Characterization of G-rich and T-rich oligonucleotides using ion-pair reversed-phase high-performance liquid chromatography/tandem electrospray ionization mass spectrometry

Analysis of global DNA methylation levels in human blood using high-performance liquid chromatography/tandem electrospray ionization mass spectrometry

DNA methylation plays an important role in both normal physiological and disease processes. In this study, a sensitive and precise liquid chromatography-electrospray ionization tandem mass spectrometry method has been optimized for quantification of global DNA -methylation levels in human peripheral blood by using multiple reaction monitoring (MRM) mode. This method was then used to analyze age-dependent association of DNA methylation. The results showed that the limit of detection was 1 pg for 5-methyl-2'-dexycytidine (5mdC) (S/N = 5.6). The linear calibration curves with correlation coefficients higher than 0.9990 were ranged 0.75-10 ppm and 0.0375-0.5 ppm for 2'-dexycytidine (dC) and 5mdC, respectively. The relative standard derivatives (RSD) of inter-day, intra-day and parallel samples were less than 5%. The analysis results of the blood samples from 60 healthy individuals showed that the child group had the highest mean 5mdC content while the adult group had the lowest values.

Analysis of single nucleotide polymorphism sites in exon 4 of the p53 gene using high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry

Three groups of four oligonucleotides with special single nucleotide polymorphisms (SNP) sites in exon 4 of the p53 gene were analyzed with ion-pair reversed-phase high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry. The retention order of four oligonucleotides with SNPs was C < G < A < T, regardless of whether the polymorphisms were at the 3' end, the 5' end, or the middle of the oligonucleotides. The charge state of the molecular ion affects the MS/MS spectra of the oligonucleotides. SNPs at the 3' end can be easily identified from the fragmentation pattern of the 2- charge state, but not from the 3- charge state, especially from the w1 fragment. The single base may be taken as the symbol of the 5' end SNP site derived from [M3H]2, but not from the [M3H]2 charge state. The oligonucleotides with SNPs in the middle were also determined from the [M2H]2 precursor ion.

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

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.

Characterization of methylated and unmethlyated CpG-ODNs by electrospray ionization tandem mass spectrometry

Methylated and unmethylated CpG-ODNs at A-rich, C-rich, G-rich and T-rich conditions were characterized by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The methylted site could be confirmed by comparison of the MS/MS spectra of methylated and unmethylated CpG-ODNs. The fragmentation patterns of the CpG-ODNs were not influenced by the presence of the methyl group but significant effects were observed for nucleobase identities and parent ion charges. The cleavage at guanine was the most facile while that at thymine was the least facile. With the increase of the parent ions charge states, the major dissociation behaviors changed from the middle to the 3' and 5' termini of the sequence.