Quantification of activated NF-kappaB/RelA complexes using ssDNA aptamer affinity-stable isotope dilution-selected reaction monitoring-mass spectrometry.

ABSTRACT: Nuclear Factor-?B (NF-?B) is a family of inducible transcription factors regulated by stimulus-induced protein interactions. In the cytoplasm, the NF-?B member RelA transactivator is inactivated by binding inhibitory I?Bs, whereas in its activated state, the serine-phosphorylated protein binds the p300 histone acetyltransferase. Here we describe the isolation of a ssDNA aptamer (termed P028F4) that binds to the activated (I?B?-dissociated) form of RelA with a K(D) of 6.4 × 10(-10), and its application in an enrichment-mass spectrometric quantification assay. ssDNA P028F4 competes with cognate duplex high affinity NF-?B binding sites for RelA binding in vitro, binds activated RelA in eukaryotic nuclei and reduces TNF?-stimulated endogenous NF-?B dependent gene expression. Incorporation of P028F4 as an affinity isolation step enriches for serine 536 phosphorylated and p300 coactivator complexed RelA, simultaneously depleting I?B?·RelA complexes. A stable isotope dilution (SID)-selected reaction monitoring (SRM)- mass spectrometry (MS) assay for RelA was developed that produced a linear response over 1,000 fold dilution range of input protein and had a 200 amol lower limit of quantification. This multiplex SID-SRM-MS RelA assay was used to quantify activated endogenous RelA in cytokine-stimulated eukaryotic cells isolated by single-step P028F4 enrichment. The aptamer-SID-SRM-MS assay quantified the fraction of activated RelA in subcellular extracts, detecting the presence of a cytoplasmic RelA reservoir unresponsive to TNF? stimulation. We conclude that aptamer-SID-SRM-MS is a versatile tool for quantification of activated NF-?B/RelA and its associated complexes in response to pathway activation.

SUBMITTER: Zhao Y 

PROVIDER: S-EPMC3108844 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature