Triplex forms of DNA act as main factors of some important cell functions. However, their positions within genome and their effect on cell functions are not known well. Triplex search algorithms often don't consider many of triplexs features and the possibility of occurrence of errors. In the other hand the complexity of full featured algorithms is extremely high. This paper shows the way to speed up the algorithm that considers all known triplex features. Parallel aproach allows due to CUDA technology acceleration up to 50.

Chemotherapy works by killing fast dividing cells. Unfortunately, these drugs are not specific to cancer tissue and can damage normal cells. Chemotherapy is like taking poison and hoping it kills the cancer cells before it kills you. As an alternative, many researchers have investigated the use of antigene therapy to selectively target cancer causing genes to avoid off target effects. Although promising, the theory is limited by the stability of the triplex structure. Here, we report the discovery of potent triplex binding ligands derived from the natural product quercetin. Chemical derivatives of 5-substituted 3, 3’, 4’, 7-tetramethoxyquercetin derivatives were characterized using several biophysical methods: thermal denaturation monitored by UV, circular dichroism, viscometry, differential scanning calorimetry, and isothermal titration calorimetry. The data revealed that these derivatives specifically stabilize triplex DNA and do not influence the stability of duplex DNA, triple RNA, or duplex RNA. Structurally, the amino containing side chains at the 5-position and the linker length are critical for the observed binding affinity and specificity. Two derivatives, 5 and 7, are comparable (if not better) to the triplex groove binder Neomycin. Our data confirm the binding mode as enthalpically driven intercalation. Piperidine or pyrrolidine 5-substituted 3, 3’, 4’, 7-tetramethoxyquercetin derivatives with a three-carbon linker are the lead compounds for development as a potential antigene enhancer.