- Chromatin Immunoprecipitation in Fused Silica Capillaries - A Miniaturization Approach to Mapping Protein-DNA Interaction in Cells (2002)
- Microsystem technology has been a fast evolving field over the last few years. Its ability to handle volumes in the sub-microliter range makes it very interesting for potential application in fields such as biology, medicine and pharmaceutical research. However, the use of micro-fabricated devices for the analysis of liquid biological samples still has to prove its applicability for many particular demands of basic research. This is particularly true for samples consisting of complex protein mixtures. The presented study therefore aimed at evaluating if a commonly used glass-coating technique from the field of micro-fluidic technology can be used to fabricate an analysis system for molecular biology. It was ultimately motivated by the demand to develop a technique that allows the analysis of biological samples at the single-cell level. Gene expression at the transcription level is initiated and regulated by DNA-binding proteins. To fully understand these regulatory processes, it is necessary to monitor the interaction of specific transcription factors with other elements - proteins as well as DNA sites - in living cells. One well-established method to perform such analysis is the Chromatin Immunoprecipitation (CHIP) assay. To map protein-DNA interactions, living cells are treated with formaldehyde in vivo to cross-link DNA-binding proteins to their resident sites. The chromatin is then broken into small fragments, and specific antibodies against the protein of interest are used to immunopurify the chromatin fragments to which those factors are bound. After purification, the associated DNA can be detected and analyzed using Polymerase Chain Reaction (PCR). Current CHIP technology is limited as it needs a relatively large number of cells while there is increasing interest in monitoring DNA-protein interactions in very few, if not single cells. Most notably this is the case in research on early organism development (embryogenesis). To investigate if microsystem technology can be used to analyze DNA-protein complexes from samples containing chromatin from only few cells, a new setup for fluid transport in glass capillaries of 75 µm inner diameter has been developed, forming an array of micro-columns for parallel affinity chromatography. The inner capillary walls were antibody-coated using a silane-based protocol. The remaining surface was made chemically inert by saturating free binding sites with suitable biomolecules. Variations of this protocol have been tested. Furthermore, the sensitivity of the PCR method to detect immunoprecipitated protein-DNA complexes was improved, resulting in the reliable detection of about 100 DNA fragments from chromatin. The aim of the study was to successively decrease the amount of analyzed chromatin in order to investigate the lower limits of this technology in regard to sensitivity and specificity of detection. The Drosophila GAGA transcription factor was used as an established model system. The protein has already been analyzed in several large-scale CHIP experiments and antibodies of excellent specificity are available. The results of the study revealed that this approach is not easily applicable to "real-world" biological samples in regard to volume reduction and specificity. Particularly, material that non-specifically adsorbed to capillary surfaces outweighed the specific antibody-antigen interaction, the system was designed for. It became clear that complex biological structures, such as chromatin-protein compositions, are not as easily accessible by techniques based on chemically modified glass surfaces as pre-purified samples. In the case of the investigated system, it became evident that there is a need for more research that goes beyond the scope of this work. It is necessary to develop novel coatings and materials to prevent non-specific adsorption. In addition to improving existing techniques, fundamentally new concepts, such as microstructures in biocompatible polymers or liquid transport on hydrophobic stripes on planar substrates to minimize surface contact, may also help to advance the miniaturization of biological experiments.