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Although many reports have revealed structural differences between DNA and RNA at the polymeric level, there are no comparative studies with 2′‐deoxyribonucleoside and ribonucleoside to explore the role of the 2′‐OH group at the monomeric level under the same conditions. Inspired by this, herein, the intrinsic contributions of the 2′‐OH group in the nucleoside have been systematically investigated by directly solving the single‐crystal structures of 2′‐deoxy‐2‐aminoadenosine (1), 2‐aminoadenosine (2), and 2‐aminoarabinofuranosyladenine (3) in water. The 2′‐OH group not only influenced the conformation and base‐pair pattern of the single‐nucleoside molecule, but also played a fundamental role in the entire supramolecular structure. Interestingly, compound 1, which did not contain the 2′‐OH group, displayed strong hydration, whereas 2 and 3 (with the 2′‐OH group in the opposite direction) exhibited no hydration, which was completely different from that observed in nucleic acids. Meanwhile, compound 1 trapped water molecules to form unique trihydrol moieties, which further served as the backbone to construct the simplest double‐chain DNA‐like structures. To this end, to investigate the effect of the biological environment on these unique structures, the solvent was changed from water to phosphate‐buffered saline (PBS). Surprisingly, such a subtle adjustment led to entirely different superstructures, consisting of 2D lamellar structures in water and 3D porous structures in PBS. These large morphological differences could be attributed to delicate ion hydration, which was also confirmed through variable‐temperature X‐ray analysis, SEM, and intermolecular interaction energy calculations. In summary, this study comprehensively investigated the intrinsic contributions of 2′‐hydroxyl to the hydration of nucleosides at the monomeric level; this is helpful to further understand the differences in DNA/RNA and the impact of their surrounding environment. [ABSTRACT FROM AUTHOR]

Formation of silver-mediated DNA was studied with oligonucleotides incorporating 8-aza-7-deazapurine, 7-deazapurine, and purine nucleosides. The investigation was performed on non-self-complementary duplexes with one or two modifications and self-complementary duplexes with an alternating dA-dT motif. Homo base pairs as well as base pair mismatches of dA analogues with dC and Watson-Crick pairs with dT were studied by stoichiometric silver ion titration and Tm measurements. N8-Glycosylated 8-aza-7-deazaadenine forms silver-ion-mediated base pairs capturing two silver ions (low silver content) whereas regularly glycosylated 8-aza-7-deazapurine, 7-deazapurine (c7Ad), and dA do not form comparable structures. Stable silver-mediated 'dA-dC' base pair mismatches were detected for all nucleosides. Two silver ions per base pair are bound by 8-aza-7-deazapurine whereas c7Ad binds only one silver ion. The situation is different when the equivalents of silver ions were increased to the number of total base pairs. Surprisingly, in 12-mer duplexes as well as in related 25-mer duplexes every base pair consumed one silver ion. [ABSTRACT FROM AUTHOR]

Structurally modified nucleosides are central players in the field of nucleic acid chemistry. Adenine-thymine (AT) pyrimido[4,5-d]pyrimidine furanosyl and pyranosyl arabinonucleosides have been synthesized for the first time. Single-crystal X-ray diffraction analysis reveals novel base pairs that, in synergy with the sugar residues, direct the emergence of distinct networks containing channels and cavities. The microscopic noncovalent connections can be translated into macroscopic levels in which robust organogels are formed by the furanoside but not the pyranoside. The influences of the sugars are also displayed by the different shaped superstructures of the free nucleosides in solution. The readout of the information in the base moiety is therefore tailored by the sugar configuration, and the interplays exert subtle effects on the structures, from solid to gel and to the solution state. The potential for forming these appealing base pairs and higher structures enables these intriguing nucleosides to serve as unique building blocks in various areas or to construct innovative nucleic acid structures. [ABSTRACT FROM AUTHOR]

Abstract: J-AT nucleoside-based organogelators 1a and 1b were designed and synthesized. They were endowed with unparalleled superiority to natural nucleobase analogues 2–6 to gelate aromatic solvents due to their excellent self-assembly properties. The J-AT nucleoside-based organogelators showed a specific self-complementary base pair recognition characteristic. The gel stabilities of 1a and 1b were drastically influenced by adenine analogue 2, hardly affected by thymine analogue 3, uracil analogue 4, cytosine analogue 5, and mildly interrupted by guanine analogue 6. [Copyright &y& Elsevier]

The intrinsic structural diversity of the nucleosides is one of the essential properties for their wide participation in myriads of chemical or biochemical processes. Two unique regio-isomeric Janus-type AT nucleosides with the 5′-deoxyribose attached on N1 or N3 position has been synthesized through Vorbrueggen or transglycosylation reactions. These two isomers display different supramolecular morphologies in solution state from their N8 glycosylated counterpart. The underneath structural details of the N3 glycosylated isomer were revealed by the single-crystal X-ray analysis. In addition to a novel base pair pattern was identified which is entirely different from the reverse Watson-Crick base pair adopted by its N8 isomer, an interesting water-filled columnar nanotuble-like structure was also found in its solid state. This study not only enriches the structural varieties of AT Janus-type nucleosides, but also provides specific information concerning the effect of the sugar glycosylation position on the properties of these new type of pyrimido[4,5-d]pyrimidine nucleosides. [ABSTRACT FROM AUTHOR]