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

• Published in: European journal of mass spectrometry (Chichester, England) England), 2005-01, Vol.11 (1), p.83-91
• Main Authors: Song, Renfang, Zhang, Wenbing, Chen, Huayong, Ma, Huimin, Dong, Yulian, Sheng, Guoying, Zhou, Zhen, Fua, Jiamo
• Format: Article
• Language: English
• Subjects: AT Rich Sequence; Buffers; Chromatography, High Pressure Liquid; Electrochemistry; Oligonucleotides - analysis; Oligonucleotides - chemistry; Spectrometry, Mass, Electrospray Ionization
• ISSN: 1469-0667; 1751-6838
• DOI: 10.1255/ejms.717

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.