Analysis of the degradation of oligonucleotide strands during the freezing/thawing processes using MALDI-MS

D. L. Davis, Edward P. O'Brien, Jr., C. M. Bentzley

Research output: Contribution to journalArticle

31 Scopus citations

Abstract

Synthetic oligonucleotide strands ranging from 5 to 25 units in length are commonly used as standards, probes, and templates in various bioanalytical applications. Until recently, their preparation, storage, and handling were regarded as unimportant, but this work provides valuable information to the contrary. The systematic degradation of oligonucleotide strands during sample preparation is investigated by repeatedly freezing/thawing short strands followed by matrix-assisted laser desorption ionization mass spectrometric (MALDI-MS) analysis. It is shown here that the longevity of an oligonucleotide strand is dependent on several factors including base composition, solution concentrations, and strand length as well as thawing conditions. Several trends in strand robustness were established. Our studies reveal that the robustness of strands is base-dependent: T-mer > A-mer > C-mer > G-mer. Likewise, an increase in the length of the strands increases the tendency of a sample to degrade. Another observation included that samples of mixed bases degrade according to structural conformations. All of these obserrations are attributed to the fact that the samples undergo degradation during sample/solvent isolation during frezing.

Original languageEnglish (US)
Pages (from-to)5092-5096
Number of pages5
JournalAnalytical Chemistry
Volume72
Issue number20
DOIs
StatePublished - Oct 15 2000

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry

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