Enabling the molecular diagnostics of genetic markers for inherited diseases.

The Polymerase Chain Reaction (PCR) is an in vitro method for rapid replication of DNA that is the workhorse of genome sequencing, genetic profiling, and forensic science. The applications of PCR are central to life science experiments and many potential breakthrough technologies. However, PCR sequencing reactions often generate inadequate yield of the target DNA sequence and amplification of undesired nonspecific products. These problems can be especially severe in case of targets with high-GC content (more GC than AT base pairs). The difficulties encountered in amplifying high-GC targets are hindering genetic diagnostics, since many DNAs of interest, particularly those that are relevant to disease risk, reside in high-GC containing segments of the genome PMC-AT has internally developed intellectual property for sequencing GC-rich segments of the genome essential for diagnosing a variety of genetically inherited diseases. In a series of papers, PMC-AT developed chemical techniques whereby small molecules could be employed to control the progress of the PCR sequencing reaction so that the amplification could be achieved for virtually any genomic template.

In order to control PCR sequencing, it is necessary to assess the thermodynamics and kinetic rate parameters of the reaction pathway for replication.  As reported in the third paper below, these quantities were measured and demonstrated that even heuristic calculations could suffice to dramatically improve amplification.  These techniques are now being used widely in practical genomics.

Selected publications:

R. Chakrabarti and C. E. Schutt, The enhancement of PCR amplification by low molecular weight amides. Nucleic Acids Res. 29: 2377-2381, 2001.

R. Chakrabarti and C.E. Schutt, The enhancement of PCR amplification by low molecular weight sulfones. Gene 274: 293-298, 2001.

R. Chakrabarti, "Novel PCR-enhancing compounds and their modes of action," In: PCR Technology: Current Innovations, 2nd Edition. Ed. T. Weissensteiner, H.G. Griffin and A. Griffin, CRC Press: Boca Raton , FL , November, 2003. [invited article].

K. Marimuthu and R. Chakrabarti, Sequence Dependent Theory of Oligonucleotide Hybridization Kinetics. J. Chem. Phys. 140: 175104, 2014.