Biophysics and bioinformatics of genomic DNA fragments very rich in guanine and adenine
|Project Period:||1/2009 - 12/2013|
|Investor:||Academy of Sciences of the Czech Republic|
|Field:||CE - Biochemistry (C - Chemistry)|
BO - Biophysics (B - Physics and mathematics)
EB - Genetics and molecular biology (E - Bio-science)
|Keywords:||DNA; primary structure; secondary structure; genomes; biophysics; bioinformatics; CD spectroscopy; NMR spectroscopy; gel electrophoresis; PCR; photochemistry; UV spectroscopy; crystal structures|
We will perform a bioinformatic analysis of the human, chimp and other genomes to identify and localize the longest blocks with an extremely high content of adenine and guanine in one strand of DNA. We will compare results obtained with various genomes to understand function of the blocks. Using NMR spectroscopy, we will determine a detailed molecular structure (GA)n and (GAA)n. Using CD spectroscopy and gel electrophoresis we will compare secondary structures of fragments related to (GA)n and (GAA)n. Using PCR we will assess their inclination to expansion that relates to genome evolution and its pathological changes. We will develop photochemical methods to find secondary structure of the fragments in genomic content. Empirical analysis of the crystal structures of DNA will serve to find the role of vertical interactions of bases and their hydrogen bonding. The project shall contribute to a better understanding of the role the very long(G+A) fragments play in the genomes.