Free energy gap and statistical thermodynamic fidelity of DNA codes

DNA nanotechnology often requires collections of oligonucleotides called "DNA free energy gap codes" that do not produce erroneous crosshybridizations in a competitive muliplexing environment. This paper addresses the question of how to design these codes to accomplish a desired amount of...

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Bibliographic Details
Published in:Journal of computational biology Vol. 14; no. 8; p. 1088
Main Authors: Bishop, Morgan A, D' Yachkov, Arkadii G, Macula, Anthony J, Renz, Thomas E, Rykov, Vyacheslav V
Format: Journal Article
Language:English
Published: United States 01.10.2007
Subjects:
Base Sequence
Computational Biology
DNA - chemistry
DNA - genetics
Mathematics
Models, Chemical
Nanotechnology
Nucleic Acid Conformation
Nucleic Acid Hybridization
Oligodeoxyribonucleotides - chemistry
Oligodeoxyribonucleotides - genetics
Thermodynamics
ISSN:1066-5277
Online Access:Get more information
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Summary:DNA nanotechnology often requires collections of oligonucleotides called "DNA free energy gap codes" that do not produce erroneous crosshybridizations in a competitive muliplexing environment. This paper addresses the question of how to design these codes to accomplish a desired amount of work within an acceptable error rate. Using a statistical thermodynamic and probabilistic model of DNA code fidelity and mathematical random coding theory methods, theoretical lower bounds on the size of DNA codes are given. More importantly, DNA code design parameters (e.g., strand number, strand length and sequence composition) needed to achieve experimental goals are identified.
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ISSN:1066-5277
DOI:10.1089/cmb.2007.0083