Warum Pentose‐ und nicht Hexose‐Nucleinsäuren??. Teil V. (Purin‐Purin)‐Basenpaarung in der homo‐DNS‐Reihe: Guanin, Isoguanin, 2,6‐Diaminopurin und Xanthin
Authors: Groebke Katrin , Hunziker Jürg , Fraser William , Peng Ling , Diederichsen Ulf , Zimmermann Kaspar , Holzner Armin , Leumann Christian , Eschenmoser Albert 
Published: December 2004

Why Pentose‐ and Not Hexose‐Nucleic Acids? Purine‐Purine Pairing in homo‐DNA: Guanine,Isoguanine, 2,6‐Diaminopurine, and Xanthine

This paper concludes the series of reports in this journal [1–4] on the chemistry of homo‐DNA, the constitutionally simplifie dmodel system of hexopyranosyl‐(6′ → 4′)‐oligonucleotide systems stidued 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 III of the series [3], a survey of what we know today about purine‐purine pairingin 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 Watson‐Crick pair between guanine and isoguanine, as well as one between 2,6‐diaminopurine and xanthinone, 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‐containg duplexes in comparison with duplexes known to be paired in the reverse guanine is replaced by 7‐carbauguanine. Isoguanine and 2,6‐diaminopurine also have the capability of self‐pariring in the reverse‐Hoogsteen mode, as previously observed for adenine and guanine [3]. In this type of pairing, the interchangeably. Fig. 36 provides an overall survey of the relative strength of pairing in all possible purine‐purine combinations.

Watson‐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 (cumulative) purine‐purine pairing in DNA (reverse‐Hoogsten or Hoogsteen) seems to occur in triplexes and tetrapalexes only, its occurrence in duplexes in a characteristic feature of homo‐DNA chemistry. The occurrence of purine‐purine Watson‐Crick base pairs is probably a consequence of homo‐DNA's quasi‐linear ladder structure [1][4]. In a double helix, the distance between the two sugar C‐atoms, on which a base pair is anchored, is expected to be constrained by the dimensions of the helix; in a linear duplex, however, there would be no restrictions with regard to base‐pair length. Homo‐DNA's ladder‐like model also allows one to recognize one of the reasons why nucleic‐acid duplexes prefer to pair in antiparallel, rather than parallel strand orientation: in homo‐DNA duplexes, (averaged) backbone and base pair axes are strongly inclined toward one another [4]; the stronger this inclination, the higher the preference for antiparallel strand orientation is expected to be (Fig. 16).

In retrospect, homo‐DNA turns out to be one of the first artificial oligonucleotide systems (cf. Footnote 65) to demonstrate in a comprehensive way that informational base pairing involving purines and pyrimidines is not a capability unique to ribofuranosyl systems. Stability and helical shape of pairing complexes are not necessary conditions of one another; it is the potential for extensive conformational cooperativity of hte backbone structure with respect to the constellational demands of base pairing and base stacking that determines whether or nor a given type of base‐carrying backbone structure is an informational pairing system. From the viewpoint of the chemical aetiology of nucleic‐acid structure, which inspired our investigations on hexopyranosyl‐(6′ → 4′)‐oligonucleotide systems in the first place, the work on homo‐DNA is only an extensive model study, because homo‐DNA is not to be considered a potential natural‐nucleic‐acid altenratie. In retrospect, it seems fortunate that the model study was carried out, because without it we could hardly have comprehended the pairing behavior of the proper nucleic‐acid alternatives which we have studied later and which will be discussed in Part VI of this series.

The English footnotes to Fig. 1–49 provide an extension of this summary.