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

Abstract

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 ...

Nucleic acid ion structures in the gas phase

“…The authors found that the loss of a nucleobases is sensitive to its identity and location in the oligodeoxynucleotide, and found a trend in the values of Ea: A<G<C. They pointed that the differences observed in Ea comes not only from the bases identity but also from the ability of the nucleobases to participate in intramolecular interactions. 53,54 Infrared multiple photon dissociation (IRMPD) can also be used in a similar way to BIRD, provided that slow heating conditions (slower dissociation rates than photon absorption/emission rates) are maintained. 55 IRMPD was recently applied to megadalton-sized DNA; note however the dissociation rates were quite fast.…”

Infrared Multiple Photon Dissociation Spectroscopy of Hydrated Cobalt Anions Doped with Carbon Dioxide CoCO2(H2O)n−, n=1–10, in the C−O Stretch Region

“…Ac opper shield, which is cooled by liquid nitrogen to T % 80 K, surrounds the cell [88,89] to minimize the amount of black body infrared radiative dissociation (BIRD). [90][91][92][93][94][95][96][97][98][99] From the rear side of the magnet, at unable IR OPO laser system (EKSPLA NT273-XIR) is coupled into the cell through aC aF 2 window. [100] When absorption events lead to photodissociation, [101] they are detected by the experiment.…”

“…These ions are guided through a system of electrostatic lenses passing three differential pumping stages to the center of the ICR cell where they are stored and mass selected in a 4.7 T magnetic field under ultra‐high vacuum (≈10 −10 mbar) conditions. A copper shield, which is cooled by liquid nitrogen to T ≈80 K, surrounds the cell to minimize the amount of black body infrared radiative dissociation (BIRD) …”

CO2/O2 Exchange in Magnesium–Water Clusters Mg+(H2O)n

“…Absolute rate coefficients k abs are obtained by analyzing the pseudo-first-order kinetic plots of different experimental runs taken over a range of pressures. The cluster distribution shrinks due to blackbody infrared radiative dissociation (BIRD) 68−76 and the exothermicity of the reaction. 58,77,78 The error of the rate coefficient was estimated to be about 30% due to the uncertainty of the pressure calibration.…”