NUCLEIC-ACID HYBRIDIZATION - TRIPLEX STABILITY AND ENERGETICS

In this chapter, we review the current state of the thermodynamic data base for triple helical oligonucleotide hybridization reactions and pr esent a critical assessment of the methods used to obtain the relevant data. The thermodynamic stability of triple-helix oligonucleotide con structs is discussed in terms of its dependence on temperature, chain length, pH, salt, base sequence, base and backbone modifications, and ligand binding. In particular, we examine the coupling of hybridizatio n equilibria to proton, cation, and drug-binding equilibria. Throughou t the chapter, we emphasize that a detailed understanding of the endog enous and exogenous variables that control tripler stability is requir ed for the rational design of oligonucleotides for specific therapeuti c, diagnostic, and/or biotechnological applications, as well as for el ucidating the potential cellular roles of these higher-order nucleic a cid complexes.