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Determination of oligonucleotide molecular masses by MALDI mass spectrometry

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Abstract

MALDI mass spectrometry (MS) of 14- to 42-mer homogeneous oligonucleotides and their mixtures was carried out using a Vision 2000 instrument (Thermo BioAnalysis, Finnigan, United States). Conditions for the determination of oligonucleotide molecular masses were optimized by applying various matrices and operation modes. The most reproducible results with minimal uncontrolled decomposition of the oligonucleotides including their apurinization during the MALDI MS registration were obtained using 2,4,6-trihydroxyacetophenone as a matrix instead of 3-hydroxypicolinic acid usually employed in the mass spectrometry of oligonucleotides. Our approach allows the determination of molecular masses of oligonucleotides obtained by chemical synthesis and the evaluation of their component composition and purity. It was applied to the mass spectrometric analysis of oligonucleotides containing a 3′-(methyl-C-phosphonate) group or a modified 1,N 6-ethenodeoxyadenosine unit.

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Abbreviations

ɛA:

1,N 6-ethenodeoxyadenosine

ɛAde:

1,N 6-ethenoadenine

ANP:

2-amino-5-nitropyridine

DBU:

1,8-diazabicyclo[5.4.0]undec-7-ene

DHB:

2,5-dihydroxybenzoic acid

HPA:

3-hydroxypicolinic acid

MALDI:

matrix-assisted laser desorption/ionization

MS:

mass spectrometry

PA:

picolinic acid

TEA:

triethylamine

THA:

2,4,6-trihydroxyacetophenone. Prefix d in oligodeoxyribonucleotide abbreviations is omitted.)

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Authors and Affiliations

  1. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia

    A. V. Streletskii, A. L. Kayushin, M. D. Korosteleva & S. E. Esipov

  2. Chair of Bioorganic Chemistry, Biological Faculty, Moscow State University, Vorob’evy gory 1, Moscow, 119992, Russia

    A. Yu. Kozlova & D. S. Esipov

Authors
  1. A. V. Streletskii
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  2. A. Yu. Kozlova
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  3. D. S. Esipov
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  4. A. L. Kayushin
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  5. M. D. Korosteleva
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  6. S. E. Esipov
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Correspondence to A. Yu. Kozlova.

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__________

Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 2, 2005, pp. 151–158.

Original Russian Text Copyright © 2005 by Streletskii, Kozlova, Esipov, Kayushin, Korosteleva, Esipov.

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Streletskii, A.V., Kozlova, A.Y., Esipov, D.S. et al. Determination of oligonucleotide molecular masses by MALDI mass spectrometry. Russ J Bioorg Chem 31, 139–145 (2005). https://doi.org/10.1007/s11171-005-0019-3

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  • DOI: https://doi.org/10.1007/s11171-005-0019-3

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