Construction of DNA codes with multiple constrained properties

DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization of its nucleotides. The formation of large stem-length secondary structures makes the sequences chemically inactive towards synthesis and sequencing processes. Furthermore, in DNA com...

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Bibliographic Details
Published in:Cryptography and communications Vol. 16; no. 5; pp. 1135 - 1149
Main Authors: Bhoi, Siddhartha Siddhiprada, Parampalli, Udaya, Singh, Abhay Kumar
Format: Journal Article
Language:English
Published: New York Springer US 01.09.2024
Springer Nature B.V
Subjects:
Algorithms
Circuits
Codes
Coding and Information Theory
Communications Engineering
Computation
Computer Science
Constraints
Data storage
Data Structures and Information Theory
Energy
Error correcting codes
Error correction
Gene sequencing
Hybridization
Information and Communication
Mathematics of Computing
Networks
Nucleotides
Reed-Solomon codes
94B15
05
94B60
Secondary structure
DNA codes
Homopolymer run length constraint
ISSN:1936-2447, 1936-2455
Online Access:Get full text
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Summary:DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization of its nucleotides. The formation of large stem-length secondary structures makes the sequences chemically inactive towards synthesis and sequencing processes. Furthermore, in DNA computing, other constraints like homopolymer run length also introduce complications. In this paper, our goal is to tackle the problems due to the creation of secondary structures in DNA sequences along with constraints such as not having a large homopolymer run length. This paper presents families of DNA codes with secondary structures of stem length at most two and homopolymer run length at most four. We identified Z 11 as an ideal structure to construct DNA codes to avoid the above problems. By mapping the error-correcting codes over Z 11 to DNA nucleotides, we obtained DNA codes with rates 0.5765 times the corresponding code rate over Z 11 , including some new secondary structure-free and better-performing codes for DNA-based data storage and DNA computing purposes.
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ISSN:1936-2447
1936-2455
DOI:10.1007/s12095-024-00718-x