TY - JOUR
T1 - A comparison of DNA fragmentation methods − Applications for the biochip technology
AU - Sapojnikova, Nelly
AU - Asatiani, Nino
AU - Kartvelishvili, Tamar
AU - Asanishvili, Lali
AU - Zinkevich, Vitaly
AU - Bogdarina, Irina
AU - Mitchell, Julian
AU - Al-humam, Abdulmohsen
PY - 2017/8/1
Y1 - 2017/8/1
N2 - 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.
AB - 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.
U2 - 10.1016/j.jbiotec.2017.06.1202
DO - 10.1016/j.jbiotec.2017.06.1202
M3 - Article
SN - 0168-1656
VL - 256
SP - 1
EP - 5
JO - Journal of Biotechnology
JF - Journal of Biotechnology
ER -