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Sapojnikova N, Asatiani N, Kartvelishvili T, Asanishvili L, Zinkevich V, Bogdarina I, Mitchell J, Al-Humam A. A comparison of DNA fragmentation methods - Applications for the biochip technology. J Biotechnol 2017; 256:1-5. [PMID: 28666852 DOI: 10.1016/j.jbiotec.2017.06.1202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/12/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
The efficiency of hybridization signal detection in a biochip is affected by the method used for test DNA preparation, such as fragmentation, amplification and fluorescent labelling. DNA fragmentation is the commonest methods used and it is recognised as a critical step in biochip analysis. Currently methods used for DNA fragmentation are based either on sonication or on the enzymatic digestion. In this study, we compared the effect of different types of enzymatic DNA fragmentations, using DNase I to generate ssDNA breaks, NEBNext dsDNA fragmentase and SaqAI restrictase, on DNA labelling. DNA from different Desulfovibrio species was used as a substrate for these enzymes. Of the methods used, DNA fragmented by NEBNext dsDNA Fragmentase digestion was subsequently labelled with the greatest efficiency. As a result of this, the use of this enzyme to fragment target DNA increases the sensitivity of biochip-based detection significantly, and this is an important consideration when determining the presence of targeted DNA in ecological and medical samples.
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Affiliation(s)
- Nelly Sapojnikova
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia.
| | - Nino Asatiani
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia
| | - Tamar Kartvelishvili
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia
| | - Lali Asanishvili
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia
| | - Vitaly Zinkevich
- School of Pharmacy and Biomedical Sciences, University of Portsmouth,St. Michael's Building, White Swan Road, PO1 2DT, UK
| | - Irina Bogdarina
- School of Pharmacy and Biomedical Sciences, University of Portsmouth,St. Michael's Building, White Swan Road, PO1 2DT, UK
| | - Julian Mitchell
- School of Biological Sciences, University of Portsmouth,King Henry Building, King Henry I Street, PO1 2DY, UK
| | - Abdulmohsen Al-Humam
- Applied Microbiology Unit, Research & Development Center Saudi Aramco, P.O. Box. 00865, 31311 Dhahran, Saudi Arabia, Saudi Arabia
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