Studying the Cycle Complexity of DNA Synthesis

TL;DR

This paper analyzes the cycle complexity of DNA synthesis for data storage, proposing new encoding methods and bounds to improve efficiency and capacity in cyclic synthesis technologies like photolithography.

Contribution

It introduces new performance metrics, extends channel capacity results, and develops encoding schemes with higher rates for DNA synthesis-based data storage.

Findings

Higher synthesis capacity than previous methods

Effective encoding achieving improved rate and capacity

Bounds and asymptotics for synthesis costs and alphabet sizes

Abstract

Storing data in DNA is being explored as an efficient solution for archiving and in-object storage. Synthesis time and cost remain challenging, significantly limiting some applications at this stage. In this paper we investigate efficient synthesis, as it relates to cyclic synchronized synthesis technologies, such as photolithography. We define performance metrics related to the number of cycles needed for the synthesis of any fixed number of bits. We first expand on some results from the literature related to the channel capacity, addressing densities beyond those covered by prior work. This leads us to develop effective encoding achieving rate and capacity that are higher than previously reported. Finally, we analyze cost based on a parametric definition and determine some bounds and asymptotics. We investigate alphabet sizes that can be larger than 4, both for theoretical completeness and since practical approaches to such schemes were recently suggested and tested in the literature.