Asymmetric charge partitioning upon dissociation of DNA duplexes

Abstract

Upon collisional activation, a series of DNA duplexes exhibited a significant degree of asymmetric dissociation with respect to charge partitioning among the single strands. That is, the charge states of the single strand product ions did not equal q/2 for even precursor charge states or (q + 1)/2 and (q-1)/2 for odd precursor charge states (where q is the charge of the precursor). The factors that affect this asymmetric charge partitioning were assessed. The smaller, lower charged duplexes resulted in more symmetric dissociation compared with larger duplexes in higher charge states, which displayed a high degree of asymmetry upon dissociation. The composition of the duplexes influenced charge partitioning, with those containing a greater number of A/T base pairs showing more symmetric dissociation relative to the more G/C rich duplexes. The use of higher collisional energies resulted in significantly more asymmetric dissociation. Comparisons were made with the dissociation behavior previously studied for protein noncovalent complexes and past studies of the gas-phase conformations and dissociation of DNA complexes.

Figure 1

CID of duplex d14-0, (a) 6- charge state, 47 mV (b) 7- charge state, 38 mV (c) 8- charge state, 34 mV. The symbol * denotes the precursor ion.

Figure 2

Comparison of symmetrical versus asymmetrical dissociation - (a) CID of d14-0, 6- charge state (47 mV), 7- charge state (38 mV), 8- charge state (34 mV) (b) CID of d14-2, 6- charge state (71 mV), 7- charge state (49 mV), 8- charge state (45 mV) (c) CID of d19-1, 7- charge state (54 mV), 8- charge state (44 mV), 9- charge state (40 mV), 10- charge state (36 mV). The peak areas of the product ions were summed for each pair of single strands and were converted to percentages. The total charge of each pair equaled the precursor charge. The area percentage of product ions involved in charge portioning (asymmetric and symmetric) is plotted against each single strand charge pair.

Figure 3

Comparison of symmetrical versus asymmetrical dissociation for 19mer base pair duplexes with varying A/T base pairs in charge states of (a) 10- (b) 9- (c) 8-. Each column represents a different duplex (e.g., d19-0, d19-1, d19-2, and d19-3). The peak areas of the product ions were summed for each pair of single strands and were converted to percentages. The total charge of each pair equaled the precursor charge. The area percentage of product ions involved in charge portioning (asymmetric and symmetric) is plotted against each single strand charge pair. For all duplexes, the CID voltage of (a) 10- charge state was 48 mV (b) 9- charge state was 51 mV, and (c) 8- charge state was 56 mV.

Figure 4

Energy variable CID o f d14-0 (8- charge state). The peak areas of the product ions were summed for each type of dissociation charge partitioning (symmetrical versus asymmetrical). The area count of product ions involved in asymmetric dissociation is plotted against CID voltage (mV). % asymmetric values of 0% mean the precursor was not significantly dissociated to produce single strands (i.e., 0% asymmetric does not equal 100% symmetric dissociation).