Biomolecular
reaction engineering
I am interested in biomolecular reaction engineering for two reasons. First, it offers a testbed for interrogation of fundamental evolutionary principles. Second, the techniques are important for integrating computational and experimental protein design. Of course, these methodologies also lie at the heart of the genomics revolution, as evidenced by Celera Genomics/Diagnostics' licensing of the patents:
1. R. Chakrabarti and C. E. Schutt, Compositions and methods for
improving polynucleotide
amplification reactions using amides, sulfones and sulfoxides: I, US
Patent 6,949,368 issued 9-27-05
for deployment in the personalized medicine industry. Please see page 2 of the following news article for details.
The polymerase chain
reaction (PCR) can
be viewed as a primitive self-replicating system akin to those
postulated to exist in the early stages of biological evolution,
rendering it ideal for experimental studies of the physics of
evolutionary dynamics as well as genomics and diagnostics. Our recently
developed theory of optimal
control of evolutionary dynamics shows that given
appropriate real-time sensing hardware, it should be possible to steer
the evolution of such systems to desired biological objectives. My
primary continuing goal in PCR research is to demonstrate that control
engineering of evolutionary dynamics is possible and to outline its
basic principles.
The PCR reaction is arguably the most important discovery in the history of biotechnology. However, the technique suffers from many drawbacks, most notably its limitations in amplifying the types of DNA sequences that are, coincidentally, the type most common in organismic genomes. Many genetic markers for diseases correspond to such sequences.
The PCR reaction is arguably the most important discovery in the history of biotechnology. However, the technique suffers from many drawbacks, most notably its limitations in amplifying the types of DNA sequences that are, coincidentally, the type most common in organismic genomes. Many genetic markers for diseases correspond to such sequences.
Molecular amplification
In a series of papers, we developed chemical techniques whereby small molecules could be employed to control the progress of the PCR evolutionary dynamics (through perturbation of the fitness measure) so that the amplification could be achieved for virtually any genomic template.
In order to control the evolution of self-replicating systems like PCR, it is necessary to assess the effect of controls on the thermodynamics and kinetic rate parameters of the reaction pathway for replication. As reported in the third paper below, we measured these quantities and demonstrated that even heuristic calculations could suffice to dramatically improve amplification. These techniques are now being used widely the practical genomics.
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.
The control parameter space thus expanded to chemical as well as thermal dimensions, it becomes essential to apply numerical tools from control theory to achieve the best possible amplification. We are currently applying the stochastic evolutionary control theory to meet this objective.
Microelectronic sensor and microreactor design
Ultimately, in order to implement these theoretical predictions, it is necessary to embed feedback control and estimation systems for real-time biomolecular amplification on microchips. These microchips, and primitive thermal control systems, were developed by us in the course of cross-disciplinary research at MIT. The ideas developed out of a course we taught in the MIT EECS department in 2003.
J. Hou, N. Milovic, M. Godin, P. R. Russo, R. Chakrabarti, and S. R. Manalis. Label-free microelectronic PCR quantification. Anal. Chem. 78: 2526-2531, 2006.
The next step is to write embedded software to control amplification according to the principles of closed-loop feedback control.