«Quantitative Analysis of Electrophoresis Data - Application to Sequence-Specific Ultrasonic Cleavage of DNA»статья

Дата последнего поиска статьи во внешних источниках: 28 мая 2015 г.

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[1] quantitative analysis of electrophoresis data - application to sequence-specific ultrasonic cleavage of dna / S. L. Grokhovsky, I. A. Il’icheva, D. Y. Nechipurenko et al. // Gel Electrophoresis - Principles and Basics, Edited by S. Magdeldin. — INTECH, 2012. — P. 217–238. The complete genomes of many different species are now being revealed in ever increasing pace. The impressive progress made in genome sequencing was largely attributed to development of high resolution denaturing polyacrylamide gel electrophoresis (PAGE). Next-generation sequencing platforms use new powerful technologies, providing gigabases of genetic information in a single run (Farias-Hesson et al., 2010). Nevertheless, scientific research often deals with situations when one needs to change the experimental conditions or the data analysis protocols, but commercial available devices and programs don’t give such an opportunity. We have faced this problem during the research focused on the phenomenon of sequence specific ultrasonic cleavage of double-stranded (ds) DNA (Grokhovsky, 2006). The observed sequence dependence of DNA cleavage efficiency was quite surprising. It seems that sequence-specificity of ultrasonic cleavage reflects the local variations in DNA structural dynamics. Thus, ultrasound may provide a basis for developing a new method for studying sequence effects on local structural dynamics of DNA fragments. It is generally accepted that recognition of various DNA binding sites by many types of transcription factors depends not only on the base pair sequence, but also on local variations in structural parameters of the DNA molecule. Among the important factors involved in these processes are conformational flexibility of sugar-phosphate backbone, geometry of DNA grooves and local bending propensities of the double helix. Local conformational parameters of DNA are sequence-dependent but in many cases different DNA sequences might carry similar structural profiles. [ DOI ]

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