Bio-Oligomer Purification, Electrophilic Oligo Synthesis, and Progress to a Genome Sequencer

CHEMISTRY SEMINAR

Michigan Technological University

Friday, December 12, 2014

3:00 pm Chemical Sciences Building Room 101

Dr. Shiyue Fang

Associate Professor, Chemistry Department

Abstract:

Bio-Oligomer Purification, Electrophilic Oligo Synthesis, and Progress to a Genome Sequencer

The progress on three projects, which are bio-oligomer purification, electrophilic oligosynthesis, and developing a new genome sequencer, will be presented. For bio-oligomer purification, we have developed two methods for oligodeoxynucleotide and one method for peptide purification. They are catching failure sequences by polymerization and catching full-length sequences by polymerization. Both methods do not require any type of chromatography,and purification is achieved through simple manipulations such as shaking and filtration. As aresult, they are suitable for large scale purification of drugs based on oligonucleotides and peptides. They are also ideal for small scale purification and high throughput purification. Currently, there are three oligonucleotide drugs and over 60 peptide drugs on the market, and many more are in various stages of clinical trials. Because known bio-oligomer purification methods such as HPLC have drawbacks such as high capital cost for instrument, labor-intensiveness and requirement of large volumes of harmful solvents, the new methods are expected to be preferred by pharmaceutical companies for drug purification, and by academic labs and biotech companies for small scale and high throughput purification. For electrophilic oligo synthesis, we have made progress on developing a new method that features using protecting groups and linkers cleavable under nearly neutral conditions. Under these conditions, electrophilic groups such as ester, thioester, alpha-halo carbonyl, epoxide and aziridine are stable. As a result, the new method is useful for the synthesis of oligonucleotide analogs that contain such  sensitive functionalities. Using known oligo synthesis methods, such analogs cannot be synthesized. The new oligo synthesis method is expected to open doors to many research projects that require  sensitive oligo analogs. For developing a new genome sequencer, we are using AFM to monitor the  conformational fluctuations of a DNA polymerase during DNA synthesis. Because different  nucleotides are expected to give different conformational fluctuations, DNA sequences can be read  out in real-time. We have made progress on mutating a polymerase and solving several potential  problems for assembling the sequencer.


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