7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization

Autor(en): Kondhare, Dasharath
Budow-Busse, Simone
Daniliuc, Constantin
Seela, Frank
Stichwörter: 5-AZA-7-DEAZA-2'-DEOXYGUANOSINE; 7-iodo-5-aza-7-deazaguanosine; all-purine RNA; base-pair prediction; Chemistry; Chemistry, Multidisciplinary; CORE; crystal packing; crystal structure; Crystallography; DNA; Hirshfeld surface analysis; OLIGONUCLEOTIDES; ORIENTATION; pK(a) values; ribonucleoside
Erscheinungsdatum: 2020
Herausgeber: INT UNION CRYSTALLOGRAPHY
Journal: ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY
Volumen: 76
Ausgabe: 5
Startseite: 513+
Zusammenfassung: 
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-deaza-guanosine. 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 center dot center dot center dot O and N-H center dot center dot center dot 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.
ISSN: 20532296
DOI: 10.1107/S2053229620004684

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