Sequencing Oligonucleotides with Blocked Termini Using Exonuclease Digestion and Electrospray Mass Spectrometry

Wu, Huaiqin; Aboleneen, Hoda

doi:10.1006/abio.2000.4827

Cited by 16 publications

(19 citation statements)

References 47 publications

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“…These results support the conclusion that phosphodiesterase I has some 5 0 -exonuclease activity, although they could also be explained by the presence of small amounts of an impurity with this activity. Support for the former explanation is provided by other studies that have reported phosphodiesterase I has the ability to hydrolyse nucleotides from the 5 0 end of oligonucleotides [36,37]. …”

Section: Total Enzymatic Digestionmentioning

confidence: 84%

Identification of bifunctional GA and AG intrastrand crosslinks formed between cisplatin and DNA

Gupta

Beck

Sheil

et al. 2005

Journal of Inorganic Biochemistry

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Section: Total Enzymatic Digestionmentioning

confidence: 84%

Identification of bifunctional GA and AG intrastrand crosslinks formed between cisplatin and DNA

Gupta

Beck

Sheil

et al. 2005

Journal of Inorganic Biochemistry

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“…6a and b), and the m/z values of the gradually shortened products, an indicator of sequence information, can be obtained from MS analysis. 112–114 For instance, Gupta et al 113 performed the partial enzymatic digestion of purified cisplatin–ODN adducts prior to LC-ESI-MS analysis to confirm the bifunctional binding sites of the metal to expected nucleobase sequences. As the period of digestion by 3′ → 5′ phosphodiesterase I prolonged (from 30 min to >5 h), ions were observed for the ODN remnants from the sequential loss of up to seven nucleotides from the 3′ end of cisplatin-adducted 16mer ODN (5′-CCTCTCC G G TCCTTCC-3′, where the sites of cisplatin conjugation were underlined), while other ions arising from the loss of more than seven nucleotides were absent.…”

Section: Qualitative Analysis Of Dna Adductsmentioning

confidence: 99%

Mass spectrometry for the assessment of the occurrence and biological consequences of DNA adducts

2015

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Exogenous and endogenous sources of chemical species can react, directly or after metabolic activation, with DNA to yield DNA adducts. If not repaired, DNA adducts may compromise cellular functions by blocking DNA replication and/or inducing mutations. Unambiguous identification of the structures and accurate measurements of the levels of DNA adducts in cellular and tissue DNA constitute the first and important step towards understanding the biological consequences of these adducts. The advances in mass spectrometry (MS) instrumentation in the past 2–3 decades have rendered MS an important tool for structure elucidation, quantification, and revelation of the biological consequences of DNA adducts. In this review, we summarized the development of MS techniques on these fronts for DNA adduct analysis. We placed our emphasis of discussion on sample preparation, the combination of MS with gas chromatography-or liquid chromatography (LC)-based separation techniques for the quantitative measurement of DNA adducts, and the use of LC-MS along with molecular biology tools for understanding the human health consequences of DNA adducts. The applications of mass spectrometry-based DNA adduct analysis for predicting the therapeutic outcome of anti-cancer agents, for monitoring the human exposure to endogenous and environmental genotoxic agents, and for DNA repair studies were also discussed.

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“…In all cases, adduct ions formed from salts used in the digestion process have limited the amount of structural information that may be obtained in a mass spectrum. An off-line desalting step [16,17] is often used to clean up the samples before ESI-MS (or MALDI) analysis. Here we demonstrate the first methodology using on-line HPLC sample clean up and separation coupled with ESI-MS for analysis of the enzyme digestion products of DNA adducts.…”

mentioning

confidence: 99%

Sequence verification of oligonucleotides containing multiple arylamine modifications by enzymatic digestion and liquid chromatography mass spectrometry (LC/MS)

Gao

Zhang

Cho

et al. 2008

J. Am. Soc. Mass Spectrom.

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An© analytical© method© for© the© structure© differentiation© of© arylamine© modified© oligonucleotides (ODNs)© using© on-line© LC/MS© analysis© of© raw© exonuclease© digests© is© described.© Six© different dodeca©ODNs©derived©from©the©reaction©of©N-acetoxy-N-(trifluoroacetyl)-2-aminofluorene with© the© dodeca© oligonucleotide© 5=-CTCGGCGCCATC-3=© are© isolated© and© sequenced© with© this LC/MS© method© using© 3=-© and© 5=-exonucleases.© When© the© three© products© modified© by© a© single aminofluorene© (AF)© are© subjected© to© 3=-exonuclease© digestion,© the© exonuclease© will© cleave© a modified© nucleotide© but© when© di-AF© modified© ODNs© are© analyzed© the© 3=-exonuclease© ceases to©cleave©nucleotides©when©the©first©modification©is©exposed©at©the©3=-terminus.©Small abundances© of© ODN© fragments© formed© by© the© cleavage© of© an© AF-modified© nucleotide© were observed©when©two©of©the©three©di-AF©modified©ODNs©were©subjected©to©5=-exonuclease digestion.© The© results© of© the© 5=-exonuclease© studies© of© the© three© di-AF© modified© ODNs© suggest that© as© the© number© of© unmodified© bases© between© two© modifications© in© an© ODN© sequence increases,© the© easier© it© becomes© to© sequence© beyond© the© modification© closest© to© the© 5© =-terminus. The© results© of© this© study© indicate© that© the© LC/MS© method© described© here© would© be© useful© in sequencing© ODNs© modified© by© multiple© arylamines© to© be© used© as© templates© for© site-specific mutagenesis© studies

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Sequencing Oligonucleotides with Blocked Termini Using Exonuclease Digestion and Electrospray Mass Spectrometry

Cited by 16 publications

References 47 publications

Identification of bifunctional GA and AG intrastrand crosslinks formed between cisplatin and DNA

Identification of bifunctional GA and AG intrastrand crosslinks formed between cisplatin and DNA

Mass spectrometry for the assessment of the occurrence and biological consequences of DNA adducts

Sequence verification of oligonucleotides containing multiple arylamine modifications by enzymatic digestion and liquid chromatography mass spectrometry (LC/MS)

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