PMR-relaxation and steric computations give unequivocal nucleoside conformations

Area of Science:

• Biophysical Chemistry
• Structural Biology
• Nucleic Acid Chemistry

Background:

• Understanding nucleoside conformation is crucial for drug design and molecular biology.
• The orientation of the base relative to the sugar moiety (glycosidic linkage) affects nucleoside properties.
• Anomeric configuration (alpha vs. beta) significantly impacts nucleoside structure and dynamics.

Purpose of the Study:

• To investigate the configuration and conformation of alpha and beta anomers of pyrazomycin, cytidine, and pseudouridine in aqueous solution.
• To utilize T1 proton relaxation measurements and proton-proton coupling constants to determine base orientation around the glycosidic linkage.
• To explore the influence of steric hindrance on nucleoside conformations.

Main Methods:

• 1H-NMR spectroscopy at 250 MHz was employed.
• T1 proton relaxation measurements were used to assess conformation.
• Proton-proton coupling constants were analyzed to determine predominant conformers (N vs. S).

Main Results:

• The N conformer is predominant in alpha anomers, while the S conformer is abundant in beta-pyrazomycin.
• Steric hindrance is greater in alpha-nucleosides, and a C-N glycosidic bond reduces base rotational freedom.
• alpha-Cytidine adopts an anti conformation (gamma = 200°), aligning with crystal structures.
• alpha-Pseudouridine shows a base orientation near the syn-anti boundary (gamma = 120°).
• beta-Cytidine exhibits equiprobable syn (gamma = 65°) and anti (gamma = 215°) conformations.
• beta-Pseudouridine displays a syn conformation with the smallest observed angle (gamma = 40°).

Conclusions:

• T1 proton relaxation is a reliable method for determining base conformation around the glycosidic linkage.
• Steric hindrance and the nature of the glycosidic bond (C-C vs. C-N) play significant roles in dictating nucleoside anomer conformations.
• Nucleoside base orientation can vary unpredictably between different nucleosides, even when syn and anti conformations are sterically accessible.
• No clear correlation exists between N/S and syn-anti conformational ratios across the studied nucleosides.