Lattice-like 3-dimensional DNA nanostructure-based bioseparation strategy for highly accurate quantification of low-abundance cancer biomarker via mass spectrometry

Abstract Disease-associated low-abundance protein biomarkers have attracted growing attention for the diagnosis and treatment of numerous diseases. Traditional immunoassays are commonly adopted for the detection of low-abundance proteins due to fast and sensitive analyses, but the used antibodies are normally lack of satisfactory selectivity that may bring about biased results. Immunoaffinity mass spectrometry approach can remedy the deficiency of antibodies and has emerged as a powerful technique for highly selective and accurate quantification assay. However, due to extremely large dynamic range of the body fluids, efficient bioseparation of low-abundance proteins is a key issue before mass spectrometry (MS) quantification. In this study, a 3-dimensional DNA tetrahedron (DNA TET) nanomaterial, MoS2@Fe3O4@AuNPs@DNA TET@Ab, was meticulously designed and constructed for the enrichment of cancer biomarker heat shock protein 90 alpha (HSP90α) in human plasma. The nanocomposites have combined advantages of quick magnetic response, a large amount of surface antibodies and excellent stability. Furthermore, through the spatial separation by pendant probes on DNA TETs, antibodies are immobilized with appropriate density and well controlled arrangement. The feasibility of this approach was demonstrated by the pleasing quantitative performance for HSP90α with fine repeatability and a dynamic range from 20 ng/g to 480 ng/g. Compared with the extraction efficiency of conventional nanomaterials with random antibody distribution, the concentrations of HSP90α captured by our materials were at least 2 folds higher, which were more close to ELISA data. Through this ingenious assay, highly efficient enrichment by controlled antibodies arrangement on the nanomaterials and accurate quantification of low-abundance proteins by MS were achieved. This promising strategy can be extended to quantify other low-abundance proteins from the biological samples in clinic.