Structure sampling for computational estimation of localized DNA interaction rates

Abstract Molecular circuits implemented using molecular components tethered to a DNA tile nanostructure have certain advantages over solution-phase circuits. Tethering components in close proximity increases the speed of reactions by reducing diffusion and improves scalability by enabling reuse of i...

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Autores principales:	Sarika Kumar, Julian M. Weisburd, Matthew R. Lakin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/19a41ae3a5a64a388c65deeb42960e93
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spelling	oai:doaj.org-article:19a41ae3a5a64a388c65deeb42960e932021-12-02T16:04:13ZStructure sampling for computational estimation of localized DNA interaction rates10.1038/s41598-021-92145-82045-2322https://doaj.org/article/19a41ae3a5a64a388c65deeb42960e932021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92145-8https://doaj.org/toc/2045-2322Abstract Molecular circuits implemented using molecular components tethered to a DNA tile nanostructure have certain advantages over solution-phase circuits. Tethering components in close proximity increases the speed of reactions by reducing diffusion and improves scalability by enabling reuse of identical DNA sequences at different locations in the circuit. These systems show great potential for practical applications including delivery of diagnostic and therapeutic molecular circuits to cells. When modeling such systems, molecular geometry plays an important role in determining whether the two species interact and at what rate. In this paper, we present an automated method for estimating reaction rates in tethered molecular circuits that takes the geometry of the tethered species into account. We probabilistically generate samples of structure distributions based on simple biophysical models and use these to estimate important parameters for kinetic models. This work provides a basis for subsequent enhanced modeling and design tools for localized molecular circuits.Sarika KumarJulian M. WeisburdMatthew R. LakinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sarika Kumar Julian M. Weisburd Matthew R. Lakin Structure sampling for computational estimation of localized DNA interaction rates
description	Abstract Molecular circuits implemented using molecular components tethered to a DNA tile nanostructure have certain advantages over solution-phase circuits. Tethering components in close proximity increases the speed of reactions by reducing diffusion and improves scalability by enabling reuse of identical DNA sequences at different locations in the circuit. These systems show great potential for practical applications including delivery of diagnostic and therapeutic molecular circuits to cells. When modeling such systems, molecular geometry plays an important role in determining whether the two species interact and at what rate. In this paper, we present an automated method for estimating reaction rates in tethered molecular circuits that takes the geometry of the tethered species into account. We probabilistically generate samples of structure distributions based on simple biophysical models and use these to estimate important parameters for kinetic models. This work provides a basis for subsequent enhanced modeling and design tools for localized molecular circuits.
format	article
author	Sarika Kumar Julian M. Weisburd Matthew R. Lakin
author_facet	Sarika Kumar Julian M. Weisburd Matthew R. Lakin
author_sort	Sarika Kumar
title	Structure sampling for computational estimation of localized DNA interaction rates
title_short	Structure sampling for computational estimation of localized DNA interaction rates
title_full	Structure sampling for computational estimation of localized DNA interaction rates
title_fullStr	Structure sampling for computational estimation of localized DNA interaction rates
title_full_unstemmed	Structure sampling for computational estimation of localized DNA interaction rates
title_sort	structure sampling for computational estimation of localized dna interaction rates
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/19a41ae3a5a64a388c65deeb42960e93
work_keys_str_mv	AT sarikakumar structuresamplingforcomputationalestimationoflocalizeddnainteractionrates AT julianmweisburd structuresamplingforcomputationalestimationoflocalizeddnainteractionrates AT matthewrlakin structuresamplingforcomputationalestimationoflocalizeddnainteractionrates
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Structure sampling for computational estimation of localized DNA interaction rates

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