SEQUENCE-SPECIFIC THERMODYNAMIC AND STRUCTURAL-PROPERTIES FOR DNA-CENTER-DOT-RNA DUPLEXES

DNA.RNA hybrid duplexes are found in many important biological process es and are involved in developing modes of disease treatment, such as antisense therapy, yet little is known about the sequence dependence o f their structure and stability. The structure and thermodynamic stabi lity of DNA.RNA hybrid model systems corresponding in composition and length and containing (1) all purine or all pyrimidine bases on each s trand or (2) mixed purine and pyrimidine bases on each strand have bee n evaluated relative to pure RNA and DNA duplexes by thermal melting, CD, and electrophoresis analyses. The spread in free energies of denat uration of the homopurine homopyrimidine systems covers over 14 kcal/m ol of single strands, while the mixed sequence free energies vary by l ess than 4 kcal/mol. The RNA-homopurine.DNA-homopyrimidine hybrid rese mbles a corresponding pure RNA duplex in both structure and stability, whereas the DNA-homopurine RNA-homopyrimidine hybrid resembles a corr esponding pure DNA duplex. The mixed sequence hybrids show intermediat e structure between the corresponding pure RNA and pure DNA duplexes a nd a stability closer to that of the pure DNA duplex. From these resul ts and the evaluation of published hybrid data [Hall, K. B., and McLau ghlin, L. W. (1998) Biochemistry 30, 10606-10613; Roberts, W. R., and Crothers, D. M. (1992) Science 258, 1463-1466], it can be predicted th at a hybrid duplex containing more RNA purine bases will have a CD spe ctrum, and probably conformation, resembling that of A-form duplexes a nd will be more stable than a corresponding hybrid duplex with fewer R NA purine bases.