2.1. Oligonucleotide Synthesis and Purification

The oligonucleotides, whose sequence is given in Table 1, were synthesized and purified in the Bioorganic Chemistry Department, Polish Academy of Science, Lodz, Poland, on a Geneworld (K & A Laborgeraete GbR, Schaafheim, Germany) synthesizer and using nucleotide phosphoroamidites purchased from the ChemGenes Corporation (Wilmington, MA, USA).

Sequence of oligonucleotides containing 2′-deoxyuridine and 5′,8-cyclo-2′-deoxyadenosine and thermal stability (Tm) of corresponding duplexes.

U = 2′-deoxyuridine; cdA = 5′,8-cyclo-2′-deoxyadenosine; Tm = melting temperature. *A larger version of Table 1 is given in the Supplementary Materials as Table S1 docx file.

The phosphoroamidite derivatives of (5′R)- and (5′S)-5′,8-cyclo-2′deoxyadenosine were synthetized as described previously by Romieu et al. [38]. The crude oligonucleotides were purified by HPLC using Varian analytics with UV detection at wavelengths λ = 260nm, Phenomenex (Synergi 4 μm Fusion-RP 80Å, 250 × 4.6 mm) C-18 column.