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

Thomas D Schneider; Vishnu Jejjala

doi:10.1371/journal.pone.0222419

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

PLoS One. 2019 Oct 31;14(10):e0222419. doi: 10.1371/journal.pone.0222419. eCollection 2019.

Authors

Thomas D Schneider¹, Vishnu Jejjala^{2

3}

Affiliations

¹ National Institutes of Health, National Cancer Institute, Center for Cancer Research, RNA Biology Laboratory, Frederick, Maryland, United States of America.
² Mandelstam Institute for Theoretical Physics, School of Physics, NITheP, and CoE-MaSS, University of the Witwatersrand, Johannesburg, South Africa.
³ David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

Abstract

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.

Publication types

Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages / genetics
Base Sequence
DNA / chemistry
DNA / genetics*
DNA Restriction Enzymes / chemistry
DNA Restriction Enzymes / genetics*
DNA-Binding Proteins / chemistry
DNA-Binding Proteins / genetics*
Deoxyribonuclease EcoRI / chemistry
Deoxyribonuclease EcoRI / genetics*
Models, Molecular

Substances

DNA-Binding Proteins
DNA
DNA Restriction Enzymes
Deoxyribonuclease EcoRI

Grants and funding

This research was supported in part by the Intramural Research Program of the National Institutes of Health (https://www.nih.gov/, TDS), National Cancer Institute, Center for Cancer Research. This work was also supported by South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation (https://www.nrf.ac.za/, grant number: SARChI 78554, VJ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.