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Comparative stability determination of oligonucleotide duplexes in gas and solution phase

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Journal of the American Society for Mass Spectrometry

Abstract

The relative stability of RNA duplexes were determined in both solution and gas phase. Solution stability as determined by a spectrophotometric method indicated that the Watson-Crick duplexes were more stable than duplexes containing one GA mismatch or two tandem GA mismatches. Gas phase stability was determined using ESI-MS through variation of the collision energy in an ion trap. Stability curves similar to the melting curves obtained in solution were observed. The relative stability in gas phase differed, however, from that in solution. The duplexes with two tandem GA mismatches were found to be more stable than the Watson-Crick and single GA mismatch duplexes. The different trends observed in solution versus gas phase can be attributed to the primary means of interaction. In solution, stacking is expected to be the dominant interaction mode. In the gas phase, hydrogen bonding is expected to be the dominant interaction mode. Duplexes with tandem GA mismatches have the potential to undergo additional hydrogen bonding relative to the other duplexes which could account for their increased stability in the gas phase.

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Authors and Affiliations

  1. Merck and Company, Rahway, New Jersey, USA

    Mei (Monica) Yang & Richard Thompson

  2. Department of Chemistry, Rutgers University, New Brunswick, New Jersey, USA

    Gene Hall

Authors
  1. Mei (Monica) Yang
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  2. Richard Thompson
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  3. Gene Hall
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Correspondence to Mei (Monica) Yang.

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Published online July 28, 2004

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Yang, M.(., Thompson, R. & Hall, G. Comparative stability determination of oligonucleotide duplexes in gas and solution phase. J Am Soc Mass Spectrom 15, 1354–1359 (2004). https://doi.org/10.1016/j.jasms.2004.06.008

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  • DOI: https://doi.org/10.1016/j.jasms.2004.06.008

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