Oligodeoxynucleotide Fragmentation in MALDI/TOF Mass Spectrometry Using 355-nm Radiation

Zhu, Lin; Parr, Gary R.; Fitzgerald, Michael C.; Nelson, Christine M.; Smith, Lloyd M.

doi:10.1021/ja00127a018

Cited by 114 publications

(94 citation statements)

References 3 publications

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“…Although many groups have reported the observation of different fragmentation in DE-reflecting and PSD spectra [22,26,28,29,32], we observed very few fragmentation pathways for both native and chargetagged forms of our 6-mers. The most likely reasons that our results differ from others are the choice of matrices and the sequences of the selected oligonucleotides.…”

Section: Discussioncontrasting

confidence: 62%

“…The stability of molecular ions of oligodeoxynucleotides is highly dependent on their base composition. Studies of homopolymer and mixed bases of oligonucleotides reveal that fragmentation often occurs at the location of a guanosine, adenosine, or cytidine base (in decreasing order of fragmentation severity) [22,37,38]. The laser wavelength does not seem to be a determining factor.…”

mentioning

confidence: 96%

“…Several hypotheses have been proposed to rationalize observed fragmentation pathways, and all of the proposed mechanisms involve protonation of a nucleobase as the initiating step [22,24,39]. It has been proposed that proton transfer occurs from either the neighboring acidic phosphodiester groups to the nucleobase, thus forming short-lived zwitterionic intermediates, or from matrix ions to form stable zwitterions upon protonation of the nucleobase.…”

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confidence: 99%

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Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

Chou

Limbach

Cole

2002

J. Am. Soc. Mass Spectrom.

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Section: Discussioncontrasting

confidence: 62%

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confidence: 96%

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confidence: 99%

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Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

Chou

Limbach

Cole

2002

J. Am. Soc. Mass Spectrom.

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“…As long as the rate of formation of f 1 (i.e., [M-B] ϩ , [a n -B] ϩ /w n ϩ ) from the precursor ions M ϩ is sufficient low (lnk[E] Ͻ 6) even for M ϩ with internal energy sufficient high to form f 2 (i.e., y n ϩ ), f 1 and f 2 ions might exclusively exist in the PSD or prompt spectrum, respectively. However, if we include fragmentation pattern reported previously in literature [31,32] by using 2,5-dihydroxybenzoic acid (DHB) as matrix (UV-MALDI), such a simple explanation might become insufficient. By using DHB as matrix, the fragmentation pathways of oligonucleotides under prompt conditions were found to resemble those of the metastable dissociation, i.e.…”

Section: Fast Vs Metastable Dissociationmentioning

confidence: 99%

A study of fast and metastable dissociations of adenine-thymine binary-base oligonucleotides by using positive-ion MALDI-TOF mass spectrometry

Chan

Fung

2002

J. Am. Soc. Mass Spectrom.

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In the present study, fast and metastable dissociations of a number of adenine-thymine binary-base oligonucleotides under the conditions of UV matrix-assisted laser desorption/ ionization mass spectrometry were investigated. 2-Aminobenzoic acid/ammonium fluoride (ABA/NH 4 F) matrix system was used. The spectra obtained under metastable and fast dissociation conditions exhibit distinctive dissociation products. From the post-source-decay analysis, all oligonucleotides underwent predominantly metastable dissociations at the 3' C-O linkages to form [a n -B] ϩ and w n ϩ complimentary ion series. Based on the present results, the so-called "[w n ϩ80] ϩ " ions were postulated to be the complimentary [z (8Ϫn) AH] ϩ ions rather than the expected phosphate rearrangement products. In addition, these oligonucleotides were found to generate fast dissociation products of b n ϩ , d n ϩ , w n S tructural characterization of short-chain nucleic acids has recently attracted much attention. They can serve as useful tools in molecular biology, as gene probes for diagnosis, or as potential drugs interacting at the level of nucleic acids. Typical short-chain DNA sequencing methods involve the use of the enzymatic or chemical cleavage algorithms [1][2][3] to produce DNA ladder products. The DNA fragments generated are then separated and identified by HPLC or gel electrophoresis. Structural verification of oligonucleotides using these methods is time-consuming and is sometimes impossible for modified oligonucleotides. Recent developments in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry [4 -9] have stimulated interest in replacing HPLC/gel electrophoresis by mass spectrometry in order to increase the speed and accuracy of the sequence determination. However, this approach still needs the time-consuming chemical or enzymatic reactions for producing sequence specific fragment ladder. A potentially more efficient method would be to obtain the DNA sequence information from fragmentation patterns in mass spectrometry through dissociation. In the present study, we attempt to evaluate the potential use of two rather direct mass spectrometric sequencing methods, namely fast and metastable dissociations for DNA sequence analysis.Fast fragmentation differs from metastable dissociation at the time of bond cleavage after the excitation of the precursor ions. In mass spectrometry, fragments are produced in a much shorter time as compared to the ion extraction time of the mass spectrometer. In the case of time-of-flight mass spectrometer, these fragment ions are therefore registered at their true masses in both linear and reflectron mode of detection. Metastable fragments, on the other hand, are usually formed at a much longer time scale (i.e., Ͼ500 ns) and are formed beyond the ion source region and before reaching the detector. Since the metastable ions are formed with the same velocity of the precursor ions, they are registered at the same mass-to-charge ratio of the precursor ion in a linear TOF instrum...

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“…Elucidating these mechanisms is of practical importance, since it will facilitate the rational development of MS-based techniques for sequencing. In addition, the dissociation of biomolecules in the gas phase reflects their intrinsic properties, which are of fundamental interest.For oligodeoxynucleotides (ODNs), sequence information can be obtained from the fragmentation behaviour of either the protonated or deprotonated gaseous ions and the dissociation behaviour of both forms has been extensively investigated [1][2][3][4][5][6][7][8][9][10]. The dissociation of deprotonated ODNs, the focus of the present study, has been shown to proceed first by the loss of a nucleobase, adenine (A), guanine (G), cytosine (C) or thymine (T), in its neutral or deprotonated form, followed by fragmentation of the phosphoester bond at the deoxyribose 3Ј C™O bond at the site of base loss to produce (a-base) and w type ions, according to the nomenclature proposed by McLuckey and coworkers [7].…”

mentioning

confidence: 99%

Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

Daneshfar

Klassen

2004

J. Am. Soc. Mass Spectrom.

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Arrhenius activation parameters (E a and A) for the loss of neutral nucleobase from a series of doubly deprotonated oligodexoynucleotide 10-mers of the type XT 9 , T 9 X, and T 5 XT 4 , where X ϭ A, C, and G, have been determined using the blackbody infrared radiative dissociation technique. At temperatures of 120 to 190°C, the anions dissociate exclusively by the loss of a neutral nucleobase (XH), followed by cleavage of the sugar 3Ј C™O bond leading to (a-XH) and w type ions or, in the case of the T 9 X 2Ϫ ions, the loss of H 2 O. The dissociation kinetics and energetics are sensitive to the nature and position of X. Over the temperature range investigated, the kinetics for the loss of AH and GH were similar, but ϳ100 times faster than for the loss of CH. For the loss of AH and GH, the values of E a are sensitive to the position of the base. The order of the E a s for the loss of XH from the 5Ј and 3Ј termini is: C Ͼ G Ͼ A; while for T 5 XT 4 the order is: C Ͼ A Ͼ G. The trends in the values of E a do not parallel the trend in deprotonation enthalpies or proton affinities of the nucleobases in the gas phase, indicating that the energetic differences do not simply reflect differences in their gas phase acidity or basicity. The pre-exponential factors (A) vary from 10 10 to 10 15 s Ϫ1 , depending on the nature and position of X. These results suggest that the reactivity of individual nucleobases is influenced by stabilizing intramolecular interactions. M ass spectrometry (MS), combined with soft ionization techniques such as electrospray (ES) and matrix assisted laser desorption/ ionization (MALDI), has become an indispensable tool for identifying the primary structure (sequence) of biopolymers: peptides, oligosaccharides, and oligonucleotides. The mass spectrometry-based sequencing approach typically involves isolating the biopolymer ion of interest in the gas phase, dissociating it to produce sequence specific fragment ions and accurately determining the mass of the ions. Sequence information is extracted from the mass differences of the sequential fragment ions of the same general structure. The MSbased sequencing approach has many attractive features, most notably its inherent speed and sensitivity and its ability to sequence biopolymers containing unnatural or unusual modifications. Despite its widespread use in the sequencing of biopolymers, fundamental questions regarding the gas phase dissociation mechanisms remain. Elucidating these mechanisms is of practical importance, since it will facilitate the rational development of MS-based techniques for sequencing. In addition, the dissociation of biomolecules in the gas phase reflects their intrinsic properties, which are of fundamental interest.For oligodeoxynucleotides (ODNs), sequence information can be obtained from the fragmentation behaviour of either the protonated or deprotonated gaseous ions and the dissociation behaviour of both forms has been extensively investigated [1][2][3][4][5][6][7][8][9][10]. The dissociation of deprotonated ODNs, the focus ...

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Oligodeoxynucleotide Fragmentation in MALDI/TOF Mass Spectrometry Using 355-nm Radiation

Cited by 114 publications

References 3 publications

Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

A study of fast and metastable dissociations of adenine-thymine binary-base oligonucleotides by using positive-ion MALDI-TOF mass spectrometry

Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

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