Comparison of A + T-rich oligonucleotides with and without self-complementary sequence using ion-pair reversed-phase high-performance liquid chromatography/tandem electrospray ionization mass spectrometry

Eur. J. Mass Spectrom. 11, 83–92 (2005)
DOI: 10.1255/ejms.717

Renfang Song,^a,b Wenbing Zhang,^a Huayong Chen,^a,b Huimin Ma,^a,b Yulian Dong,^a Guoying Sheng,^a Zhen Zhou^a and Jiamo Fu^a,*
^aState Key Laboratory of Organic Geochemistry, Guangzhou Research Center of Mass Spectrometry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China. E-mail: fujm@gig.ac.cn
^bGraduate student school of Chinese Academy of Sciences Beijing, China

ABSTRACT:

Both A + T-rich oligonucleotides with and without self-complementary sequences were analyzed using ion-pair reversed-phase liquid chromatography/electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) by tryethylammonium acetate (TEAA) and hexafluoroisopropanol (HFIP) buffer systems to study the characteristics of their retention behavior and electrospray ionization tandem mass spectrometry (ESI-MS/MS) response. The results indicated that the chain length had the same effect on the retention of A + T-rich oligonucleotides in both of TEAA and HFIP buffer systems but the sequence had a different impact on the retention in the two buffer systems. A + T-rich oligonucleotides with a self-complementary sequence were much shorter than those without in the TEAA buffer system whereas a slight difference was observed in the HFIP buffer system. Similar total ion current (TIC) intensity was observed both in oligonucleotides with or without self-complementary sequence. The opposite trend of a change in the TIC intensities with increasing chain length were observed in both the TEAA and HFIP buffer systems. A lower charge state was predominant in the TEAA buffer system whereas a higher charge state was mainly distributed in the HFIP buffer system. The oligonucleotides without self-complementary sequences had a higher charge state than those with self-complementary sequences. A- and T- are more esily formed at a higher charge state whereas the sequence fragments will be formed more easily at a lower charge state in both A + T-rich oligonucleotides with and without self-complementary sequences.

Keywords: A+T-rich oligonucleotides; self-complementary sequence; ion-pair reversed-phase high-performance liquid chromatography, electrospray ionization mass spectrometry, charge state

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