Warum Pentose‐ und nicht Hexose‐Nucleinsäuren??. Teil V. (Purin‐Purin)‐Basenpaarung in der homo‐DNS‐Reihe: Guanin, Isoguanin, 2,6‐Diaminopurin und Xanthin

Abstract

This paper concludes the series of reports in this journal [l-41 o n the chemistry of homo-DNA, the constitutionally simplified model system of hexopyranosyl-(6' + 4)-oligonucleotide systems studied in our laboratory as potentially natural-nucleic-acid alternatives in the context of a chemical aetiology of nucleic-acid structure. The report describes the synthesis and pairing properties of homo-DNA oligonucleotides which contain as nucleobases exclusively purines, and gives, together with part 111 of the series [3]. a survey of what we know today about purine-purine pairing in homo-DNA. In addition. the paper discusses those aspects of the chemistry of homo-DNA which, we think, influence the way how some of the structural features of DNA (and RNA) are to be interpreted on a qualitative level.Purine-purine pairing occurs in the homo-DNA domain in great variety. Most prominent is a novel tridentate Wutson-Crick pair between guanine and isoguanine, as well as one between 2.6-diaminopurine and xanthine, both giving rise to very stable duplexes containing the all-purine strands in antiparallel orientation. For the guanine-isoguanine pair. constitutional assignment is based on temperature-dependent UV and CD spectroscopy of various guanine-and isoguanine-containing duplexes in comparison with duplexes known to be paired in the reverse-Hoogs/rm mode. The assignment is supported by the characteristic changes observed in pairing behavior when guanine is replaced by 7-carbaguanine. Isoguanine and 2,6-diaminopurine also have the capability of self-pairing in the reverse-Hoc~gstrc.n mode, as previously observed for adenine and guanine [3]. In this type of pairing. the purine bases that contain an amino group in the 6-position (adenine. 2,6-diammopurine. and isoguanine) behave interchangeably. Fig. 36 provides an overall survey of the relative strength of pairing in all possible purine-purine combinations. Wutson-Crick pairing of isoguanine with guanine demands the former to participate in its 3H-tautomeric form; hitherto this specific tautomer had not been considered in the pairing chemistry of isoguanine. Whereas

Neighbouring bases in template influence base-pairing of isoguanine

“…In our opinion, the possible participation of these tautomers in the interactions of iG should also be taken into consideration. The participation of the 2-oxo, N3-H, 6-amino tautomeric form (structure IV, Figure 4) in various base pairs involving iG was postulated by Eschenmoser and co-workers in order to explain the formation of complexes of various unnatural polynucleotides studied in their laboratory [32,33]. Isocytosine can exist in various tautomeric forms, however, the experimental and theoretical data are consistent with the fact that 1-substituted iC adopts the 2-amino-4-oxo form ( Figure 1A) in environments of intermediate to high polarity ( [31] and references cited therein).…”

“…We cannot exclude the participation of tautomers of iG, other than structures I and II (Figure 4), in its possible plenitude of interactions with natural and non-natural bases considered by the authors quoted above [30][31][32][33]. It is worth emphasizing that relevant experimental data on the structure of iG base-pairing are rather scarce [36], whereas the evaluations of the stability and geometry of base pairs are often just of a qualitative nature [31].…”

G‐Quartets 40 Years Later: From 5′‐GMP to Molecular Biology and Supramolecular Chemistry

“…[225] Recent calculations have confirmed that formation of isoG quartets and isoG pentamers depends on the size of the templating cation. [229] Since isoG and G are self-complementary, [230,231] it is also possible that G and isoG may be able to form mixed assemblies. [232] In addition to the ligand and the cation, the anion may also affect the self-assembly of lipophilic nucleosides.…”

Preparation of pyridine-stretched 2'-deoxyhypoxanthosine phosphoramidite

“…34,35 We therefore anticipated that no protection of the carbonyl in strH 5 would be required. Dimethoxytritylation of strH 5 provided the O5-protected derivative 28 (61%) that underwent phosphitylation at O3 using compound 29 and standard conditions to give the strH nucleoside phosphoramidite 30 (51%).…”