ABSTRACT
In 1953, Watson and Crick discovered that the DNA helix is formed by two single nucleic acid strands binding noncovalently via base-pairing interaction. The thermodynamic stability of the two single strands to form a resultant DNA duplex is a function of the hydrogen bonding between pyrimidine and purine bases and the stacking of the aromatic rings. Other factors contributing to the strength of this interaction are salt concentration, strand concentration, sequence, and chemical makeup of the single strands (RNA, DNA, or otherwise modi‰ed sugars, backbones, or heterocyclic bases). In nature, the balance between a duplex and denatured state is modulated by enzymes that are responsible for the maintenance and replication of cellular function. Enzymes involved in DNA replication, transcription, recombination, and RNA processing reduce the forces necessary to denature the secondary and tertiary structures of nucleic acids, thereby facilitating performance of their respective functions. The study of these enzymes and their function is extensive. Within the ‰eld of molecular biology, understanding their thermodynamic properties is essential for successful polymerase chain reaction (PCR) primer and probe design. Likewise, thermodynamics of the binding of oligonucleotides to their molecular targets is central to the development of potent therapeutic agents.
