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High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays

Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample...

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Autores principales: Ström, Oskar E., Beech, Jason P., Tegenfeldt, Jonas O.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9611613/
https://www.ncbi.nlm.nih.gov/pubmed/36296107
http://dx.doi.org/10.3390/mi13101754
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author Ström, Oskar E.
Beech, Jason P.
Tegenfeldt, Jonas O.
author_facet Ström, Oskar E.
Beech, Jason P.
Tegenfeldt, Jonas O.
author_sort Ström, Oskar E.
collection PubMed
description Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions.
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spelling pubmed-96116132022-10-28 High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays Ström, Oskar E. Beech, Jason P. Tegenfeldt, Jonas O. Micromachines (Basel) Article Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions. MDPI 2022-10-17 /pmc/articles/PMC9611613/ /pubmed/36296107 http://dx.doi.org/10.3390/mi13101754 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ström, Oskar E.
Beech, Jason P.
Tegenfeldt, Jonas O.
High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
title High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
title_full High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
title_fullStr High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
title_full_unstemmed High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
title_short High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
title_sort high-throughput separation of long dna in deterministic lateral displacement arrays
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9611613/
https://www.ncbi.nlm.nih.gov/pubmed/36296107
http://dx.doi.org/10.3390/mi13101754
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