Why Pentose‐ and Not Hexose‐Nucleic Acids??. Part VII. Pyranosyl‐RNA (‘p‐RNA’). Preliminary communication

Abstract

Qualitative conformational analysis of the entirety of conceivable hexo-and pentopyranosyl oligonucleotide systems derived from the diastereoisomeric aldohexoses (CH,0)6 and aldopentoses (CH20), predicts the existence of a variety of pairing systems which have not been experimentally investigated so far. In particular, the analysis foresees the existence of a ribopyranosyl isomer of RNA ('p-RNA'), containing the phosphodiester linkage between the positions C(4) and C(2') of neighboring ribopyranosyl units. Double strands of p-RNA oligonucleotides are expected to have a linear structure and to show purine-pyrimidine and purine-purine (WatsonCrick) pairing comparable in strength to that observed in homo-DNA. Experimentally, synthetic fl-D-ribopyranosy1 (4+2')-oligonucleotides derived from adenine and uracil confirm this prognosis: adenine-uracil pairing in p-RNA duplexes is stronger than in the corresponding RNA duplexes. Importantly, adenine in p-Ribo(A,) does not show (reverse-Hoogsleen) self-pairing, in sharp contrast to its behavior in the homo-DNA series. The sheer existence of strong and selective pairing in a system that is constitutionally isomeric to RNA and can be predicted to have a linear structure has implications for the problem of RNA's origin. In this context, a comprehensive experimental study of the pairing properties of p-RNA, of its potential for constitutional assembly, self-replication, and intra-duplex isomerization to RNA seems mandatory.

Borate Minerals and RNA Stability

“…The following aspect of boron-sugar chemistry also deserves attention. The question was posed [46,47] about the reason why the furanose and not the pyranose forms have been selected in genetic polymers. The fact that borate affords a total selection of the furanose form [11] lends further relevance to the role of boron in the prebiotic sugar world.…”

Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

“…In recent years the groups of Eschenmoser and Herdewijn and Van Aerschot have synthesized several analogues of DNA and RNA in which the furanose ring is expanded to a six-membered ring ( Figure 11). [69][70][71][72][73] In some cases this has led to oligonucleotide analogues which hybridize more strongly to DNA and to RNA than the natural furanose-based structures do.…”

“…[66][67][68] DNA and RNA analogues with hexose sugars (and related structures) replacing ribose or deoxyribose. [69][70][71][72][73] Six-membered rings confer conformational rigidity because of their preference for the chair conformation. Examples of five different nucleoside analogues (21-25) which allow disulfide formation in DNA.…”

Toward replicatable, multifunctional, nanoscaffolded machines. A chemical manifesto

“…Moreover, because CCC is a purely chemical process, the informational material from which the scaffold is self-assembled does not necessarily need to be based on oligonucleotides. Any functional mimic, such as "spiegelmers" [16], PNA [17], pRNA [18], and many more may replace the oligonucleotide part of the scaffold. Figure 8 illustrates the self-assembly process using a single triple-function trisoligo.…”