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NITAAI-Veda.nyf > Soul Science God Philosophy > Science and Spiritual Quest > Section 4 Towards a New Biology > MOLECULAR EVOLUTION: QUANTUM MECHANICS > 2. Background

2. Background


Nature packs information into DNA molecules with remarkable efficiency. Nanometer-sized molecular engines replicate, transcribe, and otherwise process this information. New tools to detect and manipulate single molecules have made it possible to elicit how various parameters in the motor's microenvironment can control the dynamics of these nano-motors (i.e. enzymes). At small length scales, noise plays a non-negligible role in the motor's movement along DNA.Biological information in DNA is replicated, transcribed, or otherwise processed by molecular machines called polymerases. This process of reading and writing genetic   information   can  be tightly coupled or regulated by the motor's environment. Environmental parameters (like temperature, nucleoside concentrations, mechanical tension, etc.) [2 - 4] can directly couple into the conformational dynamics of the motor. Theoretical concepts in concert with emerging nanotools to probe and manipulate single molecules are elucidating how various "knobs" in a motor's environment can control its real-time dynamics. Recent single molecule experiments have shown, for example, that increasing the mechanical tension applied to a DNA template can appreciably "tune" the speed at which the motor enzyme DNA polymerase (DNAp) replicates DNA. In addition to the mning effect, a tension-induced reversal in the motor's velocity has been found to occur at high stretching forces (i.e. above -35 pN) (See Figure 1).


We have been working to understand how mechanical tension on a DNA polymer can control both the "mning" and "switching" behavior in the molecular motor. The tension-induced switching observed in single molecule experiments is similar to the natural reversal that occurs after a mistake in DNA incorporation, whereby the reaction pathways of the biochemical network are kinetically partitioned to favor the exonuclease pathway over the polymerase one. We seek to develop a framework to understand how environmental parameters (like tension, torsion, external acoustic or electromagnetic signals) can directly couple into the conformational dynamics of the motor. By understanding how these various perturbations affect (tie molecular motor's dynamics, we can develop a more holistic picture of their context-dependent function. These motors are fundamentally open systems and very little is understood today about how their (local and global) environment couples into their function. Viewing the motor as a complex adaptive system that is capable of utilizing information in its environment to evolve or learn may shed new light on how information processing and computation can be realized at the molecular level.As it becomes possible to probe the dynamics of these motors at increasingly smaller length and time scales, quantum effects, if relevant, are more likely to become experimentally detectable. Paul Davies [5] has very elegantly posed the question "Does quantum mechanics play a non-trivial role in life?" and whether quantum mechanics could somehow enhance the information processing capabilities of biological systems. Here we revisit such fundamental questions in the context of examining the information processing capabilities of motors that read DNA. We use Wigner's relations for a quantum clock to derive constraints on the information processing accuracy and precision of a molecular motor reading DNA. In order for this motor to process information quantum mechanically, it must have long decoherence times. Here we also calculate me decoherence time for our motor-DNA system.