VACLAV BRAZDA, Institute of Biophysics ASCR, Brno, Czech Republic
Local DNA structures - their presence and analyses in genomes
Local alternative DNA structures are known to exist in all life forms. The negative supercoiling of DNA can induce local nucleotide sequence-dependent conformational changes that give rise to different local structures including cruciforms, left-handed DNAs, triplexes and quadruplexes. The formation of local DNA structures is strongly dependent on base sequence, for example the presence of inverted repeats in the nucleic acid sequence is required for cruciform, or G-rich sequences are required for the formation of G-quadruplexes. Over-representation of these sequences, which occur non-randomly in the DNA of all organisms, has been demonstrated in different regulatory locations, including for example sites of replication initiation, promotor regions, RNA UTR regions, telomeres etc. Therefore, these structures are becoming important for targeted therapy studies. In this course, we will focus on the description of known local DNA structures and their biological roles, methods of analyses and DNA sequence analyses for the presence of G-quadruplexes by G4Hunter and inverted repeats by Palindrome analyzer. Course participants will be able to predict the probability and the type of local DNA structures in a given DNA molecule using in silico approaches and validate the presence of local DNA structures by biochemical methods.
1. Local DNA structures – reason for being, Variations of double stranded DNA and their biological roles
2. Multi-stranded DNA structures – biochemical characterization
3. Analyses of inverted repeats forming cruciform by Palindrome finder and G-quadruplex structures by G4Hunter – practical application
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