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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 di...

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Detalles Bibliográficos
Autores principales: Schneider, Thomas D., Jejjala, Vishnu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822723/
https://www.ncbi.nlm.nih.gov/pubmed/31671158
http://dx.doi.org/10.1371/journal.pone.0222419
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author Schneider, Thomas D.
Jejjala, Vishnu
author_facet Schneider, Thomas D.
Jejjala, Vishnu
author_sort Schneider, Thomas D.
collection PubMed
description 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.
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spelling pubmed-68227232019-11-08 Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences Schneider, Thomas D. Jejjala, Vishnu PLoS One Research Article 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. Public Library of Science 2019-10-31 /pmc/articles/PMC6822723/ /pubmed/31671158 http://dx.doi.org/10.1371/journal.pone.0222419 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Schneider, Thomas D.
Jejjala, Vishnu
Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
title Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
title_full Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
title_fullStr Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
title_full_unstemmed Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
title_short Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
title_sort restriction enzymes use a 24 dimensional coding space to recognize 6 base long dna sequences
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822723/
https://www.ncbi.nlm.nih.gov/pubmed/31671158
http://dx.doi.org/10.1371/journal.pone.0222419
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