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Rational Design of DNA Sequences with Non-Orthogonal Binding Interactions

Author Joseph Don Berleant

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Joseph Don Berleant
  • Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

Funding

Research supported in part by a National Science Foundation Graduate Research Fellowship (Grant No. 1122374). Research supported in part by the Office of Naval Research (N00014-21-1-4013), the Army Research Office (ICB Subaward W911NF-19-2-0026), and the National Science Foundation (CBET-1729397, OAC-1940231, CCF-1956054).

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Joseph Don Berleant. Rational Design of DNA Sequences with Non-Orthogonal Binding Interactions. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
https://doi.org/10.4230/LIPIcs.DNA.29.4

Abstract

Molecular computation involving promiscuous, or non-orthogonal, binding interactions between system components is found commonly in natural biological systems, as well as some proposed human-made molecular computers. Such systems are characterized by the fact that each computational unit, such as a domain within a DNA strand, may bind to several different partners with distinct, prescribed binding strengths. Unfortunately, implementing systems of molecular computation that incorporate non-orthogonal binding is difficult, because researchers lack a robust, general-purpose method for designing molecules with this type of behavior. In this work, we describe and demonstrate a process for the rational design of DNA sequences with prescribed non-orthogonal binding behavior. This process makes use of a model that represents large sets of non-orthogonal DNA sequences using fixed-length binary strings, and estimates the differential binding affinity between pairs of sequences through the Hamming distance between their corresponding binary strings. The real-world applicability of this model is supported by simulations and some experimental data. We then select two previously described systems of molecular computation involving non-orthogonal interactions, and apply our sequence design process to implement them using DNA strand displacement. Our simulated results on these two systems demonstrate both digital and analog computation. We hope that this work motivates the development and implementation of new computational paradigms based on non-orthogonal binding.

Subject Classification

ACM Subject Classification
  • Hardware → Emerging architectures
  • Hardware → Biology-related information processing
Keywords
  • DNA sequence design
  • binding networks
  • promiscuous binding
  • non-orthogonal binding
  • isometric graph embeddings

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