Accurate base composition of double-strand DNA by mass spectrometry

An accurate molecular weight (M(r)) assignment for a double-strand (ds) DNA determines or greatly restricts the possible number of each of its four bases, while the compositions for its two single-strand (ss) components can also be derived from their M(r) values. For a ds 64-mer (39 kDa), the ss- M(r) values (±0.5 Da) of its high-resolution mass spectrum from an electro- spray ionization/Fourier transform instrument yield only the correct ds- and ss-base compositions. Literature mass spectra of lower mass accuracy show that such data can also restrict their possible composition assignments, with further discrimination using the abundance vs. base composition of small fragment ions from the dissociation of the ss molecular ions.