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Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency

Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long DNA...

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Autores principales: Liu, Jingqian, Shukor, Syukri, Li, Shuxiang, Tamayo, Alfred, Tosi, Lorenzo, Larman, Benjamin, Nanda, Vikas, Olson, Wilma K., Parekkadan, Biju
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571849/
https://www.ncbi.nlm.nih.gov/pubmed/31121947
http://dx.doi.org/10.3390/biom9050199
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author Liu, Jingqian
Shukor, Syukri
Li, Shuxiang
Tamayo, Alfred
Tosi, Lorenzo
Larman, Benjamin
Nanda, Vikas
Olson, Wilma K.
Parekkadan, Biju
author_facet Liu, Jingqian
Shukor, Syukri
Li, Shuxiang
Tamayo, Alfred
Tosi, Lorenzo
Larman, Benjamin
Nanda, Vikas
Olson, Wilma K.
Parekkadan, Biju
author_sort Liu, Jingqian
collection PubMed
description Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long DNA fragments. LASSO probes are molecular inversion probes (MIP) engineered with an adapter region of user-defined length, flanked between template-specific probe sequences. Herein, we demonstrate that the adapter length is a key feature of LASSO that influences the efficiency of gene capture and cloning. Furthermore, we applied a model based on Monte Carlo molecular simulation in order to study the relationship between the long-adapter length of LASSO and capture enrichment. Our results suggest that the adapter length is a factor that contributes to the free energy of target–probe interaction, thereby determining the efficiency of capture. The results indicate that LASSOs with extremely long adapters cannot capture the targets well. They also suggest that targets of different lengths may prefer adapters of different lengths.
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spelling pubmed-65718492019-06-18 Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency Liu, Jingqian Shukor, Syukri Li, Shuxiang Tamayo, Alfred Tosi, Lorenzo Larman, Benjamin Nanda, Vikas Olson, Wilma K. Parekkadan, Biju Biomolecules Brief Report Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long DNA fragments. LASSO probes are molecular inversion probes (MIP) engineered with an adapter region of user-defined length, flanked between template-specific probe sequences. Herein, we demonstrate that the adapter length is a key feature of LASSO that influences the efficiency of gene capture and cloning. Furthermore, we applied a model based on Monte Carlo molecular simulation in order to study the relationship between the long-adapter length of LASSO and capture enrichment. Our results suggest that the adapter length is a factor that contributes to the free energy of target–probe interaction, thereby determining the efficiency of capture. The results indicate that LASSOs with extremely long adapters cannot capture the targets well. They also suggest that targets of different lengths may prefer adapters of different lengths. MDPI 2019-05-22 /pmc/articles/PMC6571849/ /pubmed/31121947 http://dx.doi.org/10.3390/biom9050199 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Brief Report
Liu, Jingqian
Shukor, Syukri
Li, Shuxiang
Tamayo, Alfred
Tosi, Lorenzo
Larman, Benjamin
Nanda, Vikas
Olson, Wilma K.
Parekkadan, Biju
Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
title Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
title_full Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
title_fullStr Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
title_full_unstemmed Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
title_short Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
title_sort computational simulation of adapter length-dependent lasso probe capture efficiency
topic Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571849/
https://www.ncbi.nlm.nih.gov/pubmed/31121947
http://dx.doi.org/10.3390/biom9050199
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