Comparison of the NMR Spectroscopy Solution Structures of Pyranosyl-RNA and Its Nucleo-δ-peptide Analogue

Abstract

The design of polymers that could mimic biomolecules in their ability to form assemblies similar to ribo- and deoxyribonucleic acids has become an attractive field of chemical research, and NMR spectroscopy has played a vital role in the determination of the three-dimensional structure of these newly designed nonnatural polymers. The structure of a self-complementary octamer duplex of pyranosyl-RNA (pRNA) has been determined by using NMR spectroscopy experimental data and an Xplor structure calculation protocol. The structure has been compared with the structure of a duplex formed by a designed nucleo-delta-peptide analogue of pRNA. The two duplexes assume one predominant conformation and show a high structural similarity. The conformation type of both structures agrees with those predicted based on qualitative conformational analysis and both structures show a good convergence toward the average torsion angles derived by NMR spectroscopy.

Etiology of Potentially Primordial Biomolecular Structures: From Vitamin B12to the Nucleic Acids and an Inquiry into the Chemistry of Life’s Origin: A Retrospective

“…The pyranose form of RNA turned out to be a superb pairing system that displays highly instructive and very special pairing characteristics. The structure of the duplex of the self‐complementary sequence 4′‐pr‐CGAATTCG was established through NMR spectroscopy by Bernhard Jaun and co‐workers,136, 142, 169 and modeled using molecular dynamics by Romain Wolf 136. The data reveal a left‐handed, weakly helical ladder structure with antiparallel strand orientation, and a strong inclination between the backbone‐ and base‐pair axes in an orientation opposite to that of homo‐DNA (Figures 39 and 40).…”

Etiology of Potentially Primordial Biomolecular Structures: From Vitamin B12to the Nucleic Acids and an Inquiry into the Chemistry of Life’s Origin: A Retrospective

“…The pyranose form of RNA turned out to be a superb pairing system that displays highly instructive and very special pairing characteristics. The structure of the duplex of the self‐complementary sequence 4′‐pr‐CGAATTCG was established through NMR spectroscopy by Bernhard Jaun and co‐workers,136, 142, 169 and modeled using molecular dynamics by Romain Wolf 136. The data reveal a left‐handed, weakly helical ladder structure with antiparallel strand orientation, and a strong inclination between the backbone‐ and base‐pair axes in an orientation opposite to that of homo‐DNA (Figures 39 and 40).…”

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

“…1b) [15]. p-RNA is capable of forming duplexes with natural RNA in antiparallel orientation [16,17], although biosensors based on p-RNA have not yet been developed. In turn, threose nucleic acid (TNA) is an analogue based on α-L-threofuranosyl units joined by 3′→2′ phosphodiester linkages (Fig.…”

Etiology of Potentially Primordial Biomolecular Structures: From Vitamin B12to the Nucleic Acids and an Inquiry into the Chemistry of Life’s Origin: A Retrospective

“…The pyranose form of RNA turned out to be a superb pairing system that displays highly instructive and very special pairing characteristics. The structure of the duplex of the self‐complementary sequence 4′‐pr‐CGAATTCG was established through NMR spectroscopy by Bernhard Jaun and co‐workers,136, 142, 169 and modeled using molecular dynamics by Romain Wolf 136. The data reveal a left‐handed, weakly helical ladder structure with antiparallel strand orientation, and a strong inclination between the backbone‐ and base‐pair axes in an orientation opposite to that of homo‐DNA (Figures 39 and 40).…”

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

“…1b) [15]. p-RNA is capable of forming duplexes with natural RNA in antiparallel orientation [16,17], although biosensors based on p-RNA have not yet been developed. In turn, threose nucleic acid (TNA) is an analogue based on α-L-threofuranosyl units joined by 3′→2′ phosphodiester linkages (Fig.…”

Etiology of Potentially Primordial Biomolecular Structures: From Vitamin B12to the Nucleic Acids and an Inquiry into the Chemistry of Life’s Origin: A Retrospective

“…The pyranose form of RNA turned out to be a superb pairing system that displays highly instructive and very special pairing characteristics. The structure of the duplex of the self‐complementary sequence 4′‐pr‐CGAATTCG was established through NMR spectroscopy by Bernhard Jaun and co‐workers,136, 142, 169 and modeled using molecular dynamics by Romain Wolf 136. The data reveal a left‐handed, weakly helical ladder structure with antiparallel strand orientation, and a strong inclination between the backbone‐ and base‐pair axes in an orientation opposite to that of homo‐DNA (Figures 39 and 40).…”

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

“…1b) [15]. p-RNA is capable of forming duplexes with natural RNA in antiparallel orientation [16,17], although biosensors based on p-RNA have not yet been developed. In turn, threose nucleic acid (TNA) is an analogue based on α-L-threofuranosyl units joined by 3′→2′ phosphodiester linkages (Fig.…”