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Volumn 9, Issue 1, 1998, Pages 25-34

Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; OLIGODEOXYNUCLEOTIDE; OLIGONUCLEOTIDE;

EID: 0031930892     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(98)80080-3     Document Type: Article
Times cited : (75)

References (79)
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    • Specific metaloligonucleotide binding studied by high resolution tandem mass spectrometry
    • 2+ complexes with oligodeoxynucleotides is used to derive information on binding sites and relative binding specificities of the metal ions. Uncertainties in the validity of this approach vis a vis solution structure clearly remain but this work points the way to additional studies.
    • 2+ complexes with oligodeoxynucleotides is used to derive information on binding sites and relative binding specificities of the metal ions. Uncertainties in the validity of this approach vis a vis solution structure clearly remain but this work points the way to additional studies.
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    • Detection of base pair mismatches in duplex DNA and RNA oligonucleotides using electrospray mass spectrometry
    • of specifial interest. Innovative experiments show that gas-phase oligonucleotide duplexes that contain a single base pair mismatch undergo selective backbone cleavage at that site upon collisional dissociation. The authors suggest that such measurements could ultimately be used to selectively identify genetic mutations, but other applications, such as probes of secondary structure, might also be possible.
    • Griffey RH, Greig MJ. Detection of base pair mismatches in duplex DNA and RNA oligonucleotides using electrospray mass spectrometry. of specifial interest Proc Int Soc Optical Eng (SPIE). 2985:1997;82-86 Innovative experiments show that gas-phase oligonucleotide duplexes that contain a single base pair mismatch undergo selective backbone cleavage at that site upon collisional dissociation. The authors suggest that such measurements could ultimately be used to selectively identify genetic mutations, but other applications, such as probes of secondary structure, might also be possible.
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    • Griffey, R.H.1    Greig, M.J.2
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    • Analysis of oligonucleotides by HPLC-electrospray ionization mass spectrometry
    • of outstanding interest. The authors attribute the effectiveness of this novel solvent system to the volatility of the hexafluoro-2-propanol buffer constituent, which is preferentially depleted at the droplet surface during desolvation. The pH then increases to -10 so that the oligonucleotide-triethylamine ion pairs dissociate, releasing the oligonucleotide into the gas phase.
    • Apffel A, Chakel JA, Fischer S, Lichtenwalter K, Hancock WS. Analysis of oligonucleotides by HPLC-electrospray ionization mass spectrometry. of outstanding interest Anal Chem. 69:1997;1320-1325 The authors attribute the effectiveness of this novel solvent system to the volatility of the hexafluoro-2-propanol buffer constituent, which is preferentially depleted at the droplet surface during desolvation. The pH then increases to -10 so that the oligonucleotide-triethylamine ion pairs dissociate, releasing the oligonucleotide into the gas phase.
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    • Apffel, A.1    Chakel, J.A.2    Fischer, S.3    Lichtenwalter, K.4    Hancock, W.S.5
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    • Characterization of oligonucleotide metabolism in vivo via liquid chromatography/electrospray tandem mass spectrometry with a quadrupole ion trap mass spectrometer
    • of outstanding interest of specifial interest. Complete identification of phosphorothioate oligonucleotide metabolites from pig kidney was achieved using LC/ESI tandem mass spectrometry in a quadrupole ion trap mass spectrometer, using an HFIP mobile phase (see Apffel 1997 [53]).
    • Griffey RH, Greig MJ, Gaus HJ, Liu K, Monteith D, Winniman M, Cummins LL. Characterization of oligonucleotide metabolism in vivo via liquid chromatography/electrospray tandem mass spectrometry with a quadrupole ion trap mass spectrometer. of outstanding interest of specifial interest J Mass Spectrom. 32:1997;305-313 Complete identification of phosphorothioate oligonucleotide metabolites from pig kidney was achieved using LC/ESI tandem mass spectrometry in a quadrupole ion trap mass spectrometer, using an HFIP mobile phase (see Apffel 1997 [53]).
    • (1997) J Mass Spectrom , vol.32 , pp. 305-313
    • Griffey, R.H.1    Greig, M.J.2    Gaus, H.J.3    Liu, K.4    Monteith, D.5    Winniman, M.6    Cummins, L.L.7
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    • Utility of organic bases for improved electrospray mass spectrometry of oligonucleotides
    • Greig M, Griffey RH. Utility of organic bases for improved electrospray mass spectrometry of oligonucleotides. Rapid Commun Mass Spectrum. 9:1995;97-102.
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    • Limbach PA, Crain PF, McCloskey JA. Molecular mass measurement of intact ribonucleic acids using electrospray ionization quadrupole mass spectrometry. J Am Soc Mass Spectrom. 6:1995;27-39.
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    • On-line HPLC electrospray mass spectrometry of phosphorothioate oligonucleotide metabolites
    • of outstanding interest of specifial interest. This paper, although written prior to report of the HFIP solvent system described by Apffel et al. 1997 [53], provides an excellent example of the uses of mass spectrometry in the identification of oligonucleotide metabolites, 2-deoxyphosphorothioates in this case. The distribution of metabolites in rat plasma, liver and kidney were determined, and were consistent with exonuclease degradation, (primarily) at the 3′-termini.
    • Gaus HJ, Owens SR, Winniman M, Cooper S, Cummins LL. On-line HPLC electrospray mass spectrometry of phosphorothioate oligonucleotide metabolites. of outstanding interest of specifial interest Anal Chem. 69:1997;313-319 This paper, although written prior to report of the HFIP solvent system described by Apffel et al. 1997 [53], provides an excellent example of the uses of mass spectrometry in the identification of oligonucleotide metabolites, 2-deoxyphosphorothioates in this case. The distribution of metabolites in rat plasma, liver and kidney were determined, and were consistent with exonuclease degradation, (primarily) at the 3′-termini.
    • (1997) Anal Chem , vol.69 , pp. 313-319
    • Gaus, H.J.1    Owens, S.R.2    Winniman, M.3    Cooper, S.4    Cummins, L.L.5
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    • On-line microdialysis sample cleanup for electrospray ionization mass spectrometry of nucleic acid samples
    • Liu C, Wu Q, Harms AC, Smith RD. On-line microdialysis sample cleanup for electrospray ionization mass spectrometry of nucleic acid samples. Anal Chem. 68:1996;3295-3299.
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    • Effect of impurities on the matrix-assisted laser desorption mass spectra of single-stranded oligodeoxynucleotides
    • Shaler TA, Wickham JN, Sannes KA, Wu KJ, Becker CH. Effect of impurities on the matrix-assisted laser desorption mass spectra of single-stranded oligodeoxynucleotides. Anal Chem. 68:1996;576-579.
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    • Shaler, T.A.1    Wickham, J.N.2    Sannes, K.A.3    Wu, K.J.4    Becker, C.H.5
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    • The use of a co-matrix for improved analysis of oligonucleotides by matrix-assisted laser desorption/ionization time of-flight mass spectrometry
    • Simmons TA, Limbach PA. The use of a co-matrix for improved analysis of oligonucleotides by matrix-assisted laser desorption/ionization time of-flight mass spectrometry. Rapid Commun Mass Spectrom. 11:1997;567-572.
    • (1997) Rapid Commun Mass Spectrom , vol.11 , pp. 567-572
    • Simmons, T.A.1    Limbach, P.A.2
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    • Influence of solvents and detergents on matrix-assisted laser desorption/ionization mass spectrometry measurements of proteins and oligonucleotides
    • Börnsen KO, Gass MAS, Bruin GJM, von Adrichem JHM, Biro MC, Kresbach GM, Ehrat M. Influence of solvents and detergents on matrix-assisted laser desorption/ionization mass spectrometry measurements of proteins and oligonucleotides. Rapid Commun Mass Spectrom. 11:1997;603-609.
    • (1997) Rapid Commun Mass Spectrom , vol.11 , pp. 603-609
    • Börnsen, K.O.1    Gass, M.A.S.2    Bruin, G.J.M.3    Von Adrichem, J.H.M.4    Biro, M.C.5    Kresbach, G.M.6    Ehrat, M.7
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    • Cryogenic frozen solution matrixes for analysis of DNA by time-of-flight mass spectrometry
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    • Controlling DNA fragmentation in MALDI-MS by chemical modification
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    • Analysis of DNA by charge tagging and matrix-assisted laser desorption/ionization mass spectrometry
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    • Vestal ML, Juhasz P, Martin SA. Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 9:1995;1044-1050.
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    • Vestal, M.L.1    Juhasz, P.2    Martin, S.A.3
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    • High resolution matrix-assisted laser desorption/ionization time-of-flight analysis of single-stranded DNA of 27 to 68 nucleotides in length
    • Christian NP, Colby SM, Giver L, Houston CT, Arnold RJ, Ellington AD, Reilly JP. High resolution matrix-assisted laser desorption/ionization time-of-flight analysis of single-stranded DNA of 27 to 68 nucleotides in length. Rapid Commun Mass Spectrom. 9:1995;1061-1066.
    • (1995) Rapid Commun Mass Spectrom , vol.9 , pp. 1061-1066
    • Christian, N.P.1    Colby, S.M.2    Giver, L.3    Houston, C.T.4    Arnold, R.J.5    Ellington, A.D.6    Reilly, J.P.7
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    • Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis
    • of outstanding interest. The authors report notable improvements in instrument performance in the linear, and in particular the reflector mode, of operation when using delayed extraction techniques, demonstrated up to 50 nucleotides in length.
    • Juhasz P, Roskey MT, Smirnov IP, Haff LA, Vestal ML, Martin SA. Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis. of outstanding interest Anal Chem. 68:1996;941-946 The authors report notable improvements in instrument performance in the linear, and in particular the reflector mode, of operation when using delayed extraction techniques, demonstrated up to 50 nucleotides in length.
    • (1996) Anal Chem , vol.68 , pp. 941-946
    • Juhasz, P.1    Roskey, M.T.2    Smirnov, I.P.3    Haff, L.A.4    Vestal, M.L.5    Martin, S.A.6
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    • High sensitivity collisionally activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer
    • of specifial interest. The instrument (Q-TOF) described consists of a quadrupole mass filter, hexapole collision cell and time-of-flight mass analyzer with reflection. Using ESI, sequencing of peptides in low femtomole to attomole amounts was demonstrated. These initial sensitivity results suggest a favorable future for this instrument design in a range of applications.
    • Morris HR, Paxton T, Dell A, Langhorne J, Berg M, Bordoli RS, Hoyes J, Bateman RH. High sensitivity collisionally activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer. of specifial interest Rapid Commun Mass Spectrom. 10:1996;889-896 The instrument (Q-TOF) described consists of a quadrupole mass filter, hexapole collision cell and time-of-flight mass analyzer with reflection. Using ESI, sequencing of peptides in low femtomole to attomole amounts was demonstrated. These initial sensitivity results suggest a favorable future for this instrument design in a range of applications.
    • (1996) Rapid Commun Mass Spectrom , vol.10 , pp. 889-896
    • Morris, H.R.1    Paxton, T.2    Dell, A.3    Langhorne, J.4    Berg, M.5    Bordoli, R.S.6    Hoyes, J.7    Bateman, R.H.8
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    • Analytical properties of the nanoelectrospray ion source
    • of specifial interest. This paper discusses the theory and practical operating aspects of the nanospray ion source. This ion source utilizes very small diameter electrospray capillary needles (1-2 μm inner diameter), which are loaded with less than 1 μl of sample solution and operate without necessity of a solvent pump. In general, the operation of the device becomes less routine, compared with the somewhat larger scale microspray ion source (see Limbach et al. 1995 [4]), as the flow rate and orifice diameter are decreased.
    • Wilm M, Mann M. Analytical properties of the nanoelectrospray ion source. of specifial interest Anal Chem. 68:1996;1-8 This paper discusses the theory and practical operating aspects of the nanospray ion source. This ion source utilizes very small diameter electrospray capillary needles (1-2 μm inner diameter), which are loaded with less than 1 μl of sample solution and operate without necessity of a solvent pump. In general, the operation of the device becomes less routine, compared with the somewhat larger scale microspray ion source (see Limbach et al. 1995 [4]), as the flow rate and orifice diameter are decreased.
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    • Wilm, M.1    Mann, M.2
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    • A gated electrostatic ion trap to repetitiously measure the charge and m/z of large electrospray ions
    • Benner WH. A gated electrostatic ion trap to repetitiously measure the charge and m/z of large electrospray ions. Anal Chem. 69:1997;4162-4168.
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    • Investigation of the 'n - 1' impurity in phosphorothioate oligodeoxynucleotides synthesized by the solid-phase beta-cyanoethyl phosphoramidite method using stepwise sulfurization
    • Fearon KL, Stults JT, Bergot BJ, Christensen LM, Raible AM. Investigation of the 'n - 1' impurity in phosphorothioate oligodeoxynucleotides synthesized by the solid-phase beta-cyanoethyl phosphoramidite method using stepwise sulfurization. Nucleic Acids Res. 23:1995;2754-2761.
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    • Fearon, K.L.1    Stults, J.T.2    Bergot, B.J.3    Christensen, L.M.4    Raible, A.M.5
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    • Mass spectrometric investigation of the reaction between 4,4-vinylenedipyridine bis[2,2:6,2-terpyridine platinum (II)] and the self-complementary oligonucleotide d(CpGpTpApCpG)
    • 2+, which neutralizes the anionic phosphodiester at the site of adduction.
    • 2+, which neutralizes the anionic phosphodiester at the site of adduction.
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    • +-1915 in domain IV from E. coli 23S ribosomal RNA as 3-methylpseudouridine
    • of specifial interest. Example of a protocol for location and characterization of modified residues in large RNAs, based on recognition of modifications in RNase T1 hydrolysis products, from mass increments (e.g. 14 Da for methyl) not allowed by the corresponding gene sequence.
    • +-1915 in domain IV from E. coli 23S ribosomal RNA as 3-methylpseudouridine. of specifial interest Nucleic Acids Res. 24:1996;688-693 Example of a protocol for location and characterization of modified residues in large RNAs, based on recognition of modifications in RNase T1 hydrolysis products, from mass increments (e.g. 14 Da for methyl) not allowed by the corresponding gene sequence.
    • (1996) Nucleic Acids Res , vol.24 , pp. 688-693
    • Kowalak, J.A.1    Bruenger, E.2    Hashizume, T.3    Peltier, J.M.4    Ofengand, J.5    McCloskey, J.A.6
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    • Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30 S subunits by a new approach using matrix-assisted laser desorption/ionization-mass spectrometry combined with N-terminal microsequencing
    • of specifial interest. This excellent paper demonstrates the considerable power of mass spectrometry for the determination of nucleic acid - protein cross-link sites. Peptide-oligonucleotide complexes formed by protease-RNase treatments were isolated by HPLC. The RNA 8-mer linked product was sequenced by measurement of a mass ladder generated by partial alkaline hydrolysis.
    • Urlaub H, Thiede B, Müller E-C, Brimacombe R, Wittmann-Liebold B. Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30 S subunits by a new approach using matrix-assisted laser desorption/ionization-mass spectrometry combined with N-terminal microsequencing. of specifial interest J Biol Chem. 272:1997;14547-14555 This excellent paper demonstrates the considerable power of mass spectrometry for the determination of nucleic acid - protein cross-link sites. Peptide-oligonucleotide complexes formed by protease-RNase treatments were isolated by HPLC. The RNA 8-mer linked product was sequenced by measurement of a mass ladder generated by partial alkaline hydrolysis.
    • (1997) J Biol Chem , vol.272 , pp. 14547-14555
    • Urlaub, H.1    Thiede, B.2    Müller E-C3    Brimacombe, R.4    Wittmann-Liebold, B.5
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    • Lysine 207 as the site of cross-linking between the 3′-end of Escherichia coli initiator tRNA and methionyl-tRNA formyltransferase
    • Gite S, RajBhandary UL. Lysine 207 as the site of cross-linking between the 3′-end of Escherichia coli initiator tRNA and methionyl-tRNA formyltransferase. J Biol Chem. 272:1997;5305-5312.
    • (1997) J Biol Chem , vol.272 , pp. 5305-5312
    • Gite, S.1    Rajbhandary, U.L.2


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