BLACKBODY INFRARED RADIATIVE DISSOCIATION OF OLIGONUCLEOTIDE ANIONS

The dissociation kinetics of a series of doubly deprotonated oligonucl eotide 7-mers [d(A)(7)(2-), d(AATTAAT)(2-), d(TTAATTA)(2-), and d(CCGG CCG)(2-)] were measured using blackbody infrared radiative dissociatio n in a Fourier-transform mass spectrometer. The oligonucleotides disso ciate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5') phosph odiester bond to produce structurally informative a-base and w type io ns. From the temperature dependence of the unimolecular dissociation r ate constants, Arrhenius activation parameters in the zero-pressure li mit are obtained for the loss of base. The measured Arrhenius paramete rs are dependent on the identity of the nucleobase. The process involv ing the loss of an adenine base from the dianions, d(A)(7)(2-), d(AATT AAT)(2-), and d(TTAATTA)(2-) has an average activation energy (E-a) of similar to 1.0 eV and a preexponential factor (A) of 10(10) s(-1). Bo th guanine and cytosine base loss occurs for d(CCGGCCG)(2-). The avera ge Arrhenius parameters for the loss of cytosine and guanine are E-a = 1.32 +/- 0.03 eV and A = 10(13.3+/-0.3) s(-1). No loss of thymine was observed for mixed adenine-thymine oligonucleotides. Neither base los s nor any other fragmentation reactions occur for d(T)(7)(2-) over a 6 00 s reaction delay at 207 degrees C, a temperature close to the upper limit accessible with our instrument. The Arrhenius parameters indica te that the preferred cleavage sites for mixed oligonucleotides of sim ilar mass-to-charge ratio will be strongly dependent on the internal e nergy of the precursor ions. At low internal energies (effective tempe ratures below 475 K), loss of adenine and subsequent cleavage of the a djacent phosphoester bonds will dominate, whereas at higher energies, preferential cleavage at C and G residues will occur. The magnitude of the A factors less than or equal to 10(13) s(-1) measured for the los s of the three nucleobases (A, G, and C) is indicative of an entropica lly neutral or disfavored process as the rate limiting step for this r eaction. (J Am Soc Mass Spectrom 1998, 9, 1117-1124) (C) 1998 American Society for Mass Spectrometry.