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Huntley MH, Murugan A, Brenner MP. Information capacity of specific interactions. Proc Natl Acad Sci U S A. 2016;113(21):5841-6doi: 10.1073/pnas.1520969113.
Huntley, M. H., Murugan, A., & Brenner, M. P. (2016). Information capacity of specific interactions. Proceedings of the National Academy of Sciences of the United States of America, 113(21), 5841-6. https://doi.org/10.1073/pnas.1520969113
Huntley, Miriam H, et al. "Information capacity of specific interactions." Proceedings of the National Academy of Sciences of the United States of America vol. 113,21 (2016): 5841-6. doi: https://doi.org/10.1073/pnas.1520969113
Huntley MH, Murugan A, Brenner MP. Information capacity of specific interactions. Proc Natl Acad Sci U S A. 2016 May 24;113(21):5841-6. doi: 10.1073/pnas.1520969113. Epub 2016 May 06. PMID: 27155013; PMCID: PMC4889362.
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Proc Natl Acad Sci U S A. 2016 May 24;113(21):5841-6. doi: 10.1073/pnas.1520969113. Epub 2016 May 06.

Information capacity of specific interactions.

Proceedings of the National Academy of Sciences of the United States of America

Miriam H Huntley, Arvind Murugan, Michael P Brenner

Affiliations

  1. Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138; Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, MA 02138;
  2. Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138; Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, MA 02138; Physics and the James Franck Institute, University of Chicago, Chicago, IL 60637;
  3. Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138; Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, MA 02138; Department of Physics, Harvard University, Cambridge, MA 02138 [email protected].

PMID: 27155013 PMCID: PMC4889362 DOI: 10.1073/pnas.1520969113

Abstract

Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in diverse contexts, from DNA hybridization to shape-sensitive depletion interactions. Despite this diversity, all systems that rely on interaction specificity operate under the constraint that increasing the number of distinct components inevitably increases off-target binding. Here we introduce "capacity," the maximal information encodable using specific interactions, to compare specificity across diverse experimental systems and to compute how specificity changes with physical parameters. Using this framework, we find that "shape" coding of interactions has higher capacity than chemical ("color") coding because the strength of off-target binding is strongly sublinear in binding-site size for shapes while being linear for colors. We also find that different specificity mechanisms, such as shape and color, can be combined in a synergistic manner, giving a capacity greater than the sum of the parts.

Keywords: colloid; crosstalk; mutual information; self-assembly; specificity

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