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Nucleic Acids Research 2005 33(11):3659-3666; doi:10.1093/nar/gki671
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Published online 28 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Secondary structural characterization of oligonucleotide strands using electrospray ionization mass spectrometry

Xinhua Guo1,2, Michael F. Bruist1, Darryl L. Davis3 and Catherine M. Bentzley1,*

1Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia 600 South 43rd Street, Philadelphia, PA 19104, USA 2Laboratory of New Drug Research and Mass Spectrometry, Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin Street, Changchun 130022, People's Republic of China 3Centocor Inc. 145 King of Prussia Road, Radnor, PA 19087, USA

*To whom correspondence should be addressed. Tel: +1 215 596 8581; Fax: +1 215 596 8543; Email: c.bentzl{at}usip.edu

Received March 3, 2005. Revised May 24, 2005. Accepted June 7, 2005.

Differences in charge state distributions of hairpin versus linear strands of oligonucleotides are analyzed using electrospray ionization mass spectrometry (ESI-MS) in the negative ion detection mode. It is observed that the linear structures show lower charge state distribution than the hairpin strands of the same composition. The concentration of ammonium acetate and the cone voltage are major factors that cause the shift of the negative ions in the charge states. The ESI data presented here are supported by UV spectra of strands acquired at 260 nm wavelength in aqueous ammonium acetate solution. We will show that the strands that demonstrate a higher charge state distribution in the gas phase also have a higher melting temperature in solution.


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