A photochemical investigation of the dynamics of oligonucleotide hybridization.

The nucleic acid double strand helix is now known to have several structural forms that are themselves rather variable or changeable in response to environmental conditions such as ionic strength, temperature, and the presence of a wide variety of solutes in the solutions in which the solvent is almost always water. A common chemistry among all of these helical forms is the reaction that separates the strands of the helices into single strands. The strands ideally may be thought of as random coils but, in reality, may fold back upon themselves and form local double stranded helical regions of secondary structure. The process of separation of the strands in the double helices is called melting by analogy to the melting of a crystal, because the transition of a long helix from double-stranded form to single-stranded form occurs in a narrow temperature interval with high temperature favoring the single strands and low temperature favoring the helix. Despite the descriptive language, it is clearly incorrect to think of the helix-coil transition as a phase transition, for there are major inhomogeneities in nucleic acid helices that invariably lead to stable intermediate states, each with its own melting temperature, in the transition from helix to coil. When a sample of melted single strands is allowed to reverse the melting process and reform the double helix, the process is