On DNA Codes With Multiple Constraints

We consider the problem of designing a set of DNA sequences (DNA codes) for various DNA computing applications, such as DNA based data storage. A chemically active DNA sequence forms unlikely secondary structure by folding back onto itself by hybridization among base pairs. DNA sequences with second...

Full description

Saved in:
Bibliographic Details
Published in:IEEE communications letters Vol. 25; no. 2; pp. 365 - 368
Main Authors: Benerjee, Krishna Gopal, Banerjee, Adrish
Format: Journal Article
Language:English
Published: New York IEEE 01.02.2021
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subjects:
Bats
Data storage
Deoxyribonucleic acid
DNA
DNA codes
DNA computing
DNA data storage
Gene sequencing
Hamming distance
homopolymers
Memory
Prediction algorithms
reverse-complement constraint
secondary structures
Sequential analysis
Writing
ISSN:1089-7798, 1558-2558
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We consider the problem of designing a set of DNA sequences (DNA codes) for various DNA computing applications, such as DNA based data storage. A chemically active DNA sequence forms unlikely secondary structure by folding back onto itself by hybridization among base pairs. DNA sequences with secondary structures are less active chemically and are needed to unfold before reading. On the other side, during synthesis and sequencing of DNA sequences with homopolymers of large run-length, errors occur frequently. In this letter, we have presented families of DNA codes with several properties such as DNA sequences free from secondary structures of stem length more than two and also free from homopolymers of run-length more than four. All constructed DNA sequences of any DNA codes are sufficiently dissimilar to their reverse-complement DNA sequences. Further, DNA sequences obtained by concatenating all those DNA sequences also avoid secondary structures and homopolymers.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
ISSN:1089-7798
1558-2558
DOI:10.1109/LCOMM.2020.3029071