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Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization

Sensitive and specific DNA hybridization is essential for nucleic acid chemistry. Competitive composition of probe and blocker has been the most adopted probe design for its relatively high sensitivity and specificity. However, the sensitivity and specificity were inversely correlated over the lengt...

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Autores principales: Chen, Xin, Liu, Na, Liu, Liquan, Chen, Wei, Chen, Na, Lin, Meng, Xu, Jiaju, Zhou, Xing, Wang, Hongbo, Zhao, Meiping, Xiao, Xianjin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791858/
https://www.ncbi.nlm.nih.gov/pubmed/31611572
http://dx.doi.org/10.1038/s41467-019-12593-9
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author Chen, Xin
Liu, Na
Liu, Liquan
Chen, Wei
Chen, Na
Lin, Meng
Xu, Jiaju
Zhou, Xing
Wang, Hongbo
Zhao, Meiping
Xiao, Xianjin
author_facet Chen, Xin
Liu, Na
Liu, Liquan
Chen, Wei
Chen, Na
Lin, Meng
Xu, Jiaju
Zhou, Xing
Wang, Hongbo
Zhao, Meiping
Xiao, Xianjin
author_sort Chen, Xin
collection PubMed
description Sensitive and specific DNA hybridization is essential for nucleic acid chemistry. Competitive composition of probe and blocker has been the most adopted probe design for its relatively high sensitivity and specificity. However, the sensitivity and specificity were inversely correlated over the length and concentration of the blocker strand, making the optimization process cumbersome. Herein, we construct a theoretical model for competitive DNA hybridization, which disclose that both the thermodynamics and kinetics contribute to the inverse correlation. Guided by this, we invent the 4-way Strand Exchange LEd Competitive DNA Testing (SELECT) system, which breaks up the inverse correlation. Using SELECT, we identified 16 hot-pot mutations in human genome under uniform conditions, without optimization at all. The specificities were all above 140. As a demonstration of the clinical practicability, we develop probe systems that detect mutations in human genomic DNA extracted from ovarian cancer patients with a detection limit of 0.1%.
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spelling pubmed-67918582019-10-17 Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization Chen, Xin Liu, Na Liu, Liquan Chen, Wei Chen, Na Lin, Meng Xu, Jiaju Zhou, Xing Wang, Hongbo Zhao, Meiping Xiao, Xianjin Nat Commun Article Sensitive and specific DNA hybridization is essential for nucleic acid chemistry. Competitive composition of probe and blocker has been the most adopted probe design for its relatively high sensitivity and specificity. However, the sensitivity and specificity were inversely correlated over the length and concentration of the blocker strand, making the optimization process cumbersome. Herein, we construct a theoretical model for competitive DNA hybridization, which disclose that both the thermodynamics and kinetics contribute to the inverse correlation. Guided by this, we invent the 4-way Strand Exchange LEd Competitive DNA Testing (SELECT) system, which breaks up the inverse correlation. Using SELECT, we identified 16 hot-pot mutations in human genome under uniform conditions, without optimization at all. The specificities were all above 140. As a demonstration of the clinical practicability, we develop probe systems that detect mutations in human genomic DNA extracted from ovarian cancer patients with a detection limit of 0.1%. Nature Publishing Group UK 2019-10-14 /pmc/articles/PMC6791858/ /pubmed/31611572 http://dx.doi.org/10.1038/s41467-019-12593-9 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Chen, Xin
Liu, Na
Liu, Liquan
Chen, Wei
Chen, Na
Lin, Meng
Xu, Jiaju
Zhou, Xing
Wang, Hongbo
Zhao, Meiping
Xiao, Xianjin
Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
title Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
title_full Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
title_fullStr Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
title_full_unstemmed Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
title_short Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
title_sort thermodynamics and kinetics guided probe design for uniformly sensitive and specific dna hybridization without optimization
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791858/
https://www.ncbi.nlm.nih.gov/pubmed/31611572
http://dx.doi.org/10.1038/s41467-019-12593-9
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