Segmented Synthesis of GammaPNA Oligomers

DESCRIPTION provided by applicant The proposed Phase I project will result in the development of an efficient method for synthesizing gammaPNA PNA oligomers of customer defined sequence for broad applications in biomedical and biotechnological research Current oligonucleotide and oligopeptide synthesis methods involve consecutive addition of single residues at a time whereas our proposed method will involve synthesis and storage of PNA segments consisting of residues in bulk All possible sequences of each length will be synthesized and will be functionalized with reactive groups that are appropriate for coupling via reductive amination For example a mer probe can be synthesized in only three reactions using tetramer segments whereas traditional synthesis would require sequential coupling reactions of single residue reactants In addition the coupling reactions will be performed using a solid supported DNA template which will a accelerate the reaction b insure coupling of segments in the correct order and c simplify purification Phase I will consist of three specific aims Synthesis of trimer and tetramer PNA segments bearing terminal amine and aldehyde functional groups DNA templated synthesis of PNA oligomers from segments prepared during Aim and assessment of their hybridization properties Testing of segmented probes for telomere fluorescence in situ hybridization and PCR clamping assays where PNAs have recently shown improved performance compared to traditional PNA The significance of the proposed research will come from the ability to reduce our synthesis and purification time ca fold for custom designed sequences leading to throughput that rivals that of RNA oligonucleotide synthesis Not only will the customer obtain their PNA oligomers much faster but the production costs will be substantially lower leading to lower costs for our customers as well as a higher profit margin for PNA Innovations PUBLIC HEALTH RELEVANCE The goal of this project is to develop an efficient method for rapid synthesis and purification of PNA oligomers that are of growing utility in biomedical and biotechnological research Ultimately the oligomers will be constructed from pre synthesized segments of defined length and sequence such that an order from a customer for a particular sequence will require far fewer synthesis steps than is currently needed when each oligomer is synthesized one residue at a time Purification of oligomers synthesized in this manner will also be streamlined due to the difference in length between the full length product and the short segments used for its construction The significance of this goal is that synthesis will be ca fold less expensive than our current method which will allow us to price our oligomers more aggressively than our competitors while also increasing our profit margin The Phase I aims will focus on synthesis of PNA trimer and tetramer segments assembly of segments into PNA oligomers using a solid supported DNA template and assessing the hybridization affinity and specificity and testing of segmented probes in fluorescence in situ hybridization of telomeric DNA and PCR clamping assays