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Abstract: The work deals with rational design of strong DNA binder. The first part concerns with a new way of acridine peptide conjugates synthesis, either on solid phase or in solution. Suitability of various linkers in solid phase synthesis of head-and-tail bis-acridinylated peptide-conjugates is compared. This knowledge was utilized in synthesis of positional scanning libraries such as a mini-library from 5 amino acids containing 250 (2 x 53) members and a library made from 17 amino acids with 9826 (2 x 173) members. The work deals with rational library design and selection of compounds, which influence interaction between synthetic peptide HuPrP106-126 and DNA. Two candidates exhibit approximately two-order higher DNA-binding constant than the starting building block - 9-amino acridine. The high-throughput assay for HuPrP106-126/dsDNA interaction screening was also developed. It is very cheap because it requires minimal amount of biologically active components and relatively simple instrumentation like digital camera. The utilization of fluorescence scanner, which is used for micro-arrays scanning of dry samples, was found as a significant improvement for the screening of libraries in water solution. The minimal volume of water drop and water border, which offer a reproducibility of measurement, were found. New methods and compounds described in the work may facilitate the understanding of nucleic acid role in pathogenesis of prions. counter