The objective of this proposal is to study how sequence and solution salt concentration influence the structural, thermodynamic and kinetic properties of a DNA-RNA hybrid oligomer. Questions to be addressed are: Do DNA-RNA hybrid duplexes exist only as A-form helices or do they display a sequence dependent shape?, What is the role of nearest neighbor sequence determining the stability of a hybrid duplex? and How does salt concentration affect the physical properties and behavior of hybrid molecules? Work will include: 1. Circular dichroism studies of hybrid duplex conformation as a function of sequence and salt concentration 2. Optical melting studies to develop a basis set of free energy parameters for the prediction of stability and conformation of hybrid duplexes in 1.0 M Na+ 3. Optical melting studies of the effects of salt on the thermodynamics of duplex formation 4. The construction of a laser Raman temperature jump spectrophotometer to measure kinetic properties of hybrid duplex formation as a function of base sequence and salt concentration.
