Sequential and Structural Biophysical Aspects of Combinatorial Oligo FISH in Her2/neu Breast Cancer Diagnostics

Fluorescence in situ Hybridization (FISH) is an important tool in medical diagnostics to determine the genetic status to monitor tumor progression in breast cancer. The newly developed method of COMBO-FISH allows a more refined diagnosis by using a set of short oligonucleotides which cluster at the Her2/neu gene and indicate the multiplicity of amplification. A careful image analysis of the fluorescence microscopic image also provides insights in the nanolocal nuclear architecture. Designing a set of short oligonucleotides which can form triple helical structures with double stranded DNA and cluster exclusively at the Her2/neu gene locus is based on the analysis of the sequence of the whole human genome, while understanding the properties of the hybridization process, namely its kinetics and energetics, depends on the detailed knowledge of the dynamics of the molecular interactions which are exemplified by molecular dynamics simulations of triplex forming oligonucleotides.