DNA conformational dynamics: approach to the physical mapping of genome

• Main Authors: Yurii Dmitrievich Nechipurenko, Dmitrii Yurievich Nechipurenko, Irina Alekseevna Il’icheva, Mikhail Viktorovich Golovkin, Larisa Andreevna Panchenko, Robert Valentinovich Polozov, Sergey L'vovich Grokhovsky
• Format: Article
• Language: Russian
• Published: Institute of Computer Science 2010-12-01
• Series: Компьютерные исследования и моделирование
• Subjects: ultrasonic cleavage of DNA; sequence effects on DNA structure; DNA flexibility; d(CpG) dinucleotide
• Online Access: http://crm.ics.org.ru/uploads/crmissues/crm2010-2-4/crm100410.pdf

Recently we have developed a new method for studying DNA based on ultrasound - induced cleavage of DNA sugar-phosphate backbone. Relative cleavage rates of the phosphodiester bonds in all 16 dinucleotides have been determined. The increased amount of data sampling (of more than 20 000 nucleotides) made it also possible to obtain cleavage rates in all 256 possible tetranucleotides. These values quantitatively characterize sequence effects on conformational dynamics of DNA sugar phosphate backbone. Same type of DNA heterogeneity have been discovered and studied using its chemical cleavage induced by various chemical agents and DNAse I. The presence of essential heterogeneity in structural properties of DNA might be a key for physical mapping of the genomes, i.e. determining the structural profiles being responsible for DNA recognition by gene expression regulation machinery.