DeepAI AI Chat
Log In Sign Up

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

02/06/2019
by   Thomas D. Schneider, et al.
University of the Witwatersrand
National Institutes of Health
0

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.

READ FULL TEXT

page 1

page 2

page 3

page 4

01/15/2018

Coding over Sets for DNA Storage

In this paper we study error-correcting codes for the storage of data in...
12/09/2022

Computability questions in the sphere packing problem

We consider the sets of dimensions for which there is an optimal sphere ...
06/20/2022

Dual Linear Programming Bounds for Sphere Packing via Discrete Reductions

The Cohn-Elkies linear program for sphere packing, which was used to sol...
11/08/2022

Multiple Packing: Lower Bounds via Infinite Constellations

We study the problem of high-dimensional multiple packing in Euclidean s...
03/15/2023

Wilson matrix kernel for lattice QCD on A64FX architecture

We study the implementation of the even-odd Wilson fermion matrix for la...
08/30/2020

On Communication for Distributed Babai Point Computation

We present a communication-efficient distributed protocol for computing ...
01/06/2023

Echoes of the hexagon: remnants of hexagonal packing inside regular polygons

Based on numerical simulations that we have carried out, we provide evid...