ABSTRACT
This chapter introduces DNA and its properties and describes molecular dynamics simulations and the necessary force fields required for DNA. Nucleic acids play crucial roles in biological processes including cell division and protein synthesis. Cancerous cells are characterized by the uncontrolled cell division, which differs from the normal healthy cell division. The stability of DNA is largely affected by its length, base composition, sequence, and presence of nucleotide mismatches. It is also strongly perturbed by changes in pH, temperature, and solvent as well as by the binding of proteins such as helicases, polymerases, or topoisomerases in living cells. The three-dimensional structures of the DNA-intra-strand cross links (ICLs) are variable, which could influence the efficiency of ICL recognition and repair. ICLs are thought to form a link between the same strand or complimentary strand and thereby increase the stability of DNA, which forbids processes like replication and transcription.
