Nanotechnologies for biomolecular detection and medical diagnostics Mark Ming Cheng Cheng1 Giovanni Cuda2 Yuri L Bunimovich3 Marco Gaspari2 James R Heath3 Haley D Hill4 Chad A Mirkin4 A Jasper Nijdam1 Rosa Terracciano2 Thomas Thundat5 and Mauro Ferrari1 Nanotechnology based platforms for the high throughput multiplexed detection of proteins and nucleic acids in heretofore unattainable abundance ranges promise to bring substantial advances in molecular medicine The emerging approaches reviewed in this article with reference to their diagnostic potential include nanotextured surfaces for proteomics a two particle sandwich assay for the biological amplification of low concentration biomolecular signals and silicon based nanostructures for the transduction of molecular binding into electrical and mechanical signals respectively Addresses 1 Division of Hematology and Oncology Internal Medicine The Ohio State University 473 West 12 Avenue Columbus OH 43210 1002 USA 2 Universita degli Studi Magna Graecia Campus Universitario di Germaneto Viale Europa Germaneto 88100 Catanzaro Italy 3 Caltech Chemistry MC 127 72 1200 East California Blvd Pasadena CA 91125 USA 4 International Institute for Nanotechnology and Chemistry Department Northwestern University 2145 Sheridan Rd Evanston IL 60208 3003 USA 5 Nanoscale Science and Devices Group Oak Ridge National Laboratory Bethel Valley Road Mail stop 6123 Rm H 150 4500S Oak Ridge TN 37831 6123 USA These authors contributed equally to this work Corresponding author Ferrari Mauro ferrari 5 osu edu Current Opinion in Chemical Biology 2006 10 11 19 This review comes from a themed issue on Proteomics and genomics Edited by Garry P Nolan and Emanuel F Petricoin the clinical deployment of personalized medicine 1 in domains such as the early detection and the treatment of malignant disease Early detection is particularly important in the case of cancer and other pathologies because the early stages of disease are typically treated with the greatest probability of success The repeated screening of large populations for signs of precancerous developments or the establishment of early malignant lesions is only conceivable in the context of the analysis of biological fluids such as blood urine and sputum samples To date this has been impossible largely because there are no contemporary approaches for the reliable quantitative detection of multiple lowabundance protein markers comprised within a formidable complexity of diverse biomolecular species in each bio fluid specimen Nanotechnology offers promise as a broad spectrum of highly innovative approaches emerges for the overcoming of this challenge 2 3 4 11 Four emerging approaches are reviewed below nanostructured surfaces for the enhancement of proteomic analysis via mass spectrometry MS and reverse phase protein microarrays the bio bar code method for the amplification of protein signatures via the use of two particle sandwich assay nanowires as biologically gated transistors transducing molecular binding events into real time electrical signals and silicon cantilevers for the mechanics based recognition of biomolecular populations Available online 18th January 2006 1367 5931 see front matter 2005 Elsevier Ltd All rights reserved DOI 10 1016 j cbpa 2006 01 006 Introduction As medicine steadily progresses toward diagnostics based on molecular markers and highly specific therapies aimed at molecular targets the necessity for high throughput methods for the detection of biomolecules and their abundance concomitantly increases Technology platforms that provide the reliable rapid quantitative lowcost and multi channel identification of biomarkers such as genes and proteins are de facto the rate limiting steps for www sciencedirect com Nanostructured surfaces for proteomic analyses via MS and reverse phase protein microarrays MS is currently the gold standard for the protein expression profiling of biological fluids and tissues 12 14 with mounting evidence that matrix assisted laser desorption ionization time of flight MALDI TOF MS can be employed for the early detection of malignant disease Current limitations of this approach include the complexity and reproducibility of the 2 D gel electrophoresis prefractionation steps required for its implementation on biological fluids It is also recognized that the number of different biomolecular species in the plasma proteome probably exceeds 300 000 and could be as high as 106 with differences of as many as 12 orders of magnitude in Current Opinion in Chemical Biology 2006 10 11 19 12 Proteomics and genomics relative abundances It is hypothesized that the low molecular weight proteome LMWP comprising proteolyic fragments at extremely low concentration contains a wealth of information of diagnostic and prognostic utility 15 Current MS methodologies do not enable the routine profiling of the LMWP The physico chemical modification of nanoscale domains nanotexturing on an MS planar or nanoparticle substrate has been proposed Terracciano R et al and Gaspari M et al unpublished data with the objective of the size exclusion based elective capture and enrichment of selected regions of the LMWP from body fluids In proof of principle validation experiments silicon oxide particles obtained starting from silica gels and silicon chips coated with a 500 nm thick nanoporous film were challenged with a human plasma diluted sample MALDI TOF analysis was then performed as a means of detecting and assessing the extracted proteins Figure 1 Spiking experiments performed by adding peptide standards to human plasma at different concentrations showed that a MALDI TOF signal can be detected from peptide amounts down to the ng ml range Figure 2 This demonstrates the effectiveness of silica platforms for increasing the sensitivity of MS analysis roughly 400fold The selective enrichment achieved by the use of the different nanostructured surfaces depends on the pore size the fabrication procedure and the experimental conditions and represents a powerful tool to further improve the selectivity of peptide harvesting Moreover chemical and or structural modifications of the surface of the silica substrate contribute to the tailoring of the device for selective enrichment of specific protein peptide classes High throughput MALDI TOF MS analysis of LMWenriched serum plasma is an attractive strategy to rapidly and efficiently screen and profile a large number of samples in the search for disease