Abstract

Several ultrasound-based platforms for DNA sample preparation were evaluated in terms of effective fragmentation of DNA (plasmid and genomic DNA)-ultrasonic probe, sonoreactor, ultrasonic bath and the newest Vialtweeter device. The sonoreactor showed the best efficiency of DNA fragmentation while simultaneously assuring no cross-contamination of samples, and was considered the best ultrasonic tool to achieve effective fragmentation of DNA at high-throughput and avoid sample overheating. Several operation variables were studied-ultrasonication time and amplitude, DNA concentration, sample volume and sample pre-treatment-that allowed optimisation of a sonoreactor-based strategy for effective DNA fragmentation. Optimal operating conditions to achieve DNA fragmentation were set to 100% ultrasonic amplitude, 100 μL sample volume, 8 min ultrasonic treatment (2 min/sample) for a DNA concentration of 100 μg mL-1. The proposed ultrasonication strategy can be easily implemented in any laboratory setup, providing fast, simple and reliable means for effective DNA sample preparation when fragmentation is critical for downstream molecular detection and diagnostics protocols.

Original languageEnglish
Pages (from-to)881-886
Number of pages6
JournalTalanta
Volume81
Issue number3
DOIs
Publication statusPublished - 15 May 2010

Fingerprint

Ultrasonics
DNA
DNA Probes
Plasmids
Contamination
Throughput

Keywords

  • DNA fragmentation
  • Restriction enzyme
  • Sample preparation
  • Sonoreactor
  • Ultrasound

Cite this

@article{67f0dc2c795f402fa7bffca2f804da99,
title = "Development of a fast and efficient ultrasonic-based strategy for DNA fragmentation",
abstract = "Several ultrasound-based platforms for DNA sample preparation were evaluated in terms of effective fragmentation of DNA (plasmid and genomic DNA)-ultrasonic probe, sonoreactor, ultrasonic bath and the newest Vialtweeter device. The sonoreactor showed the best efficiency of DNA fragmentation while simultaneously assuring no cross-contamination of samples, and was considered the best ultrasonic tool to achieve effective fragmentation of DNA at high-throughput and avoid sample overheating. Several operation variables were studied-ultrasonication time and amplitude, DNA concentration, sample volume and sample pre-treatment-that allowed optimisation of a sonoreactor-based strategy for effective DNA fragmentation. Optimal operating conditions to achieve DNA fragmentation were set to 100{\%} ultrasonic amplitude, 100 μL sample volume, 8 min ultrasonic treatment (2 min/sample) for a DNA concentration of 100 μg mL-1. The proposed ultrasonication strategy can be easily implemented in any laboratory setup, providing fast, simple and reliable means for effective DNA sample preparation when fragmentation is critical for downstream molecular detection and diagnostics protocols.",
keywords = "DNA fragmentation, Restriction enzyme, Sample preparation, Sonoreactor, Ultrasound",
author = "Miguel Larguinho and Santos, {Hugo M.} and Gon{\cc}alo Doria and H. Scholz and Baptista, {Pedro V.} and Capelo, {Jos{\'e} L.}",
note = "We thank FCT/MCTES for financial support: project PTDC/BIO/66514/2006; PTDC/SAU-BEB/66511/2006 and CIGMH: SRFH/BD/38509/2007 for H. M. Santos; SFRH/BD/64026/2009 for Miguel Larguinho. SFRH/BDE/15544/2005 and STAB Vida, Lda for G.Doria. FCGulbenkian ref. 76436. Dr. J.L. Capelo acknowledges Xunta de Galicia (Spain) for their Parga-Pondal Research contract and Universidade de Vigo (Spain) for Project ref. 2009-INOU-15.",
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T1 - Development of a fast and efficient ultrasonic-based strategy for DNA fragmentation

AU - Larguinho, Miguel

AU - Santos, Hugo M.

AU - Doria, Gonçalo

AU - Scholz, H.

AU - Baptista, Pedro V.

AU - Capelo, José L.

N1 - We thank FCT/MCTES for financial support: project PTDC/BIO/66514/2006; PTDC/SAU-BEB/66511/2006 and CIGMH: SRFH/BD/38509/2007 for H. M. Santos; SFRH/BD/64026/2009 for Miguel Larguinho. SFRH/BDE/15544/2005 and STAB Vida, Lda for G.Doria. FCGulbenkian ref. 76436. Dr. J.L. Capelo acknowledges Xunta de Galicia (Spain) for their Parga-Pondal Research contract and Universidade de Vigo (Spain) for Project ref. 2009-INOU-15.

PY - 2010/5/15

Y1 - 2010/5/15

N2 - Several ultrasound-based platforms for DNA sample preparation were evaluated in terms of effective fragmentation of DNA (plasmid and genomic DNA)-ultrasonic probe, sonoreactor, ultrasonic bath and the newest Vialtweeter device. The sonoreactor showed the best efficiency of DNA fragmentation while simultaneously assuring no cross-contamination of samples, and was considered the best ultrasonic tool to achieve effective fragmentation of DNA at high-throughput and avoid sample overheating. Several operation variables were studied-ultrasonication time and amplitude, DNA concentration, sample volume and sample pre-treatment-that allowed optimisation of a sonoreactor-based strategy for effective DNA fragmentation. Optimal operating conditions to achieve DNA fragmentation were set to 100% ultrasonic amplitude, 100 μL sample volume, 8 min ultrasonic treatment (2 min/sample) for a DNA concentration of 100 μg mL-1. The proposed ultrasonication strategy can be easily implemented in any laboratory setup, providing fast, simple and reliable means for effective DNA sample preparation when fragmentation is critical for downstream molecular detection and diagnostics protocols.

AB - Several ultrasound-based platforms for DNA sample preparation were evaluated in terms of effective fragmentation of DNA (plasmid and genomic DNA)-ultrasonic probe, sonoreactor, ultrasonic bath and the newest Vialtweeter device. The sonoreactor showed the best efficiency of DNA fragmentation while simultaneously assuring no cross-contamination of samples, and was considered the best ultrasonic tool to achieve effective fragmentation of DNA at high-throughput and avoid sample overheating. Several operation variables were studied-ultrasonication time and amplitude, DNA concentration, sample volume and sample pre-treatment-that allowed optimisation of a sonoreactor-based strategy for effective DNA fragmentation. Optimal operating conditions to achieve DNA fragmentation were set to 100% ultrasonic amplitude, 100 μL sample volume, 8 min ultrasonic treatment (2 min/sample) for a DNA concentration of 100 μg mL-1. The proposed ultrasonication strategy can be easily implemented in any laboratory setup, providing fast, simple and reliable means for effective DNA sample preparation when fragmentation is critical for downstream molecular detection and diagnostics protocols.

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KW - Restriction enzyme

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