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PCR-based evaluation of sequence specificity of DNA fragmentation by ultrasound

  • Genomics. Transcriptomics
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Abstract

Ultrasonic fragmentation, which is a simple and convenient method for the mechanical degradation of DNA, is widely used in modern genome studies as one of the sample preparation steps. It has been recently found that the DNA breaks occur more often in the regions containing 5'-CG-3' dinucleotides. We studied the influence of the 5'-CG-3' dinucleotides on the efficiency of the 28S rRNA gene amplification during PCR with sonicated DNA of Mantis religiosa. It was shown that the amplification rate depends on the template length and the number of 5'-CG-3' dinucleotides. Amplification of the DNA regions with a higher 5'-CG-3' density is less efficient because of their higher sensitivity to ultrasound. The amount of the amplified DNA templates is inversely proportional to the 5'-CG-3'number.

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Authors and Affiliations

  1. Institute of Biochemistry and Genetics of Ufa Science Center of Russian Academy of Sciences, Ufa, 450054, Russia

    R. R. Garafutdinov, A. A. Galimova, A. R. Sakhabutdinova & A. V. Chemeris

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  1. R. R. Garafutdinov
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  2. A. A. Galimova
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  3. A. R. Sakhabutdinova
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  4. A. V. Chemeris
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Correspondence to R. R. Garafutdinov.

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Original Russian Text © R.R. Garafutdinov, A.A. Galimova, A.R. Sakhabutdinova, A.V. Chemeris, 2016, published in Molekulyarnaya Biologiya, 2016, Vol. 50, No. 2, pp. 272–278.

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Garafutdinov, R.R., Galimova, A.A., Sakhabutdinova, A.R. et al. PCR-based evaluation of sequence specificity of DNA fragmentation by ultrasound. Mol Biol 50, 236–241 (2016). https://doi.org/10.1134/S0026893316020059

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  • DOI: https://doi.org/10.1134/S0026893316020059

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