Analysis of Double-Stranded Oligonucleotides by Electrospray Mass Spectrometry

Bayer, Ernst; Bauer, Tatjana.; Schmeer, Karl; Bleicher, Konrad H.; Maier, Martin A.; Gaus, Hans

doi:10.1021/ac00094a004

Cited by 78 publications

(55 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This information has been used to determine exact nuclease cleavage sites in antisense metabolism studies and has helped to identify aspects of the siRNA mechanism [10][11][12]. The soft ionization process of ESI also allows duplex oligonucleotides to be mass analyzed intact and not denatured into single strands, a characteristic of the technique particularly applicable to siRNA analysis [13][14][15][16][17][18][19][20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Liquid chromatography electrospray ionization mass spectrometry analysis of the ocular metabolites from a short interfering RNA duplex

Beverly

Hartsough

Machemer

et al. 2006

Journal of Chromatography B

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

Liquid chromatography electrospray ionization mass spectrometry analysis of the ocular metabolites from a short interfering RNA duplex

Beverly

Hartsough

Machemer

et al. 2006

Journal of Chromatography B

View full text Add to dashboard Cite

“…Commonly applied off-line and on-line sample purification protocols for nucleic acids prior to mass spectrometric analysis include multiple ethanol precipitation [19], membrane filtration [20], solid-phase extraction [21], microdialysis [14], affinity purification [22,23], cation-exchange [24], ligand-exchange [13], magnetic particles [25], size exclusion chromatography [26], and high-performance liquid chromatography (HPLC) [27,28]. Ion-pair reversed-phase high-performance liquid chromatography hyphenated to electrospray ionization mass spectrometry (ICEMS) has been demonstrated to be a rapid and highly effective analytical tool for the characterization of PCR amplified sequences [15, 29 -31].…”

mentioning

confidence: 99%

Optimized suppression of adducts in polymerase chain reaction products for semi-quantitative SNP genotyping by liquid chromatography-mass spectrometry

Oberacher

Parson

Hölzl³

et al. 2004

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

While electrospray ionization mass spectrometry has shown great potential for the identification of genotypes in DNA sequences amplified by polymerase chain reaction (PCR), the quantitative determination of allele frequencies remains challenging because of the presence of cationic adducts in the mass spectra which severely impairs accuracy of quantitation. We report here on the elaboration of an optimized desalting protocol for ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (ICEMS) of PCR amplicons which facilitates the genotyping of single nucleotide polymorphisms (SNPs). Chromatographic purification at temperatures between 50 and 70°C using monolithic reversed-phase columns and acetonitrile gradients in aqueous, 20 -30 mmol/l butyldimethylammonium bicarbonate enabled the mass spectrometric analysis of nucleic acid solutions containing up to 1.7 mol/l sodium chloride. A further improvement in removal of metal cations was achieved upon the addition of 5-10 mmol/l ethylenediaminetetraacetic acid (EDTA) to the sample solution prior to liquid chromatography. ICEMS was used for the semi-quantitative genotyping of SNPs amplified from the tetraploid genome of potato cultivars. Using a quadrupole ion trap mass spectrometer, allele frequencies were determined with an accuracy of 2-9% by measuring the relative intensities of the signals corresponding to the molecular mass of each of the alleles in the deconvoluted mass spectra. ICEMS results correlated well with those obtained by pyrosequencing, single nucleotide primer extension, and conventional dideoxy

show abstract

“…While lack of fragmentation is a distinct disadvantage for those seeking information on deoxynucleotide sequence, others have taken advantage of the characteristic stability of the molecular ion to analyze noncovalently bound complexes which remain intact throughout the electrospray process. ESI mass spectra of duplex DNA have been obtained in which intense molecular ions of the duplex form are found distributed among the molecular ions of each single strand (34). Conditions have also been determined for the analysis of higher order complexes, such as the quadruplex structure formed by the decamer, 5 '-CGCGGGGGCG-3' (35), and drug-DNA noncovalent complexes (36).…”

Section: Fisons Instruments 55 Cherry Hill Drive Beverly Ma 01915mentioning

confidence: 99%

Application of Electrospray Ionization Mass Spectrometry to the Analysis of Oligodeoxynucleotides

Iden

Rieger

Torres

et al. 1996

ACS Symposium Series

View full text Add to dashboard Cite

Electrospray mass spectrometry is a powerful technique for the analysis of oligodeoxynucleotides providing accurate molecular masses from the multiply charged negative ions formed by the electrospray volatilization/ionization process. Fragment ions are generally absent unless formed by secondary collisions near the exit of the source where pressures are relatively high. Use of the electrospray technique for the analysis of oligodeoxynucleotides is superior to other ionization techniques for verification of site-specific incorporation of modified deoxynucleotides, especially for oligomers containing more than ten deoxynucleotides where FAB/MS is not effective. ESI spectra may be generated on 10-100 picomoles of an oligomer on a single quadrupole mass spectrometer system, and mass accuracy of ±0.01% is attainable with careful calibration of the instrument. Spectra are presented for oligomers containing modified nucleobases and sugar moieties, as well as a hybrid DNA/RNA oligomer in which an O-methyl moiety is positioned at the 2'-position of adenosine. The technique is also effective for the elucidation of mechanisms by which unstable oligomers may disintegrate into unknown products, and the known sensitivity of 8-oxo-2-deoxyguanosine-containing oligomers to the postsynthetic ammonia deprotection procedure has been examined. ESI/MS was used to characterize the major products of oligomer decomposition. Deoxynucleotide sequence of an oligomer cannot be determined from the electrospray mass spectrum. However, MS/MS experiments were conducted on multiply charged oligodeoxynucleotide molecular ions generated by ESI on a triple quadrupole instrument. Product ion spectra from collision induced dissociation are complex, and product ions may differ in charge state from the precursor ion. However, families of ions were identified from which the sequence of the oligomer was verified.

show abstract

Analysis of Double-Stranded Oligonucleotides by Electrospray Mass Spectrometry

Cited by 78 publications

References 26 publications

Liquid chromatography electrospray ionization mass spectrometry analysis of the ocular metabolites from a short interfering RNA duplex

Liquid chromatography electrospray ionization mass spectrometry analysis of the ocular metabolites from a short interfering RNA duplex

Optimized suppression of adducts in polymerase chain reaction products for semi-quantitative SNP genotyping by liquid chromatography-mass spectrometry

Application of Electrospray Ionization Mass Spectrometry to the Analysis of Oligodeoxynucleotides

Contact Info

Product

Resources

About