Low‐frequency modes in the raman spectrum of DNA

Low-Frequency Modes in the Raman Spectrum of DNAIt is becoming increasingly clear that the molecular dynamics of nucleic acids play a key role in their structure and function.The conformational flexibility of DNA in solution has been demonstrated by theoretical calculation' and hydrogen-deuterium exchange s t u d i e ~. ~-~ Dynamic properties have been invoked to explain the relative ease of drug intercalation: and in a more speculative vein, Robson7 has pointed out that the kinetic accessibility of some recently proposed unconventional DNA structures will also be determined by molecular dynamics, providing that such structures have free energies comparable to the double helix.In a number of these studies it has been proposed that the normal modes of vibration that are excited a t thermal energies provide the basis for dynamic behavior.For example, in order to obtain a satisfactory interpretation of the exchange kinetics of DNA, Teitelhaum and Englander2 suggested the existence of traveling loops within which base pairs are open and exposed to solvent.This model requires two torsional fluctuations in order to carry base pairs through opening and closing reactions.Sobell et a1.6 proposed a different type of motion, a dynamically kinked-unkinked structure involving partial unstacking and tilting of base pairs to explain the incorporation of drugs a t intercalation sites.It was suggested that the normal modes involved are highly coupled bending, stretching, and unwinding (presumably torsional) vibrations.Modes that are thermally populated a t ambient temperatures appear 30