As it was stated before the naturally occurring DNA structure can be recognised by specific proteins. In modern organisms proteins are everywhere around the DNA and everything what happens on the DNA level is strongly connected with the DNA-protein interactions. In Eukaryota the genome is organised in chromosomes. This enables the eukaryotic cells to pack very long DNA threads (measured in centimetres) into the nuclei (measured in micrometers). Apart from the fact that DNA is flexible enough to be wrapped around a complex of histones (nucleosom) the primary structure having its impact on the secondary structure determines which regions of DNA are bound to the nucleosom and which cannot form the interactions (as it is for the DNA regions reach in C-G pairs). In regulation of replication or transcription an important role play proteins (so called trans factors) bound to certain regions of the chromosome, activating or inhibiting the process. Changed by the mismatch (T-T dimers, as jpg file or pdb file; G-A mismatch, as a jpg file or pdb file) DNA structure is recognised by proteins (repair nucleases) which specifically cleave the mismatch, what finally leads to incorporation of a proper nucleotide.
The mechanisms in which DNA structure play an important role will be discussed in detail later on.
