Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Natural RNAs undergo extensive modifications, particularly uracil, to diversify structure and function.
• Over 76% of uracil modifications occur at the 5-position, highlighting its significance.
• Transfer RNAs (tRNAs) are heavily modified, influencing their roles in translation.

Purpose of the Study:

• To investigate the structural and functional implications of the natural 5-methoxy (5-O-CH(3)) modification of uracil in an A-form oligonucleotide duplex.
• To elucidate the atomic-level interactions mediated by the 5-methoxy uracil modification.

Main Methods:

• X-ray crystallography was employed to determine the structure of the A-form oligonucleotide duplex containing 5-methoxy uracil.
• Computational studies were performed to complement experimental observations.
• Comparative analysis with selenium and sulfur substitutions at the 5-position was conducted.

Main Results:

• A novel hydrogen bond was identified between the 5-methoxy group of uracil and its 5'-phosphate in the A-form duplex.
• This specific hydrogen bond was absent when oxygen was replaced by larger atoms like selenium or sulfur.
• The 5-methoxy modification did not induce significant alterations in the overall structure or stability of the oligonucleotide duplex.
• Computational results corroborated the experimental findings regarding the hydrogen bond formation.

Conclusions:

• The 5-position of uracil is critical for RNA modification, with the 5-methoxy group playing a specific role.
• A general interaction pattern between the nucleobase and the RNA backbone was suggested.
• The 5-methoxy uracil modification in tRNAs may serve to rigidify local conformation, potentially facilitating translation.