Abstract: Development and Simulation of Fluorescent Peptide-Based Molecular Probes for Cancer Diagnosis Circulating p53-autoantibodies, as an answer of the humoral immunosystem to p53-tumor?suppressor?protein accumulation, are found in a significant part of cancer patients with a specifity of 100%, independent on the type of cancer. Hence, sereological screening for p53-autoantibodies at very low concentration levels has become increasingly relevant for early stage diagnosis of a malignant disease like lung and liver cancer. I present a new method for the highly sensitive detection of p53-antibodies in a homogeneous assay format. A 15mer peptide of the immunodominant N-terminal region of the human p53 protein was used as tracer to search for p53-autoantibodies. Upon N-terminal conjugation of the peptide epitope with the oxazine dye MR121, the fluorescence intensity of the dye decreases. The predominantly static fluorescence quenching results from an interaction of the oxazine dye with the tryptophan residue W23. Specific antibody recognition by the monoclonal mouse clone BP53-12 induces a conformational change in tracer structure, repealing the dye-tryptophan interactions. Consequently, a 2-fold fluorescence increase upon antibody binding signals the binding event. The application of confocal fluorescence microscopy to that system increases the detection sensitivity dramatically and allows measurements in the clinical relevant concentration range. However, detection sensitivity can be further increased by optimization of the developed probes. This can be done by support from Molecular Dynamics Simulations (MDS). They are performed by integrating Newtons equation of motion for the peptide structure in an empirical force field. MDS open an insight into molecular interactions between dye and tryptophan at microscopic detail.