DNA Codes that Avoid Secondary Structures

TL;DR

This paper addresses the challenge of designing DNA sequences for storage and computing that minimize secondary structure formation, focusing on enumeration and practical code construction methods.

Contribution

It introduces new approaches for enumerating and constructing DNA codes that avoid secondary structures, advancing the reliability of DNA-based systems.

Findings

Developed enumeration techniques for secondary structure-free DNA sequences

Proposed practical code construction algorithms for DNA storage

Enhanced understanding of DNA sequence design constraints

Abstract

In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the issue of enumerating the sequences with such properties and the problem of practical code construction.