Characterization of Base Modifications and Covalent Adducts

5-dihydroxybenzoic acid (DHB), or a mixture of anthranilic acid and nicotinic acid were used to prompt the formation of structurally significant fragments. A time delay was also inserted between the laser-desorption and ion-detection steps to enable metastable decomposition [60]. Alternatively, informative sequence ions were produced by collision-induced dissociation (CID) [61] in the FT-ICR cell. 

The position of modified nucleotides can be located according to any of the sequencing approaches described earlier, which rely on either gas-phase fragmentation techniques, or the analysis of appropriate ladders generated in solution by chemical/enzymatic methods. Although the gas-phase sequencing of oHgonu-cleotides up to 100 nt has been reported [66, 67], the practical Umit for these 

RNase digestion products of 5S rRNA of S. acidocaldarius (b) Post-source decay mass spectrum obtained from the precursor ion 

When ethidium bromide and methylene blue were evaluated under the same conditions, duplex stabilization was modest, whereas relatively stable complexes could be detected between the ligands and the double-stranded substrate [105]. These results were consistent with the intercalating properties of such molecules, which are responsible for their specific binding to helical structures. In contrast, electrostatic interactions were shown to contribute prominently to the stability of noncovalent complexes between single-stranded deoxyoligonucleotides and 

4 amol of glycerol. The sum of 22 single-shot spectra was recorded. Reproduced with permission from Ref. [111]. the American Society for Biochemistry and Molecular Biology. 

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