When protiens interact with DNA, they interact on the major groove because the minor groove is too small. Nucleotides make up the DNA strand and form a polymer. Each nucleotide contains a phosphate group, a sugar, and a nitrogenous base. Base pairing occurs where A attaches to T and G attaches to C. The 1’ carbon is attached to base all the way to 5’ carbon at the phosphate in the sugar. This is important to the directionality of the polymer. The 3’ end of DNA/polymer is on the sugar, 5’ is where the phosphate is exposed. Polymers attach by hydrogen (non-covalent) bonding to create the DNA strand. The DNA runs antiparallel fashion. A primer is required for DNA polymerase to begin adding nucleotides.
RNA has a difference in its sugar as compared to DNA. The 2’ carbon has OH coming off of it, DNA has 2’ H. RNA is less stable, the oxygen allows it to act as a catalyst in chemical reactions. RNA can make intramolecular reactions on itself, like a protein, but structures are limited (ribosomes & splicasome). RNA has uracil instead of thymine. When DNA is damaged, cytosine can change to uracil and base paring then does not occur properly. It is possible for double stranded RNA to be formed and DNA can bind with it. It is a hybrid double helix, a slightly different shape. DNA replication is semi-conservative (a mix). Originally there were three methods thought up, Semi-conserve, Conservative and dispersive.