Interstrand Complex Formation of Purine Oligonucleotides and Their Nonionic Analogs: The Model System of d(AG)8 and Its Complement, d(CT)8

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Abstract
We have investigated the role of purines in interstrand complex formation with regard to substitution of the negatively-charged, phosphodiester backbone by a nonionic, internucleoside linkage. Using the purine oligomer, d(AG)8, its methylphosphonate analog, d(AG)8, and the complementary pyrimidine oligomer, d(CT)8, as a model system, the stoichiometry, conformation, and stability of complexes formed at pH 8 were studied by spectroscopic and electrophoretic methods. When there is only one oligomer species in solution, d(AG)8 behaves as a single-stranded molecule. In contrast, the d(AG)8 oligomer readily forms an intermolecular self-complex, particularly in the presence of magnesium ion. Using either purine oligomer, duplexes can form with the d(CT)8 strand which differ in terms of their conformation and in the dependence of their thermal stability on sodium and magnesium ions. All studies show that a stable triplex forms with a 1:2 d(CT)8:d(AG)8 stoichiometry which does not require high concentrations of sodium or magnesium ions. Triplex formation between the d(CT)8 strand and two d(AG)8 strands was not observed. Native gel electrophoresis suggests that a 1:1:1 d(CT) 8:d(AG)8:d(AG)8 complex may be formed. In regard to triplex formation, the advantage of the methylphosphonate backbone on the purine strand is clearly demonstrated. Nucleic acid interactions which involve base-recognition motifs other than the familiar Watson-Crick (W‚C)1 T(U)‚A and C‚G base pairs have been the focus of many physical studies. In particular, interest in the formation of three- stranded helices, or triplexes, has been rekindled from two general aspects. (1) The ability of certain naturally-occurring sequences to adopt intramolecular triplex conformations (H- form) has led to the proposal that such structures may play roles in ViVo (Wells et al., 1988). (2) Triplex formation through binding of a nucleotide probe to a double-stranded DNA target site has been proposed as a means of regulation of gene expression at the DNA level (Miller & Sobell, 1966; Cooney et al., 1988; Maher et al., 1989; Francois et al., 1989).