Chemical Etiology of Nucleic Acid Structure: The Pentulofuranosyl Oligonucleotide Systems: The (1′→3′)-β-L-Ribulo, (4′→3′)-α-L-Xylulo, and (1′→3′)-α-L-Xylulo Nucleic Acids

• Published in: Chemistry : a European journal Vol. 19; no. 45; pp. 15336 - 15345
• Main Authors: Stoop, Matthias, Meher, Geeta, Karri, Phaneendrasai, Krishnamurthy, Ramanarayanan
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 04-11-2013; WILEY‐VCH Verlag
• Subjects: chemical evolution; Humans; Nucleic Acid Conformation; nucleic acids; Nucleic Acids - chemistry; Nucleic Acids - genetics; Oligonucleotides - chemistry; Oligonucleotides - genetics; pentuloses; prebiotic chemistry; RNA; RNA - chemistry; RNA - genetics; prebiotic chemistry; nucleic acids; RNA; pentuloses; chemical evolution
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.201302219

Under potentially prebiotic scenarios, ribose (pentose), the component of RNA is formed in meager amounts, as opposed to ribulose and xylulose (pentuloses). Consequently, replacement of ribose in RNA, with pentulose sugars, gives rise to prospective oligonucleotide candidates that are potentially prebiotic structural variants of RNA that could be formed by the same type of chemical pathways that gave rise to RNA from ribose. The potentially natural alternative (1′→3′)‐ribulo oligonucleotides and (4′→3′)‐ and (1′→3′)‐xylulo oligonucleotides consisting of adenine and thymine were synthesized and found to exhibit no self‐pairing or cross‐pairing with RNA. This signifies that even though pentulose sugars may have been abundant in a prebiotic scenario, the pentulose nucleic acids (NAs), if and when formed, would not have been competitors of RNA, or interfered with the emergence of RNA as a functional informational system. The reason for the lack of base pairing in pentulose NA highlights the contrasting and central role played by the furanosyl ring in RNA and pentulose NA, enabling and optimizing the base pairing in RNA, while impeding it in pentulose NA.
Which side are you on? The potentially natural and alternative ribulo‐ and xylulo‐oligonucleotides (see figure: B=base) exhibit no self‐pairing or cross‐pairing with RNA. Although pentulose sugars may have been abundant in a prebiotic scenario, the pentulose nucleic acids (NAs) would not have been RNA competitors nor interfered with the emergence of RNA. This result highlights the contrasting role played by the sugar moiety in optimizing the base pairing in RNA while hindering it in pentulose NA.