Design and Application of an Easy to Use Oligonucleotide Mass Calculation Program

  • Jiong Yang
  • Peter Leopold
  • Roy Helmy
  • Craig Parish
  • Becky Arvary
  • Bing Mao
  • Fanyu Meng
Application Note

Abstract

With the development of new synthesis procedures, an ever increasing number of chemical modifications can now be incorporated into synthetic oligonucleotides, representing new challenges for analytical chemists to efficiently identify and characterize such molecules. While conventional mass spectrometry (MS) has proven to be a powerful tool to study nucleic acids, new and improved methods and software are now needed to address this emerging challenge. In this report, we describe a simple yet powerful program that affords great flexibility in the calculation of theoretical masses for conventional as well as modified oligonucleotide molecules. This easy to use program can accept input oligonucleotide sequences and then calculate the theoretical mass values for full length products, process impurities, potential metabolites, and gas phase fragments. We intentionally designed this software so that modified nucleotide residues can be incorporated into oligonucleotide sequences, and corresponding mass values can be rapidly calculated. To test the utility of this program, two oligonucleotides that contain a large number of chemical modifications were synthesized. We have analyzed these samples using a Q-TOF mass spectrometer and compared the calculated masses to the observed ones. We found that all of the data matched very well with less than 30 ppm mass errors, well within the expectation for our instrument operated in its current mode. These data confirmed the validity of calculations performed with this new software.

Key words

Oligonucleotide Chemical modifications Mass calculation Software 

Notes

Acknowledgments

The authors especially acknowledge Gary Martin and Chris Welch for their helpful comments on this manuscript. The authors thank Huimin Yuan, Vinny Antonucci, and Zhihong Ge for their managerial support. In addition, we thank Jef Rozenski for access of the SOS software and helpful discussions.

Supplementary material

13361_2013_643_MOESM1_ESM.ppt (952 kb)
ESM 1 (PPT 952 KB)
13361_2013_643_MOESM2_ESM.doc (157 kb)
ESM 2 (DOC 157 KB)

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Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  • Jiong Yang
    • 1
  • Peter Leopold
    • 2
  • Roy Helmy
    • 1
  • Craig Parish
    • 3
  • Becky Arvary
    • 3
  • Bing Mao
    • 1
  • Fanyu Meng
    • 1
  1. 1.Analytical ChemistryMerck Research Labs, Merck and Co., Inc.RahwayUSA
  2. 2.BioAnalyte Inc.PortlandUSA
  3. 3.Process ChemistryMerck Research Labs, Merck and Co., Inc.RahwayUSA

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