Ultrafast dynamics of normal and damaged DNA

Thermal fluctuations away from the average structure of DNA may play an important role in its biological function. Computer simulations predict that the amplitude of these fluctuations is quite large in the picosecond and nanosecond time scales. The resulting flexibility may be important for the ''indirect readout'' of sequence information by proteins, including the detection of damage by natural repair systems. These fluctuations may also be responsible for ''gating'' the transfer of charge along the DNA and thereby affect the course of oxidative damage. This chapter presents experimental evidence that DNA damage results in specific changes to its dynamics. Two kinds of prototypical DNA damage are studied and compared with an equivalent undamaged sequence. An ''abasic'' sample reproduces the most common type of in vivo damage to DNA, the loss of a single base. The ''chain-end'' sample explores a more severe type of damage, the disruption of the helical structure at the severed end of a DNA chain.