## 4 Glycol and Butyl Nucleic Acids (GNA and BuNA)
The calculations also utilized data collected for a new crystal of a GNA duplex (with a resolution of 1.8 A--it belongs to the condensed N-type) obtained from the self-complementary GNA 3\({}^{\prime}\)-CTC(\({}^{\text{(SPU)}}\))AGAG-2\({}^{\prime}\). All bases form standard Watson-Crick hydrogen bonds, with the negligible distortion effect coming from the presence of the 5-bromouracil nucleotides. The MD simulations of dsGNA explained the high thermal stability of the duplex by a combination of enthalpic and entropic factors, but also revealed a pronounced \"twisting/untwisting\" behavior of the dsGNA backbone. This feature can significantly complicate the design of GNA probes intended for sequence-specific recognition. In the field of molecular biology, GNA oligomers have been tested as templates for template-dependent synthesis of DNA using the polymerases Taq, Bst, DeepVent (exo-), Therminator, Sequenase and SuperScript II DNA [42]. The chances of success were not good because GNA and DNA oligomers do not form stable duplexes. The DNA primer (5\({}^{\prime}\)-TAATACGACTACTATAGG-3\({}^{\prime}\)) was labeled at the 5\({}^{\prime}\) end with 3\({}^{2}\)P-phosphate and annealed to a DNA-GNA chimeric templates 3\({}^{\prime}\)-ATTAGCTGAGTATCCCatatacq-5\({}^{\prime}\), or 3\({}^{\prime}\)-ATTAGCTGAGTATCCCDtDgcDgtcA-5\({}^{\prime}\), where lowercase letters denote GNA nucleotides and \"D\" stands for a diaminopurine nucleotide (see structure 36). For most polymerases, the primer extension process stalled after elongation of the primer by two or three deoxynucleotides. However, the Bst DNA polymerase catalyzed full-length DNA synthesis on a dodecamer GNA template. In another study, the ability of various DNA polymerases (_vide supra_) to use GNA triphosphates as substrates for GNA synthesis on DNA templates was investigated [43]. It was found that the Therminator DNA polymerase was able to extend the primer by incorporating two GNA units, whereas extension with up to five GNA nucleotides was much less efficient. Some improvement was achieved by using 5-propyl-substituted GNA-C, where the propynyl substituent was assumed to enhance stacking interactions. This assumption was incorrect for a GNA-(5-propyl-T) nucleotide. In another type of experiment, a GNA-T unit was introduced into a molecule of the thrombin-binding aptamer mentioned above, the important part of which is a G-quadruplex [44]. The GNA-T nucleotide was introduced at position 3, 4, 7, 9, 12 or 13, and in all cases, these substitutions decreased the melting temperature (by approximately 10 \({}^{\circ}\)C), except at position 7, where Tm increased by 5 \({}^{\circ}\)C. However, no data were shown on the effects of these substitutions on the activity of the aptamer. The effect of GNA substitution on the potency of the siRNA probe was also investigated. First, the effect of incorporation of (_S_)- or (_R_)-GNA nucleotides on the RNA duplex structure was investigated using three individual crystal structures [45]. It was found that the (_S_)-GNA nucleotide backbone adopts a near-neutral conformation for the overall duplex structure, while the (_R_)-nucleotide dislocates the phosphate backbone and alters the hydrogen bonding of an adjacent base pair. Modification of an siRNA with (_S_)-GNA resulted in higher in vitro efficacy than analogs with (_R_)-GNA. Notably, duplexes modified with GNA were able to maintain their efficacy in vivo when injected subcutaneously into mice. For potential applications in molecular biology, sufficient resistance to light-induced damage is an important factor. Therefore, it is promising information that regardless of the absolute configuration of the GNA-T units, GNA-TT dinucleotides are not photocrosslinked in aqueous solution [46]. Samples were exposed to 254 nm radiation for 3 h. UVspectra showed no significant change in UV absorbance around 270 and 330 nm, indicating that the thymine chromophore remained intact. This resistance was explained by a small overlap interaction between adjacent thymine residues.