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Nucleic Acids Res. 1997 Dec 15;25(24):5072-6.

Test of the potential of a dATP surrogate for sequencing via MALDI-MS.

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  • 1Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.


1-(2'-Deoxy-beta-d-ribofuranosyl)-3-nitropyrrole phosphate was incorporated into a DNA decamer and analyzed via matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The extent and composition of the various fragment peaks were compared with those in the MALDI-MS spectrum of dT4AT5. The nitropyrrole-containing oligomer proved to be more robust. Two different DNA template assays were then used to attempt to identify DNA replicating enzymes that would incorporate the corresponding triphosphate, i.e. 1-(2'-deoxy-beta-d-ribofuranosyl)-3-nitropyrrole triphosphate (dXTP). It was shown that dXTP was not incorporated by some enzymes and it inhibited others. However, DNA polymerase I Klenow fragment and avian myeloblastosis virus reverse transcriptase incorporated dXTP in place of dATP and then replicated the template overhang in the usual way. The potential of dXTP as a surrogate for dATP in DNA sequencing with MALDI-MS analysis is discussed.

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