{"title":"Construction of Primers for DNA-Based Storage Systems.","authors":"Siddhartha Siddhiprada Bhoi, Abhay Kumar Singh, Kishan","doi":"10.1109/TNB.2026.3720321","DOIUrl":null,"url":null,"abstract":"<p><p>To enable random access in artificial DNA-based storage systems, it is essential to develop a balanced and stable address sequence with minimal cross-correlation, ensuring address independence. The goal of our paper is to design primers suitable for use as addresses within these systems. We extend the construction of secondary structure-avoiding DNA codes from [1] and modify these codes to create primers that meet the necessary specifications. To achieve the desired functionality, the paper presented three methods of primer construction. The first method generates the set of 13<sup>8</sup> primer sequences of length 64 which are mutually uncorrelated, while the other constructions generate a much higher number of primer sequences with weak uncorrelatedness. Finally, the paper concludes with the analysis and the examples for each construction. We also stimulated the primers under insertion, deletion, and substitutuion channels and also provided a further direction for the scheme.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":4.2000,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IEEE Transactions on NanoBioscience","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1109/TNB.2026.3720321","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
To enable random access in artificial DNA-based storage systems, it is essential to develop a balanced and stable address sequence with minimal cross-correlation, ensuring address independence. The goal of our paper is to design primers suitable for use as addresses within these systems. We extend the construction of secondary structure-avoiding DNA codes from [1] and modify these codes to create primers that meet the necessary specifications. To achieve the desired functionality, the paper presented three methods of primer construction. The first method generates the set of 138 primer sequences of length 64 which are mutually uncorrelated, while the other constructions generate a much higher number of primer sequences with weak uncorrelatedness. Finally, the paper concludes with the analysis and the examples for each construction. We also stimulated the primers under insertion, deletion, and substitutuion channels and also provided a further direction for the scheme.
期刊介绍：
The IEEE Transactions on NanoBioscience reports on original, innovative and interdisciplinary work on all aspects of molecular systems, cellular systems, and tissues (including molecular electronics). Topics covered in the journal focus on a broad spectrum of aspects, both on foundations and on applications. Specifically, methods and techniques, experimental aspects, design and implementation, instrumentation and laboratory equipment, clinical aspects, hardware and software data acquisition and analysis and computer based modelling are covered (based on traditional or high performance computing - parallel computers or computer networks).
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