A rapid and efficient zirconia bead-mediated ultrasonic strategy for DNA fragmentation up to 10 kbp.

Pan Fu, Taowa Zhao, Pengyao Wei, Tong Kong, Sihua Qian, Yuhui Wang, Lei Yu, Jianping Zheng

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Article in RSC advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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8 authors.

Pan FuNingbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315300 China zhengjianping@nimte.ac.cn yulei@nimte.ac.cn wangyuhui@nimte.ac.cn.ORCID https://orcid.org/0000-0002-6438-669X

Taowa ZhaoCixi Biomedical Research Institute, Wenzhou Medical University Wenzhou 325035 China.

Pengyao WeiCixi Biomedical Research Institute, Wenzhou Medical University Wenzhou 325035 China.

Tong KongNingbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315300 China zhengjianping@nimte.ac.cn yulei@nimte.ac.cn wangyuhui@nimte.ac.cn.

Sihua QianNingbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315300 China zhengjianping@nimte.ac.cn yulei@nimte.ac.cn wangyuhui@nimte.ac.cn.ORCID https://orcid.org/0000-0003-4023-9545

Yuhui WangNingbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315300 China zhengjianping@nimte.ac.cn yulei@nimte.ac.cn wangyuhui@nimte.ac.cn.ORCID https://orcid.org/0000-0001-9430-6614

Lei YuNingbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315300 China zhengjianping@nimte.ac.cn yulei@nimte.ac.cn wangyuhui@nimte.ac.cn.

Jianping ZhengNingbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315300 China zhengjianping@nimte.ac.cn yulei@nimte.ac.cn wangyuhui@nimte.ac.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Single-molecule sequencing (SMS), a long-read DNA sequencing technology, plays a crucial role in genomics research. However, traditional ultrasonic shearing techniques struggle to efficiently produce DNA fragments ≥10 kbp, limiting the efficiency of SMS library preparation. Here, we developed a zirconia bead-mediated ultrasonic shearing method that enables precise DNA fragmentation through zirconia bead mechanical agitation induced by sonication cavitation. By optimizing parameters such as zirconia bead size, quantity, ultrasonic probe distance, ultrasonic time, water bath temperature, DNA sample volume, and DNA concentration, we obtained target fragments in the 10-20 kbp range. The results demonstrated that this method sheared purified λDNA (48.5 kbp) into fragments averaging 15 kbp within 20 seconds, achieving performance comparable to commercial g-TUBE methods. The method was also successfully applied to human genomic DNA. This simple, rapid and reliable DNA fragmentation method provides an effective solution for SMS library preparation with great potential for molecular detection and diagnostic applications.

Identifiers

PMID39995453

DOI10.1039/d5ra00027k

PMCPMC11848711

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.