Design and application of an easy to use oligonucleotide mass calculation program

Area of Science:

• Analytical Chemistry
• Biochemistry
• Molecular Biology

Background:

• Advancements in synthetic oligonucleotide production introduce complex chemical modifications.
• Characterizing these modified oligonucleotides presents significant analytical challenges.
• Conventional mass spectrometry (MS) requires enhanced methods for novel nucleic acid analysis.

Purpose of the Study:

• To develop and validate a flexible software program for calculating theoretical masses of oligonucleotides.
• To facilitate the identification and characterization of both conventional and chemically modified oligonucleotides.
• To address the growing need for efficient analytical tools in oligonucleotide synthesis.

Main Methods:

• Development of a user-friendly software program for theoretical mass calculations.
• Input of oligonucleotide sequences, including modified residues.
• Calculation of masses for full-length products, impurities, metabolites, and fragments.
• Experimental validation using synthesized oligonucleotides with extensive modifications.
• Analysis via quadrupole-time-of-flight (Q-TOF) mass spectrometry.

Main Results:

• The software successfully calculates theoretical masses for diverse oligonucleotide structures.
• Experimental mass spectrometry data closely matched calculated values (<30 ppm error).
• The program demonstrated high accuracy and reliability for modified oligonucleotides.
• Validation confirmed the software's utility in characterizing complex synthetic nucleic acids.

Conclusions:

• The developed software provides a powerful and flexible solution for oligonucleotide mass analysis.
• It effectively supports the characterization of synthetic oligonucleotides with numerous chemical modifications.
• This tool enhances the capabilities of analytical chemists in the field of nucleic acid research.