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Yin J, Huang H, Zheng M, Hu J. An ultrasonic biosample disruptor with two triangular teeth on its radiation face. Biotechnol J 2024; 19:e2300263. [PMID: 38009259 DOI: 10.1002/biot.202300263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
Ultrasound has been used in biosample disruption such as disruption of algal cell and DNA. New structure of ultrasonic biosample disruptor (UBD) needs to be explored to increase the energy efficiency. In this study, an UBD with two triangular teeth on the bottom radiation face of the water tank has been proposed, to concentrate the acoustic energy into the slot between the two neighboring triangular teeth, in order to raise the acoustic energy utilization and fragmentation performance. The acoustic energy concentration into the slot is verified by the FEM computation, and the improvement of fragmentation performance is experimentally confirmed with spirulina and tribonema, compared to the traditional UBD which has a flat radiation face. The number proportion of fragment in the length range of 10-20 μm generated by the UBD proposed in this work is 17.08% and 10.82% more than that generated by the traditional UBD for the two samples, respectively. Besides, the UBD proposed in this work has a much smaller standard deviation of DNA fragment length (47 bp) than the traditional UBD (249 bp), with a similar mean length of fragments. Moreover, the maximum weight proportion of fragment in the range of 100-300 bp, generated by the UBD proposed in this work, is 71.4%.
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Affiliation(s)
- Jia Yin
- State Key Lab of Mechanics and Control for Aerospace Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Huiyu Huang
- State Key Lab of Mechanics and Control for Aerospace Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | | | - Junhui Hu
- State Key Lab of Mechanics and Control for Aerospace Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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Sun L, Liu Y, Lehnert T, Gijs MAM, Li S. The enhancement of DNA fragmentation in a bench top ultrasonic water bath with needle-induced air bubbles: Simulation and experimental investigation. BIOMICROFLUIDICS 2022; 16:044103. [PMID: 35909646 PMCID: PMC9337879 DOI: 10.1063/5.0101740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Shearing DNA to a certain size is the first step in many medical and biological applications, especially in next-generation gene sequencing technology. In this article, we introduced a highly efficient ultrasonic DNA fragmentation method enhanced by needle-induced air bubbles, which is easy to operate with high throughput. The principle of the bubble-enhanced sonication system is introduced and verified by flow field and acoustic simulations and experiments. Lambda DNA long chains and mouse genomic DNA short chains are used in the experiments for testing the performance of the bubble-enhanced ultrasonic DNA fragmentation system. Air bubbles are an effective enhancement agent for ultrasonic DNA fragmentation; they can obviously improve the sound pressure level in the whole solution, thus, achieving better absorption of ultrasound energy. Growing bubbles also have a stretched function on DNA molecule chains and form a huge pressure gradient in the solution, which is beneficial to DNA fragmentation. Purified λDNA is cut from 48.5 to 2 kbp in 5 min and cut to 300 bp in 30 min. Mouse genomic DNA (≈1400 bp) decreases to 400 bp in 5 min and then reduces to 200 bp in 30 min. This bubble-enhanced ultrasonic method enables widespread access to genomic DNA fragmentation in a standard ultrasonic water bath for many virus sequencing demands even without good medical facilities.
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Affiliation(s)
| | | | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Martin A. M. Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Songjing Li
- Department of Fluid Control and Automation, School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150000, China
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Kechin A, Boldyreva D, Borobova V, Boyarskikh U, Scherbak S, Apalko S, Makarova M, Mosyakin N, Kaftyreva L, Filipenko M. An inexpensive, simple, and effective method of genome DNA fragmentation for NGS libraries. J Biochem 2021; 170:675-681. [PMID: 34382083 DOI: 10.1093/jb/mvab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/29/2021] [Indexed: 11/12/2022] Open
Abstract
NGS-library preparation for whole-genome sequencing (WGS) starts with DNA fragmentation, and sonication is a physical approach used most often due to its simplicity and reproducibility. However, the commercially available Covaris instrument has a high price for both the device and consumables. Here we describe our in-house method of DNA shearing by sonication with small (100-600 µm) glass beads and an ultrasonic bath. The fragmentation conditions were optimized for the bacterial WGS with ∼550 bp fragment size (the ultrasonic bath water temperature 5-10 °C, glass beads 0.06 g, the fragmentation time 50 seconds), and for human DNA with ∼250 bp (fragmentation with the same parameters for 4 minutes). Fragmentation results were compared with the Covaris instrument for preparing several bacterial NGS libraries for Illumina NGS platforms by several characteristics. We obtained close mean fragment lengths (523-623 vs 480-646), similar mono- and dinucleotide specificity of shearing, and comparable indicators of read alignment and de novo assembly for both methods. Thus, the described method is a new fast, and effective DNA fragmentation approach that can be used in different WGS applications.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Darya Boldyreva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Viktoriya Borobova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Sergey Scherbak
- Saint-Petersburg State University, Saint-Petersburg, 199034, Russia.,Saint-Petersburg State Medical Academy "City Hospital No, 40 of the Resort Administrative District", Saint-Petersburg, 195067, Russia
| | - Svetlana Apalko
- Saint-Petersburg State Medical Academy "City Hospital No, 40 of the Resort Administrative District", Saint-Petersburg, 195067, Russia
| | - Maria Makarova
- Saint-Petersburg Pasteur Institute, St Petersburg, 197101, Russia
| | - Nikolay Mosyakin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Lidia Kaftyreva
- Saint-Petersburg Pasteur Institute, St Petersburg, 197101, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
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A simple approach for effective shearing and reliable concentration measurement of ultra-high-molecular-weight DNA. Biotechniques 2021; 71:439-444. [PMID: 34232102 DOI: 10.2144/btn-2021-0051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Pipetting and concentration measurement of viscous ultra-high-molecular-weight (UHMW) DNA samples is challenging and often highly imprecise. Effective guidelines for handling UHMW samples are missing in the field. Herein, a simple and low-cost workflow is presented that enables accurate pipetting and reliable concentration measurement. Central to the workflow is the shearing of representative small aliquots of UHMW DNA samples to a fragment size <150 kb by vortexing them for 1 min with a glass bead in a round-bottomed 2-ml tube. Additionally, a solution is provided for accurate quantitation of high-molecular-weight DNA with fluorometric (Qubit [Thermo Fisher Scientific, MA, USA]) methods by using an appropriate genomic DNA standard, resulting in values that match spectrophotometric (Nanodrop [Thermo Fisher Scientific]) optical density readings.
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Lin Z, Nielsen J, Liu Z. Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters. Front Bioeng Biotechnol 2020; 8:526. [PMID: 32582659 PMCID: PMC7290108 DOI: 10.3389/fbioe.2020.00526] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
Since the discovery of penicillin, natural products and their derivatives have been a valuable resource for drug discovery. With recent development of genome mining approaches in the post-genome era, a great number of natural product biosynthetic gene clusters (BGCs) have been identified and these can potentially be exploited for the discovery of novel natural products that can find application as pharmaceuticals. Since many BGCs are silent or do not express in native hosts under laboratory conditions, heterologous expression of BGCs in genetically tractable hosts becomes an attractive route to activate these BGCs to discover the corresponding products. Here, we highlight recent achievements in cloning and discovery of natural product biosynthetic pathways via intact BGC capturing, and discuss the prospects of high-throughput and multiplexed cloning of rational-designed gene clusters in the future.
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Affiliation(s)
- Zhenquan Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,BioInnovation Institute, Copenhagen, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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