Jejjala, V. | Search bioRxiv

bioRxiv2019

Dynamics of genetic code evolution: The emergence of universality

AO_SCPLOWBSTRACTC_SCPLOWWe study the dynamics of genetic code evolution. The algorithm of Vetsigian et al. [1] provides a solution that is both optimal and universal. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on achieving universality. We show that by allowing specific parameters to vary with time, the algorithm converges much faster to a universal solution. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions in order to understand the origin of universality and find that there is a direct link to mutation rate.

genomics↗

bioRxiv2019

Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences

Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.

bioinformatics↗