Photofragmentation of 2-deoxy-D-ribose molecules in the gas phase.

Research paper by Gemma G Vall-Llosera, Michael A MA Huels, Marcello M Coreno, Antti A Kivimäki, Katarzyna K Jakubowska, Marek M Stankiewicz, Elisabeth E Rachlew

Indexed on: 21 Mar '08Published on: 21 Mar '08Published in: ChemPhysChem


We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C(5)H(10)O(4)) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule's ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH(3) (+), OH(+), H(3)O(+), C(2)H(3) (+), C(2)H(4) (+), CH(x)O(+) (x=1,2,3), C(2)H(x)O(+) (x=1-5), C(3)H(x)O(+) (x=3-5), C(2)H(4)O(2) (+), C(3)H(x)O(2) (+) (x=1,2,4-6), C(4)H(5)O(2) (+), C(4)H(x)O(3) (+) (x=6,7), C(5)H(7)O(3) (+), and C(5)H(8)O(3) (+). The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C(3)H(5)O(+)), whereas a general intensity decrease is observed for all other fragments- relative to the m/q=57 fragment-with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH(3) (+), H(3)O(+), C(2)H(4) (+), CH(3)O(+), and C(2)H(5)O(+), involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar-phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.