Force spectroscopy platform for label free genome sequencing

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DESCRIPTION (provided by applicant): Ability to obtain genetic information of individuals efficiently and rapidly is critical to the advancement of preventive medicine, as well as to introduction of new therapies and medical devices in all areas of clinical medicine. The new healthcare paradigm of pharmacogenomics will match the prescribed treatment to the genomics profile of the individual; however, such a profile must be made available in real time and within certain cost constraints. To meet the challenge of delivering fast and affordable genome sequencing, a new basic concept for DNA sequencing is proposed: detection of a single nucleotide addition (SNA) can be based on changes in mechanical properties and molecular structure of single DNA fragments. Force spectroscopy of DNA undergoing arrested polymerization will be used to implement one-molecule-at-the-time analysis of changes in molecular mechanics with a single nucleotide resolution. The ability of force spectroscopy to determine the end-to-end distance with the accuracy of a single chemical bond (approximately 0.1 nm) is recognized as a new "molecular ruler" with which to study changes in molecular conformation. By using optical near field probes, the methods of force spectroscopy can be advanced into techniques having massively parallel format, where millions of SNA additions can be followed at the same time. The technique will not require labeling of nucleotide bases, and base calling will be done exclusively on the basis of changes experienced by the molecule as a whole. Exclusion of separation and amplification steps further speeds up the timeframe of the whole genome sequencing. The development of force spectroscopy in the highly parallel format allows for further miniaturization of the sequencing device and automation of the procedures by employing microfluidics for steps involving SNA cycle. This parallelization will be implemented in a low cost table-top setup suitable for adaptation in a majority of biological, chemical, and hospital laboratories. Demonstration of single nucleotide sensitivity in force spectroscopy experiments can lead to a wide acceptance of the technique as a genomics tool in biological research. Successful demonstration of molecular mechanics assay will help to move from the present day uniform medical treatment to a diversified, patient-centered treatment with determination of a full genome as a routine test.