Pentopyranosyl Oligonucleotide Systems. 9th Communication

Abstract

Dulio Arigoni zu seinem 75. Geburtstag gewidmet, in Erinnerung an gute alte Zeiten Pyranosyl-RNA (−p-RNA× ) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chemical, and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature×s evolutionary choice of the molecular basis of genetic function. We consider the study of the chemistry of p-RNA as etiologically relevant in the sense that knowledge of its structural, chemical, and informational properties on the chemical level offers both a perspective and reference points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biology as we know it today. The paper describes the chemical synthesis of b-d-(and l)ribopyranosyl-(4' 3 2')-oligonucleotide sequences, presents a resume of their structural and chemical properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA×s origin. see [1 ± 8]. The label −Chemistry of Pyranosyl-RNA× previously used for the series of papers on p-RNA [1 ± 8] has been changed (see [9]) into −Pentopyranosyl Oligonucleotide Systems× as a consequence of the extension of our work on p-RNA to a whole family of diastereoisomeric pentopyranosyl oligonucleotides. In [9], the present paper had been assigned No. 9 in this series. The follow-up papers No. 10 [9], 11 [10], 12 [11], and 13 [12] in the series have already appeared. The present paper also is communication No. 30 in the series −Chemistry of a-Aminonitriles×. 4271 hexopyranosyl systems. Such hindrance is expected to occur between an equatorial 2'-OH group of a pyranosyl unit and the neighboring (downstream-positioned) nucleobase; it is clearly to be inferred from model considerations based on homo-DNA×s two types of pairing conformations (À g/ À g and t/ À g), which were derived by qualitative conformational analysis [29] 5 ) ( Fig. 2), and were found to co-exist in a homo-DNA duplex by an NMR structure analysis by Otting et al [26]. The results of experimental studies on 2'-deoxy-and 3'-deoxyallopyranosyl model systems [24] [46] [47] (Table 1) corroborated this interpretation.It was this insight into the consequences of the steric bulk of fully hydroxylated (6' 3 4')-hexopyranosyl building blocks that led us to ask whether base pairing might be Helvetica Chimica Acta ± Vol. 86 (2003) 4275 8 ) See Scheme 1 in [1]. It seems worth pointing out that an analogously built hexopyranosyl-(4' 3 2')oligonucleotide system, e.g., the b-allopyranosyl member depicted below, by the same reasoning, would not be expected to be a base-pairing system. The (repetitive) pairing conformation would suffer serious steric hindrance (see arrow) and, therefore, not become populated in competition with less strained (nonrepetitive) conformations. 9 ) ...

Ätiologie potentiell primordialer Biomolekül‐Strukturen: Vom Vitamin B12zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens – ein Rückblick

“…[133,134,141] Wie bei der homo-DNA ist die Duplexierung durch Watson-Crick-Paarung in antiparalleler Strangorientierung gegenüber Paarung in paralleler Orientierung viel stärker bevorzugt als bei der DNA: [99,141] Für ein Adenin-und Thymin-haltiges Hexadecamer der p-RNAReihe, dessen Duplex mit dem antiparallel-komplementären Strang unter Standardbedingungen über 60 8C schmilzt, wurde keinerlei Duplexierung mit seinem parallel-komplementären Strang beobachtet. [141] Dies entspricht der Erwartung, dass Oligomersysteme mit starker Rückgratneigung aus geometrischen Gründen [99] keine [41][42][43]. [137,139,140] Gleiches gilt für die Erwartung, wonach sogenannte "dangling bases" einen p-RNA-Duplex nur dann stabilisieren, wenn sie am 2'-Ende eines Stranges sitzen, und dass sie dies als Purine stärker tun, als in Form von Pyrimidinen (Abbildung 43 und 44).…”

“…Einfluss überhängender Basen auf die Stabilität von p-RNA-Haarnadel-Komplexen. [140,141] A. Eschenmoser…”

Prebiotic Chemistry and the Origin of the RNA World

“…Consequently, it is not possible to form chimeric double helices between a strand of homo-DNA and a strand of RNA. The discovery of a structurally regular isomer of RNA, pyranosyl RNA, or pRNA (Figure 9c still possible to form a double-stranded, base-paired double helix (Pitsch et al, 2003). Again, the structure of the helix is incompatible with that of RNA.…”

Facula, Faculae

“…One study revealed limitations of the conformational diversity of canonical nucleic acids by systematically synthesizing alternative nucleic acid structures. Markedly lower level of helicity was exhibited by pentopyranosyl nucleic acids in comparison to ribonucleic acid, lending support to the idea that the pentofuranose structure is responsible for the helical shape of the duplex in RNA and ▶ DNA (Eschenmoser and Dobler 1992;Pitsch et al 2003). Another study explored the assemblage and accumulation of pentofuranoses through a borate-mediated stabilization of cis-diols in furanose form (Prieur 2001;).…”