Determination of Nearest Neighbors in Nucleic Acids by Mass Spectrometry

Abstract

The identification of nearest-neighbor residues in nucleic acids provides useful constraints on establishment of base composition and sequence and is potentially applicable to a range of structural problems involving synthetic and natural polynucleotides. A new approach to this problem using electrospray ionization tandem mass spectrometry is based on measurement of precursor-product relationships derived from small fragment ions produced in the high-pressure ionization ("nozzle-skimmer") region of the instrument. Measured mass values of dinucleotide or other fragments, which give rise to mononucleotide ions N formed in the collision cell and transmitted by the second mass analyzer, establish the identities of residues adjacent to N. The technique is applicable to RNA and DNA, whether modified, or not, and is demonstrated using modified residues in nucleic acids up to the size of intact tRNA (76-mer). By monitoring of selected ion reaction channels, the method has been extended to LC/MS and to nearest-neighbor determinations directly in oligonucleotide mixtures.

Characterization and sequence verification of thiolated deoxyoligonucleotides used for microarray construction

“…Ions at m/z 110, 125, 134, and 150 can be assigned for base anions of C, T, A ,and G, respectively, while single nucleotides can be found having lost a water molecule (e.g., m/z 303 for T). When the phosphodiester backbone is cleaved twice, the so-called internal fragments (e.g., 481 for a TT subsequence) are formed, giving information about the presence of neighbor residues [16]. In our case, the 5= end a-B ion series gives information about the presence of the sulfhydryl group.…”

Differentiation and sequencing of three constitutional isobaric 18-mer DNA oligomers using low-energy collision tandem mass spectrometry

“…As expected, the ESI-QqTOF-MS analysis of the three constitutional isobaric 18-mer DNA oligomers gave the equivalent series of highly charged deprotonated molecular anions with the same m/z values. It is also well known that the DNA molecular anions, when highly charged, are extremely easy to fragment [30,31,[33][34][35]43]. In addition the three analyzed isobaric 18-mer oligomers, formed in the gas-phase the same series of sodiated adduct anions.…”

“…Rozenski and McCloskey developed a novel approach for the nearest-neighbor determination, based on the analysis of fragment ions of the nucleic acid formed in the ionization region of the mass spectrometer, along with the product ions obtained from MS/MS of the precursor oligonucleotide anion [33]. The same authors wrote a software for the ab initio determination of unknown oligonucleotide sequences up to the mer-20 level and was termed Simple Oligonucleotide Sequencer (SOS) [34].…”

RNase mapping of intact nucleic acids by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) and 18O labeling

“…Although MALDI-MS offers several advantages when analyzing complex mixtures of oligonucleotides arising from the generation of primarily singly charged ions and its higher tolerance towards salts typically present in oligonucleotide samples, the implementation of MALDI-based sequencing of oligonucleotides by post-source decay is usually more difficult than correspond- ing ESI-based collisionally induced dissociation (CID) approaches. In addition, several reports illustrate that multiply charged oligonucleotides can provide significant sequence information during low-energy CID [10,[19][20][21][22][23][24][25][26].…”