an N-dimethylformamidine protecting group was chosen for adenine and guanine and an acetamide group for cytosine [36]. The new phosphoramidite derivative of GNA-G\({}^{\text{d}\text{m}\text{f}}\) proved to be stable when chromatographed on a silica gel column, and the monomer was obtained in a significantly higher yield (30% vs. 8%). Using these new monomers, several GNA oligonucleotides were prepared following the general procedures for the synthesis of DNA oligonucleotides, except that the coupling time of 3 min was applied.