Abstract
The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson-Crick proton donor site N3-H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4'-endo) for the ribose moiety, with an antiperiplanar orientation of the 5'-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2' of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O-H...O and N-H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine-purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.
Highlights
The specific recognition of complementary nucleobases in the DNA coding system is based on the combination of purine and pyrimidine bases (Watson & Crick, 1953)
The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine
The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O40endo) for the ribose moiety, with an antiperiplanar orientation of the 50-hydroxy group
Summary
The specific recognition of complementary nucleobases in the DNA coding system is based on the combination of purine and pyrimidine bases (Watson & Crick, 1953). Purines glycosylated at nitrogen-9 (adenine and guanine) base pair with purines glycosylated at nitrogen-3 (motif I xanthine and motif II isoguanine, see Fig. 1; purine numbering is used throughout this article). Recent advances in the construction of ‘all-purine’ DNA used purine nucleosides glycosylated at nitrogen-9 (Seela et al, 1997, 2001; Seela & Melenewski, 1999; Seela & Rosemeyer, 2002). In this context, 5-aza-7-deazaguanine (imidazo[1,2-a]-1,3,5-triazine) 20-deoxyribonucleoside (2b) has emerged as a promising purine analogue mimicking the pyrimidine site of a Watson–Crick base pair (Fig. 2).
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