Trimethylsilyl derivatization of nucleic acid anions in the gas phase

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Abstract

Ion-molecule reactions between nucleic acid anions, [M-nH]n, formed via electrospray ionization, and trimethylsilylchloride have been investigated in an ion trap mass spectrometer at a helium bath gas pressure of 1 mtorr. Three types of reactions are observed: (i) SN2(Si) when n > 1 ; (ii) adduct formation when n = 1 ; and (iii) addition followed by elimination of HCl when n = 1 and where an acidic phosphate proton is present (e.g., 5′-pdA). The kinetics of these reactions have been studied for various anions derived from the following deoxyadenosine species: 5′-pdA; 5′-pppdA, 5′-d(AA)-3′; 5′-d(AAA)-3′ and 5′-d(AAAA)-3′. The following reactivity order is observed: [M-2H]2− of 5′-pppdA > [M-2H]2− of 5′-d(AAA)-3′ > [M-3H]3− of 5′-d(AAAA)-3′ > [M-3H + TMS]2− of 5′-d(AAAA)-3′ > [M-2H]2− of 5′-d(AAAA)-3′ > [M-H] of 5′-pdA ≫ [M-H] of 5′-d(AA)-3′ > [M-H] of 5′-d(AAA)-3′. In addition, the collision-induced dissociation reactions of the products of these reactions have been studied. Decomposition reactions are consistent with trimethylsilyl attachment on the phosphodiester linkage(s) in oligonucleotides and on the phosphate moieties of 5′-pdA and 5′-pppdA. Comparison of data acquired for modified and unmodified oligonucleotide anions of the same charge state reveal that TMS modification can significantly alter the favored dissociation channels, giving rise to sequence information. The results suggest that gas phase TMS derivatization of oligonucleotide anions, combined with tandem mass spectrometry, can provide sequence information complementary to that derived from unmodified anions.

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      Citation Excerpt :

      Sevugarajan and Menon have reported on a simulation study of the effect of geometric aberration, space charge, dipolar excitation, and damping on ion axial secular frequencies in a nonlinear Paul trap [38]. Trimethylsilyl derivatization of nucleic acid anions in the gas phase has been investigated [39] and the derivatization of alkylphenols has been employed for molecular ion stabilization [40]. A comparison of cation-binding affinities of quinones [41] and an evaluation of binding selectivities of caged crown ligands towards heavy metals has been carried out by Brodbelt and coworkers [42], and the noncovalent inclusion complexes of protonated amines with crown ethers [43] has been reported.

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