Synthesis and Electron Paramagnetic Resonance Studies of Oligodeoxynucleotides Containing 2-N-tert-Butylaminoxyl-2'-deoxyadenosines.

Oligodeoxynucleotides (ODNs) containing 2-N-tert-butylaminoxyl-2'-deoxyadenosine (A*) residues were synthesized to allow accurate monitoring of adenine motion by EPR spectroscopy through the agency of direct linkage of the acyclic aminoxyl group to the nucleobase, and EPR studies of the ODNs in single- and double-stranded forms were performed. Upon duplex formation, peak broadening and decreases in peak height were observed in EPR spectra, and the synthesized ODNs were shown to be excellent monitors of hybridization. Comparison of peak height and the h1 /h0 signal ratio provided information on the relative mobility of A* in duplexes with different stability. A second set of ODNs each containing two A* residues at different intervals and four dA residues were also synthesized. For these ODNs, correlations were observed between the EPR spectral shapes of the duplexes and the number of dA residues between A* residues, thus demonstrating the potential of A* residues in monitoring of the structures of nucleic acids.

Evaluation of mobility of 2-N-tert-butylaminoxyladenosine incorporated into oligodeoxynucleotides.

We synthesized oligodeoxynucleotide (ODN, 3) containing 2-N-tert-butylaminoxyladenosine (1) and studied EPR spectra of 3 and its duplexes. The h(+)/h(0) values in the EPR spectra of duplexes between 3 and 5-8 well correlated with Tm values. We also synthesized ODN 4 containing 2, which has a cyclic aminoxyl via a linker, to compare with ODN 3. The h(+)/h(0) values in the EPR spectra of duplexes between 4 and 5-8 did not correlate with Tm values. These results indicate that 1 has a potential to monitor of motion of the nucleobase.

Dynamics of 2-N-tert-butylaminoxyladenosine incorporated into oligodeoxynucleotides.

We synthesized oligodeoxynucleotide (ODN, 3) containing 2-N-tert-butylaminoxyladenosine (1) and studied EPR spectra of 1 and its duplexes with varied sequences. Duplex formation resulted in a broadening of spectrum and a significant decrease in peak-to-peak height and peak height ratio values. The h(+)/ho values in EPR spectra well correlated with stability of duplex which indicated ODN containing 1 has the potential to monitor DNA structure.