System and method for using nucleic acid barcodes to monitor biological, chemical, and biochemical materials and processes

Abstract

Aspects of the embodiments use nucleic acid sequence (NS) based barcodes (NS tracking barcodes) in different capacities to track, trace, monitor, optimize, and troubleshoot complex biological, chemical, and biochemical processes. At least two forms of the NS tracking barcodes are described herein: ported NS tracking barcodes and process NS tracking barcodes. Ported NS tracking barcodes are designed such that they will not be modified during the process, and their sequence can indicate time or location of manufacture information, as well as an indication of success of a DNA processing step. Process NS tracking barcodes can be more complicated than the ported NS tracking barcodes, as they can be modified during the course of DNA processing, so that they can provide specific information regarding whether a desired nucleic acid process or reaction worked or did not. Process NS tracking barcodes can be synthesized such that they can used as a substrate for the reaction and get modified. Many nucleic acid sequencing or other molecular counting techniques are used to quantify the modified and unmodified NS tracking barcodes to calculate conversion efficiency, and correct for amplification bias or inefficiencies, as well as identifying other processing issues. The nucleic acids used in NS tracking barcodes have robust structures, dense information content, and can be readily synthesized and sequenced.

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