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Biosensors based on DNA-protein interactions

In all known organisms, DNA molecules containing genetic instructions interact with diverse proteins as they carry out their function. Based on these molecular interactions, we have been developing “biosensors” for diagnostic and therapeutic applications. Oligonucleotides known as “aptamers”, which specifically recognize target proteins, have been developed for diagnosis of various diseases, including cancer, Alzheimer’s disease, and bacterial infections. We also focus on zinc finger proteins that recognize specific DNA sequences to detect bacterial genome DNAs for pathogen detection.

Development of aptameric biosensors

Aptamers are short oligonucleotides with unique 3D structures, displaying strong interactions with specific targets. We are using both in vitro and in silico evolutionary approaches to develop functional aptamers that bind to tumor markers and pathogens. We have been developing “in silico maturation” techniques to improve particular functions of aptamers, and the resulting highly functional aptamers have been used to make aptameric biosensors. Based on nano-structural changes of aptamer and enzyme complexes, we have developed unique aptameric sensors for rapid and simple detection of targets.

Specific detection of pathogenic bacteria using PCR and zinc finger proteins.

Zinc finger proteins, which are small DNA-binding proteins from mammals, can bind strongly to specific DNA base pairs. We applied this specific DNA recognition of zinc finger proteins in a PCR-based method to detect bacterial genomic DNA. Zinc finger proteins can discriminate specific amplicons from nonspecific amplicons, allowing specific bacterial genome detection.
We succeeded in detection of PCR-amplified DNA fragments from Legionella pneumophila, Escherichia coli O157 and Salmonella species by using zinc finger proteins that recognize a specific sequence within the amplified fragments. Moreover, we have also developed a zinc finger protein-based system for the detection of DNA methylation related to the onset of cancer.

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