Sequencing Regular and Labeled Oligonucleotides Using Enzymatic Digestion and Ionspray Mass Spectrometry

Wu, Huaiqin; Chan, Clifford; Aboleneen, Hoda

doi:10.1006/abio.1998.2812

Cited by 15 publications

(31 citation statements)

References 22 publications

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“…As demonstrated previously (2,19,20), such truncated oligonucleotides from SVP digestion can be analyzed directly by ESImass spectrometry. The MWs of truncated oligonucleotides determined by MS form sequence ladders, and oligonucleotide sequences are obtained.…”

Section: Resultsmentioning

confidence: 99%

“…The instrument used was as described previously (20). The potential on the sampling orifice was set at 35 V during calibration and was changed to Ϫ65 V for oligonucleotide samples.…”

Section: Methodsmentioning

confidence: 99%

“…However, the method can be hampered by the interference of nucleotides produced during the digestion (20). This is especially true with ESI-MS detection (20) when the oligonucleotide to be sequenced is greater than 25 bases long. Similarly, such interference has been suggested with MALDItof-MS detection (23).…”

mentioning

confidence: 98%

“…The method is straight forward in principle, the procedure is easy to follow, and data interpretation is simple. Both MALDI-tof-MS (16 -18) or 19,20) have been reported for the molecular weight (MW) determination of 3Ј-phosphodiesterase (3Ј-PDE) and 5Ј-phosphodiesterase (5Ј-PDE) digestion products. However, the method can be hampered by the interference of nucleotides produced during the digestion (20).…”

mentioning

confidence: 99%

“…Both MALDI-tof-MS (16 -18) or ESI-MS (2,19,20) have been reported for the molecular weight (MW) determination of 3Ј-phosphodiesterase (3Ј-PDE) and 5Ј-phosphodiesterase (5Ј-PDE) digestion products. However, the method can be hampered by the interference of nucleotides produced during the digestion (20). This is especially true with ESI-MS detection (20) when the oligonucleotide to be sequenced is greater than 25 bases long.…”

mentioning

confidence: 99%

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Improved Oligonucleotide Sequencing by Alkaline Phosphatase and Exonuclease Digestions with Mass Spectrometry

Aboleneen

2001

Analytical Biochemistry

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Section: Resultsmentioning

confidence: 99%

“…The instrument used was as described previously (20). The potential on the sampling orifice was set at 35 V during calibration and was changed to Ϫ65 V for oligonucleotide samples.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 98%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Improved Oligonucleotide Sequencing by Alkaline Phosphatase and Exonuclease Digestions with Mass Spectrometry

Aboleneen

2001

Analytical Biochemistry

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Structural characterization of carcinogen‐modified oligodeoxynucleotide adducts using matrix‐assisted laser desorption/ionization mass spectrometry

et al. 2002

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The aim of this study was to determine the chemical structure of in vitro 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)-modified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization mass spectrometry. A single-stranded 11-mer ODN, 5-d(CCATCGCTACC), was reacted with N-acetoxy-PhIP, resulting in the formation of one major and eight minor PhIP-ODN adducts. A 10 min treatment of the major and one minor PhIP-ODN adduct with a 3-exonuclease, bovine intestinal mucosa phosphodiesterase (BIMP), and a 5-exonuclease, bovine spleen phosphodiesterase, results in inhibition of the primary exonuclease activity at deoxyguanosine (dG) producing 5-d(CCATCG(PhIP)) and 5-d(G(PhIP)CTACC) product ions, respectively. Post-source decay (PSD) of these enzymatic end products identifies dG as the sole modification site in two 11-mer ODN-PhIP adducts. PSD of the minor PhIP-ODN adduct digestion end product, 5-d(CCATCG(PhIP)), also reveals that the PhIP adducted guanine moiety is in an oxidized form. Prolonged treatment of the PhIP-ODN adducts at 37 • C with BIMP induces a non-specific, or endonuclease, enzymatic activity culminating in the formation of deoxyguanosine 5-monophosphate-PhIP (5-dGMP-PhIP). The PSD fragmentation pattern of the 5-dGMP-PhIP [M + H] + ion of the major adduct confirms PhIP binds to the C-8 position of dG. For the minor adduct, PSD results suggest that PhIP binds to the C-8 position of an oxidized guanine, supporting the hypothesis that this adduct arises from oxidative degradation, resulting in a spirobisguanidino structure.

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Therapeutic Oligonucleotides, Impurities, Degradants, and Their Characterization by Mass Spectrometry

Pourshahian

2019

Mass Spectrometry Reviews

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Oligonucleotides are an emerging class of drugs that are manufactured by solid‐phase synthesis. As a chemical class, they have unique product‐related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product‐related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas‐phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev

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Sequencing Regular and Labeled Oligonucleotides Using Enzymatic Digestion and Ionspray Mass Spectrometry

Cited by 15 publications

References 22 publications

Improved Oligonucleotide Sequencing by Alkaline Phosphatase and Exonuclease Digestions with Mass Spectrometry

Improved Oligonucleotide Sequencing by Alkaline Phosphatase and Exonuclease Digestions with Mass Spectrometry

Structural characterization of carcinogen‐modified oligodeoxynucleotide adducts using matrix‐assisted laser desorption/ionization mass spectrometry

Therapeutic Oligonucleotides, Impurities, Degradants, and Their Characterization by Mass Spectrometry

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