Method for degradation and sequencing of polymers which sequentially

Abstract

A method and apparatus for sequentially degrading at least a portion of a polymer of backbone repeating units, the polymer having a terminal repeating unit comprised of a nucleophile and a backbone carbonyl carbon distant from the nucleophile, comprising the steps of first initiating attack of said nucleophile upon said backbone carbonyl carbon by raising the energy level to activate said nucleophile for said attack. Secondly, forming a ring comprising the terminal repeating unit, thereby simultaneously releasing the ring and generating a shortened polymer having a terminal repeating unit capable of nucleophile attack upon the backbone carbonyl carbon and, lastly, maintaining the reaction conditions necessary for repeating steps a and b until the portion of the polymer desired is degraded. In a related embodiment, polyamide nucleic acid (PNA) sequences can be determined by generating a nested set of polymer fragments, each fragment having N-x repeating units where N is the total number of repeating units in the parent polymer and x is the number of degradation cycles the fragment has been subjected to, and then analyzing the nested set of polymer fragments to determine polymer sequence. An apparatus embodying the method of sequential degradation is also described. Analysis may be by MALD-TOF.